Journal articles: 'Heterogeneous-Nuclear Ribonucleoprotein U'

1

Kawano, Shinji, Mary Miyaji, Shoko Ichiyasu, Kimiko M. Tsutsui, and Ken Tsutsui. "Regulation of DNA Topoisomerase IIβ through RNA-dependent Association with Heterogeneous Nuclear Ribonucleoprotein U (hnRNP U)." Journal of Biological Chemistry 285, no. 34 (June 16, 2010): 26451–60. http://dx.doi.org/10.1074/jbc.m110.112979.

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Godbout, Roseline, Margaret Hale, and Dwayne Bisgrove. "A human DEAD box protein with partial homology to heterogeneous nuclear ribonucleoprotein U." Gene 138, no. 1-2 (January 1994): 243–45. http://dx.doi.org/10.1016/0378-1119(94)90816-8.

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Eggert, Heike, Martin Schulz, Frank O. Fackelmayer, Rainer Renkawitz, and Martin Eggert. "Effects of the heterogeneous nuclear ribonucleoprotein U (hnRNP U/SAF-A) on glucocorticoid-dependent transcription in vivo." Journal of Steroid Biochemistry and Molecular Biology 78, no. 1 (July 2001): 59–65. http://dx.doi.org/10.1016/s0960-0760(01)00074-7.

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Winteringham, Louise N., Raelene Endersby, Simon Kobelke, Ross K. McCulloch, James H. Williams, Justin Stillitano, Scott M. Cornwall, Evan Ingley, and S. Peter Klinken. "Myeloid Leukemia Factor 1 Associates with a Novel Heterogeneous Nuclear Ribonucleoprotein U-like Molecule." Journal of Biological Chemistry 281, no. 50 (September 28, 2006): 38791–800. http://dx.doi.org/10.1074/jbc.m605401200.

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5

von Kries, Jens P., Friedrich Buck, and Wolf H. Sträting. "Chicken MAR binding protein p120 is identical to human heterogeneous nuclear ribonucleoprotein (hnRNP) U." Nucleic Acids Research 22, no. 7 (1994): 1215–20. http://dx.doi.org/10.1093/nar/22.7.1215.

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6

Gupta, Ashim K., Judith A. Drazba, and Amiya K. Banerjee. "Specific Interaction of Heterogeneous Nuclear Ribonucleoprotein Particle U with the Leader RNA Sequence of Vesicular Stomatitis Virus." Journal of Virology 72, no. 11 (November 1, 1998): 8532–40. http://dx.doi.org/10.1128/jvi.72.11.8532-8540.1998.

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ABSTRACT The 3′ ends of the genome and antigenome RNA of vesicular stomatitis virus (VSV) serve as the promoter sites for the RNA-dependent RNA polymerase in the initiation of transcription and replication, respectively. The leader RNA, the first transcript synthesized during the RNA synthetic step, contains sequences to initiate encapsidation with the nucleocapsid protein, which is a prerequisite for replication. It also plays a role in the inhibition of cellular RNA synthesis. To search for a specific cellular factor(s) which may interact with the leader RNA sequences and regulate these processes, we used a gel mobility shift assay to identify such a protein(s). By using nuclear extract, it was found that in addition to the previously reported La protein, a 120-kDa nuclear protein specifically interacts with the leader RNA. Biochemical and immunological studies identified the 120-kDa protein as heterogeneous nuclear ribonucleoprotein particle U (hnRNP U), which is involved in pre-mRNA processing. We also demonstrate that hnRNP U is associated with the leader RNA in the nuclei of VSV-infected cells and also packaged within the purified virions. By double immunofluorescence labeling and confocal microscopy, hnRNP U appears to colocalize with the virus in the cytoplasm of infected cells. These results strongly suggest that hnRNP U plays an important role in the life cycle of VSV.

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Swanson, M. S., and G. Dreyfuss. "Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities." Molecular and Cellular Biology 8, no. 5 (May 1988): 2237–41. http://dx.doi.org/10.1128/mcb.8.5.2237.

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Several proteins of heterogeneous nuclear ribonucleoprotein (hnRNP) particles display very high binding affinities for different ribonucleotide homopolymers. The specificity of some of these proteins at high salt concentrations and in the presence of heparin allows for their rapid one-step purification from HeLa nucleoplasm. We show that the hnRNP C proteins are poly(U)-binding proteins and compare their specificity to that of the previously described cytoplasmic poly(A)-binding protein. These findings provide a useful tool for the classification and purification of hnRNP proteins from various tissues and organisms and indicate that different hnRNP proteins have different RNA-binding specificities.

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Swanson, M. S., and G. Dreyfuss. "Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities." Molecular and Cellular Biology 8, no. 5 (May 1988): 2237–41. http://dx.doi.org/10.1128/mcb.8.5.2237-2241.1988.

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Several proteins of heterogeneous nuclear ribonucleoprotein (hnRNP) particles display very high binding affinities for different ribonucleotide homopolymers. The specificity of some of these proteins at high salt concentrations and in the presence of heparin allows for their rapid one-step purification from HeLa nucleoplasm. We show that the hnRNP C proteins are poly(U)-binding proteins and compare their specificity to that of the previously described cytoplasmic poly(A)-binding protein. These findings provide a useful tool for the classification and purification of hnRNP proteins from various tissues and organisms and indicate that different hnRNP proteins have different RNA-binding specificities.

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Mondal, Samiran, Nasim A. Begum, Wenjun Hu, and Tasuku Honjo. "Functional requirements of AID’s higher order structures and their interaction with RNA-binding proteins." Proceedings of the National Academy of Sciences 113, no. 11 (February 29, 2016): E1545—E1554. http://dx.doi.org/10.1073/pnas.1601678113.

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Activation-induced cytidine deaminase (AID) is essential for the somatic hypermutation (SHM) and class-switch recombination (CSR) of Ig genes. Although both the N and C termini of AID have unique functions in DNA cleavage and recombination, respectively, during SHM and CSR, their molecular mechanisms are poorly understood. Using a bimolecular fluorescence complementation (BiFC) assay combined with glycerol gradient fractionation, we revealed that the AID C terminus is required for a stable dimer formation. Furthermore, AID monomers and dimers form complexes with distinct heterogeneous nuclear ribonucleoproteins (hnRNPs). AID monomers associate with DNA cleavage cofactor hnRNP K whereas AID dimers associate with recombination cofactors hnRNP L, hnRNP U, and Serpine mRNA-binding protein 1. All of these AID/ribonucleoprotein associations are RNA-dependent. We propose that AID’s structure-specific cofactor complex formations differentially contribute to its DNA-cleavage and recombination functions.

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10

Tazi, J., T. Forne, P. Jeanteur, G. Cathala, and C. Brunel. "Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome." Molecular and Cellular Biology 13, no. 3 (March 1993): 1641–50. http://dx.doi.org/10.1128/mcb.13.3.1641.

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Mammalian U6 small nuclear RNA (snRNA) is heterogeneous with respect to the number of 3' terminal U residues. The major form terminates with five U residues and a 2',3' cyclic phosphate. Because of the presence in HeLa cell nuclear extracts of a terminal uridylyl transferase, a minor form of U6 snRNA is elongated, producing multiple species containing up to 12 U residues. In this study we have used glycerol gradients to demonstrate that these U6 snRNA forms are assembled into U6 ribonucleoprotein (RNP), U4/U6 snRNPs, and U4/U5/U6 tri-snRNP complexes. Furthermore, glycerol gradients combined with affinity selection of biotinylated pre-mRNAs led us to show that elongated forms of U6 snRNAs enter the spliceosome and that some of these become shortened with time to a single species having the same characteristics as the major form of U6 snRNA present in mammalian nuclear extracts. We propose that this elongation-shortening process is related to the function of U6 snRNA in mammalian pre-mRNA splicing.

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Tazi, J., T. Forne, P. Jeanteur, G. Cathala, and C. Brunel. "Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome." Molecular and Cellular Biology 13, no. 3 (March 1993): 1641–50. http://dx.doi.org/10.1128/mcb.13.3.1641-1650.1993.

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Mammalian U6 small nuclear RNA (snRNA) is heterogeneous with respect to the number of 3' terminal U residues. The major form terminates with five U residues and a 2',3' cyclic phosphate. Because of the presence in HeLa cell nuclear extracts of a terminal uridylyl transferase, a minor form of U6 snRNA is elongated, producing multiple species containing up to 12 U residues. In this study we have used glycerol gradients to demonstrate that these U6 snRNA forms are assembled into U6 ribonucleoprotein (RNP), U4/U6 snRNPs, and U4/U5/U6 tri-snRNP complexes. Furthermore, glycerol gradients combined with affinity selection of biotinylated pre-mRNAs led us to show that elongated forms of U6 snRNAs enter the spliceosome and that some of these become shortened with time to a single species having the same characteristics as the major form of U6 snRNA present in mammalian nuclear extracts. We propose that this elongation-shortening process is related to the function of U6 snRNA in mammalian pre-mRNA splicing.

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12

Hegde, Muralidhar L., Srijita Banerjee, Pavana M. Hegde, Larry J. Bellot, Tapas K. Hazra, Istvan Boldogh, and Sankar Mitra. "Enhancement of NEIL1 Protein-initiated Oxidized DNA Base Excision Repair by Heterogeneous Nuclear Ribonucleoprotein U (hnRNP-U) via Direct Interaction." Journal of Biological Chemistry 287, no. 41 (August 17, 2012): 34202–11. http://dx.doi.org/10.1074/jbc.m112.384032.

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13

Fakan, S., G. Leser, and T. E. Martin. "Immunoelectron microscope visualization of nuclear ribonucleoprotein antigens within spread transcription complexes." Journal of Cell Biology 103, no. 4 (October 1, 1986): 1153–57. http://dx.doi.org/10.1083/jcb.103.4.1153.

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The ultrastructural distribution of nuclear ribonucleoproteins (RNP) within spread active chromatin has been investigated using specific anti-RNP antibodies. Monoclonal antibodies directed against the core proteins of heterogeneous nuclear (hn)RNP or against small nuclear (sn)RNP have been incubated directly with lysed mouse or Drosophila tissue culture cells and the bound antibodies visualized by means of a protein A-colloidal gold complex. The hnRNP core proteins have been localized on growing RNP fibrils within non-nucleolar transcription complexes. Anti-snRNP antibodies, directed either against the Sm-antigen (common for nucleoplasmic snRNP species containing U1, U2, U4, U5, and U6 RNAs) or against U1-snRNP, were bound by two morphological types of RNP structures. Within areas of chromatin that do not completely disperse, labeling was observed on RNP-fibril gradient type structures or on groups of fibrogranular material. In the well dispersed regions containing individual nonribosomal transcription complexes, snRNP antigens were associated with growing RNP fibrils. Our results provide direct evidence for association of some U-snRNP species (including U1-snRNP) with extranucleolar RNA as early as during transcription elongation. In addition, the presence of core hnRNP proteins on the same type of nascent RNA transcripts has been confirmed.

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Ameyar-Zazoua, Maya, Mouloud Souidi, Lauriane Fritsch, Philippe Robin, Audrey Thomas, Ali Hamiche, Piergiorgio Percipalle, Slimane Ait-Si-Ali, and Annick Harel-Bellan. "Physical and Functional Interaction between Heterochromatin Protein 1α and the RNA-binding Protein Heterogeneous Nuclear Ribonucleoprotein U." Journal of Biological Chemistry 284, no. 41 (July 17, 2009): 27974–79. http://dx.doi.org/10.1074/jbc.m109.037929.

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15

Zhao, Wei, Lijuan Wang, Meng Zhang, Peng Wang, Jianni Qi, Lei Zhang, and Chengjiang Gao. "Nuclear to Cytoplasmic Translocation of Heterogeneous Nuclear Ribonucleoprotein U Enhances TLR-Induced Proinflammatory Cytokine Production by Stabilizing mRNAs in Macrophages." Journal of Immunology 188, no. 7 (February 17, 2012): 3179–87. http://dx.doi.org/10.4049/jimmunol.1101175.

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16

Gao, Chengjiang, Hongtao Guo, Zhiyong Mi, Philip Y. Wai, and Paul C. Kuo. "Transcriptional Regulatory Functions of Heterogeneous Nuclear Ribonucleoprotein-U and -A/B in Endotoxin-Mediated Macrophage Expression of Osteopontin." Journal of Immunology 175, no. 1 (June 21, 2005): 523–30. http://dx.doi.org/10.4049/jimmunol.175.1.523.

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17

Zietzer, A., H. Wang, M. Rabiul Hosen, G. Nickenig, N. Werner, and F. Jansen. "Heterogeneous nuclear ribonucleoprotein U binds microRNA-30c and negatively regulates the export of microRNA-30c in endothelial microvesicles." Journal of Molecular and Cellular Cardiology 120 (July 2018): 49. http://dx.doi.org/10.1016/j.yjmcc.2018.05.144.

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18

Feliers, Denis, Myung-Ja Lee, Goutam Ghosh-Choudhury, Karol Bomsztyk, and B. S. Kasinath. "Heterogeneous nuclear ribonucleoprotein K contributes to angiotensin II stimulation of vascular endothelial growth factor mRNA translation." American Journal of Physiology-Renal Physiology 293, no. 2 (August 2007): F607—F615. http://dx.doi.org/10.1152/ajprenal.00497.2006.

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ANG II rapidly increases VEGF synthesis in proximal tubular epithelial cells through mRNA translation. The role of heterogeneous nuclear ribonucleoprotein K (hnRNP K) in ANG II regulation of VEGF mRNA translation initiation was examined. ANG II activated hnRNP K as judged by binding to poly(C)- and poly(U)-agarose. ANG II increased hnRNP K binding to VEGF mRNA at the same time as it stimulated its translation, suggesting that hnRNP K contributes to VEGF mRNA translation. Inhibition of hnRNP K expression by RNA interference significantly reduced ANG II stimulation of VEGF synthesis. ANG II increased hnRNP K phosphorylation on both tyrosine and serine residues with distinct time courses; only Ser302 phosphorylation paralleled binding to VEGF mRNA. Src inhibition using PP2 or RNA interference inhibited PKCδ activity and prevented hnRNP K phosphorylation on both tyrosine and serine residues and its binding to VEGF mRNA. Under these conditions, ANG II-induced VEGF synthesis was inhibited. ANG II treatment induced redistribution of both VEGF mRNA and hnRNP K protein from light to heavy polysomal fractions, suggesting increased binding of hnRNP K to VEGF mRNA that is targeted for increased translation. This study shows that hnRNP K augments efficiency of VEGF mRNA translation stimulated by ANG II.

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19

Ye, Junqiang, Nadine Beetz, Sean O’Keeffe, Juan Carlos Tapia, Lindsey Macpherson, Weisheng V. Chen, Rhonda Bassel-Duby, Eric N. Olson, and Tom Maniatis. "hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function." Proceedings of the National Academy of Sciences 112, no. 23 (May 26, 2015): E3020—E3029. http://dx.doi.org/10.1073/pnas.1508461112.

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We report that mice lacking the heterogeneous nuclear ribonucleoprotein U (hnRNP U) in the heart develop lethal dilated cardiomyopathy and display numerous defects in cardiac pre-mRNA splicing. Mutant hearts have disorganized cardiomyocytes, impaired contractility, and abnormal excitation–contraction coupling activities. RNA-seq analyses of Hnrnpu mutant hearts revealed extensive defects in alternative splicing of pre-mRNAs encoding proteins known to be critical for normal heart development and function, including Titin and calcium/calmodulin-dependent protein kinase II delta (Camk2d). Loss of hnRNP U expression in cardiomyocytes also leads to aberrant splicing of the pre-mRNA encoding the excitation–contraction coupling component Junctin. We found that the protein product of an alternatively spliced Junctin isoform is N-glycosylated at a specific asparagine site that is required for interactions with specific protein partners. Our findings provide conclusive evidence for the essential role of hnRNP U in heart development and function and in the regulation of alternative splicing.

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Kim, Jong Heon, Ki Young Paek, Kobong Choi, Tae-Don Kim, Bumsuk Hahm, Kyong-Tai Kim, and Sung Key Jang. "Heterogeneous Nuclear Ribonucleoprotein C Modulates Translation of c-myc mRNA in a Cell Cycle Phase-Dependent Manner." Molecular and Cellular Biology 23, no. 2 (January 15, 2003): 708–20. http://dx.doi.org/10.1128/mcb.23.2.708-720.2003.

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ABSTRACT The c-myc proto-oncogene plays a key role in the proliferation, differentiation, apoptosis, and regulation of the cell cycle. Recently, it was demonstrated that the 5′ nontranslated region (5′ NTR) of human c-myc mRNA contains an internal ribosomal entry site (IRES). In this study, we investigated cellular proteins interacting with the IRES element of c-myc mRNA. Heterogeneous nuclear ribonucleoprotein C (hnRNP C) was identified as a cellular protein that interacts specifically with a heptameric U sequence in the c-myc IRES located between two alternative translation initiation codons CUG and AUG. Moreover, the addition of hnRNP C1 in an in vitro translation system enhanced translation of c-myc mRNA. Interestingly, hnRNP C was partially relocalized from the nucleus, where most of the hnRNP C resides at interphase, to the cytoplasm at the G2/M phase of the cell cycle. Coincidently, translation mediated through the c-myc IRES was increased at the G2/M phase when cap-dependent translation was partially inhibited. On the other hand, a mutant c-myc mRNA lacking the hnRNP C-binding site, showed a decreased level of translation at the G2/M phase compared to that of the wild-type message. Taken together, these findings suggest that hnRNP C, via IRES binding, modulates translation of c-myc mRNA in a cell cycle phase-dependent manner.

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Kiledjian, M., C. T. DeMaria, G. Brewer, and K. Novick. "Identification of AUF1 (heterogeneous nuclear ribonucleoprotein D) as a component of the alpha-globin mRNA stability complex." Molecular and Cellular Biology 17, no. 8 (August 1997): 4870–76. http://dx.doi.org/10.1128/mcb.17.8.4870.

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mRNA turnover is an important regulatory component of gene expression and is significantly influenced by ribonucleoprotein (RNP) complexes which form on the mRNA. Studies of human alpha-globin mRNA stability have identified a specific RNP complex (alpha-complex) which forms on the 3' untranslated region (3'UTR) of the mRNA and appears to regulate the erythrocyte-specific accumulation of alpha-globin mRNA. One of the protein activities in this multiprotein complex is a poly(C)-binding activity which consists of two proteins, alphaCP1 and alphaCP2. Neither of these proteins, individually or as a pair, can bind the alpha-globin 3'UTR unless they are complexed with the remaining non-poly(C) binding proteins of the alpha-complex. With the yeast two-hybrid screen, a second alpha-complex protein was identified. This protein is a member of the previously identified A+U-rich (ARE) binding/degradation factor (AUF1) family of proteins, which are also known as the heterogeneous nuclear RNP (hnRNP) D proteins. We refer to these proteins as AUF1/hnRNP-D. Thus, a protein implicated in ARE-mediated mRNA decay is also an integral component of the mRNA stabilizing alpha-complex. The interaction of AUF1/hnRNP-D is more efficient with alphaCP1 relative to alphaCP2 both in vitro and in vivo, suggesting that the alpha-complex might be dynamic rather than a fixed complex. AUF1/hnRNP-D could, therefore, be a general mRNA turnover factor involved in both stabilization and decay of mRNA.

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22

Malik, Karl F., Howard Jaffe, John Brady, and W. Scott Young. "The class III POU factor Brn-4 interacts with other class III POU factors and the heterogeneous nuclear ribonucleoprotein U." Molecular Brain Research 45, no. 1 (April 1997): 99–107. http://dx.doi.org/10.1016/s0169-328x(96)00238-0.

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23

Chun, Younghwa, Raehyung Kim, and Soojin Lee. "Centromere Protein (CENP)-W Interacts with Heterogeneous Nuclear Ribonucleoprotein (hnRNP) U and May Contribute to Kinetochore-Microtubule Attachment in Mitotic Cells." PLOS ONE 11, no. 2 (February 16, 2016): e0149127. http://dx.doi.org/10.1371/journal.pone.0149127.

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24

Samuels, M. E., D. Bopp, R. A. Colvin, R. F. Roscigno, M. A. Garcia-Blanco, and P. Schedl. "RNA binding by Sxl proteins in vitro and in vivo." Molecular and Cellular Biology 14, no. 7 (July 1994): 4975–90. http://dx.doi.org/10.1128/mcb.14.7.4975.

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Sxl has been proposed to regulate splicing of specific target genes by directly interacting with their pre-mRNAs. We have therefore examined the RNA-binding properties of Sxl protein in vitro and in vivo. Gel shift and UV cross-linking assays with a purified recombinant MBP-Sxl fusion protein demonstrated preferential binding to RNAs containing poly(U) tracts, and the protein footprinted over the poly(U) region. The protein did not appear to recognize either branch point or AG dinucleotide sequences, but an adenosine residue at the 5' end of the poly(U) tract enhanced binding severalfold. MBP-Sxl formed two shifted complexes on a tra regulated acceptor site RNA; the doubly shifted form may have been stabilized by protein-protein interactions. Consistent with its proposed role in pre-mRNA processing, in nuclear extracts Sxl was found in large ribonucleoprotein (RNP) complexes which sedimented significantly faster than bulk heterogeneous nuclear RNP and small nuclear RNPs. Anti-Sxl staining of polytene chromosomes showed Sxl protein at a number of chromosomal locations, among which was the Sxl locus itself. Sxl protein could also be targeted to a new chromosomal site carrying a transgene containing splicing regulatory sequences from the Sxl gene, following transcriptional induction. After prolonged heat shock, all Sxl protein was restricted to the heat-induced puff at the hs93D locus. In contrast, a presumptive small nuclear RNP protein was observed at several heat puffs following shock.

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Samuels, M. E., D. Bopp, R. A. Colvin, R. F. Roscigno, M. A. Garcia-Blanco, and P. Schedl. "RNA binding by Sxl proteins in vitro and in vivo." Molecular and Cellular Biology 14, no. 7 (July 1994): 4975–90. http://dx.doi.org/10.1128/mcb.14.7.4975-4990.1994.

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Sxl has been proposed to regulate splicing of specific target genes by directly interacting with their pre-mRNAs. We have therefore examined the RNA-binding properties of Sxl protein in vitro and in vivo. Gel shift and UV cross-linking assays with a purified recombinant MBP-Sxl fusion protein demonstrated preferential binding to RNAs containing poly(U) tracts, and the protein footprinted over the poly(U) region. The protein did not appear to recognize either branch point or AG dinucleotide sequences, but an adenosine residue at the 5' end of the poly(U) tract enhanced binding severalfold. MBP-Sxl formed two shifted complexes on a tra regulated acceptor site RNA; the doubly shifted form may have been stabilized by protein-protein interactions. Consistent with its proposed role in pre-mRNA processing, in nuclear extracts Sxl was found in large ribonucleoprotein (RNP) complexes which sedimented significantly faster than bulk heterogeneous nuclear RNP and small nuclear RNPs. Anti-Sxl staining of polytene chromosomes showed Sxl protein at a number of chromosomal locations, among which was the Sxl locus itself. Sxl protein could also be targeted to a new chromosomal site carrying a transgene containing splicing regulatory sequences from the Sxl gene, following transcriptional induction. After prolonged heat shock, all Sxl protein was restricted to the heat-induced puff at the hs93D locus. In contrast, a presumptive small nuclear RNP protein was observed at several heat puffs following shock.

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Anderson, J. T., S. M. Wilson, K. V. Datar, and M. S. Swanson. "NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability." Molecular and Cellular Biology 13, no. 5 (May 1993): 2730–41. http://dx.doi.org/10.1128/mcb.13.5.2730.

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A variety of nuclear ribonucleoproteins are believed to associate directly with nascent RNA polymerase II transcripts and remain associated during subsequent nuclear RNA processing reactions, including pre-mRNA polyadenylation and splicing as well as nucleocytoplasmic mRNA transport. To investigate the functions of these proteins by using a combined biochemical and genetic approach, we have isolated nuclear polyadenylated RNA-binding (NAB) proteins from Saccharomyces cerevisiae. Living yeast cells were irradiated with UV light to covalently cross-link proteins intimately associated with RNA in vivo. Polyadenylated RNAs were then selectively purified, and the covalent RNA-protein complexes were used to elicit antibodies in mice. Both monoclonal and polyclonal antibodies which detect a variety of NAB proteins were prepared. Here we characterize one of these proteins, NAB2. NAB2 is one of the major proteins associated with nuclear polyadenylated RNA in vivo, as detected by UV light-induced cross-linking. Cellular immunofluorescence, using both monoclonal and polyclonal antibodies, demonstrates that the NAB2 protein is localized within the nucleus. The deduced primary structure of NAB2 indicates that it is composed of at least two distinct types of RNA-binding motifs: (i) an RGG box recently described in a variety of heterogeneous nuclear RNA-, pre-rRNA-, mRNA-, and small nucleolar RNA-binding proteins and (ii) CCCH motif repeats related to the zinc-binding motifs of the largest subunit of RNA polymerases I, II, and III. In vitro RNA homopolymer/single-stranded DNA binding studies indicate that although both the RGG box and CCCH motifs bind poly(G), poly(U), and single-stranded DNA, the CCCH motifs also bind to poly(A). NAB2 is located on chromosome VII within a cluster of ribonucleoprotein genes, and its expression is essential for cell growth.

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Anderson, J. T., S. M. Wilson, K. V. Datar, and M. S. Swanson. "NAB2: a yeast nuclear polyadenylated RNA-binding protein essential for cell viability." Molecular and Cellular Biology 13, no. 5 (May 1993): 2730–41. http://dx.doi.org/10.1128/mcb.13.5.2730-2741.1993.

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A variety of nuclear ribonucleoproteins are believed to associate directly with nascent RNA polymerase II transcripts and remain associated during subsequent nuclear RNA processing reactions, including pre-mRNA polyadenylation and splicing as well as nucleocytoplasmic mRNA transport. To investigate the functions of these proteins by using a combined biochemical and genetic approach, we have isolated nuclear polyadenylated RNA-binding (NAB) proteins from Saccharomyces cerevisiae. Living yeast cells were irradiated with UV light to covalently cross-link proteins intimately associated with RNA in vivo. Polyadenylated RNAs were then selectively purified, and the covalent RNA-protein complexes were used to elicit antibodies in mice. Both monoclonal and polyclonal antibodies which detect a variety of NAB proteins were prepared. Here we characterize one of these proteins, NAB2. NAB2 is one of the major proteins associated with nuclear polyadenylated RNA in vivo, as detected by UV light-induced cross-linking. Cellular immunofluorescence, using both monoclonal and polyclonal antibodies, demonstrates that the NAB2 protein is localized within the nucleus. The deduced primary structure of NAB2 indicates that it is composed of at least two distinct types of RNA-binding motifs: (i) an RGG box recently described in a variety of heterogeneous nuclear RNA-, pre-rRNA-, mRNA-, and small nucleolar RNA-binding proteins and (ii) CCCH motif repeats related to the zinc-binding motifs of the largest subunit of RNA polymerases I, II, and III. In vitro RNA homopolymer/single-stranded DNA binding studies indicate that although both the RGG box and CCCH motifs bind poly(G), poly(U), and single-stranded DNA, the CCCH motifs also bind to poly(A). NAB2 is located on chromosome VII within a cluster of ribonucleoprotein genes, and its expression is essential for cell growth.

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ARAO, Yukitomo, Atsumi KIKUCHI, Kazuhiro IKEDA, Satoshi NOMOTO, Hyogo HORIGUCHI, and Fujio KAYAMA. "A+U-rich-element RNA-binding factor 1/heterogeneous nuclear ribonucleoprotein D gene expression is regulated by oestrogen in the rat uterus." Biochemical Journal 361, no. 1 (December 17, 2001): 125–32. http://dx.doi.org/10.1042/bj3610125.

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Oestrogen-mediated gene expression is regulated at both the transcriptional and post-transcriptional levels. The molecular mechanism of transcriptional regulation has been well characterized. On the other hand, there is little understanding of the mechanism of post-transcriptional regulation. To clarify the mechanism of oestrogen-mediated post-transcriptional regulation, we focused on A+U-rich-element RNA-binding factor 1/heterogeneous nuclear ribonucleoprotein D (AUF1/hnRNP D), which is known as a regulator of cytosolic mRNA degradation and nuclear pre-mRNA maturation. However, little is known about the expression levels and the regulation of AUF1/hnRNP D mRNA in tissues. We further investigated the expression levels of AUF1/hnRNP D isoform mRNAs to determine whether AUF1/hnRNP D gene expression is regulated by oestrogen in the ovariectomized adult female rat uterus. Uterine AUF1/hnRNP D mRNA was induced by a single subcutaneous injection (1μg/kg) of 17β-oestradiol (E2), reaching a peak level within 6h. Furthermore, we observed that the E2-induced AUF1/hnRNP D isoform mRNAs are p45 and p40 transcripts, and that E2-mediated induction is suppressed by the oestrogen receptor antagonist ICI 182,780. Finally, using the transcriptional inhibitor actinomycin D, we confirmed that the E2-mediated increase in AUF1/hnRNP D mRNA is caused by E2-dependent AUF1/hnRNP D mRNA stabilization.

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Dolcino, Marzia, Elisa Tinazzi, Antonio Puccetti, and Claudio Lunardi. "In Systemic Sclerosis, a Unique Long Non Coding RNA Regulates Genes and Pathways Involved in the Three Main Features of the Disease (Vasculopathy, Fibrosis and Autoimmunity) and in Carcinogenesis." Journal of Clinical Medicine 8, no. 3 (March 7, 2019): 320. http://dx.doi.org/10.3390/jcm8030320.

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Systemic sclerosis (SSc) is an autoimmune disease characterized by three main features: vasculopathy, immune system dysregulation and fibrosis. Long non-coding RNAs (lncRNAs) may play a role in the pathogenesis of autoimmune diseases and a comprehensive analysis of lncRNAs expression in SSc is still lacking. We profiled 542,500 transcripts in peripheral blood mononuclear cells (PBMCs) from 20 SSc patients and 20 healthy donors using Clariom D arrays, confirming the results by Reverse Transcription Polymerase-chain reaction (RT-PCR). A total of 837 coding-genes were modulated in SSc patients, whereas only one lncRNA, heterogeneous nuclear ribonucleoprotein U processed transcript (ncRNA00201), was significantly downregulated. This transcript regulates tumor proliferation and its gene target hnRNPC (Heterogeneous nuclear ribonucleoproteins C) encodes for a SSc-associated auto-antigen. NcRNA00201 targeted micro RNAs (miRNAs) regulating the most highly connected genes in the Protein-Protein interaction (PPI) network of the SSc transcriptome. A total of 26 of these miRNAs targeted genes involved in pathways connected to the three main features of SSc and to cancer development including Epidermal growth factor (EGF) receptor, ErbB1 downstream, Sphingosine 1 phosphate receptor 1 (S1P1), Activin receptor-like kinase 1 (ALK1), Endothelins, Ras homolog family member A (RhoA), Class I Phosphoinositide 3-kinase (PI3K), mammalian target of rapamycin (mTOR), p38 mitogen-activated protein kinase (MAPK), Ras-related C3 botulinum toxin substrate 1 (RAC1), Transforming growth factor (TGF)-beta receptor, Myeloid differentiation primary response 88 (MyD88) and Toll-like receptors (TLRs) pathways. In SSc, the identification of a unique deregulated lncRNA that regulates genes involved in the three main features of the disease and in tumor-associated pathways, provides insight in disease pathogenesis and opens avenues for the design of novel therapeutic strategies.

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INOUE, Akira, Yukitomo ARAO, Akira OMORI, Sachiyo ICHINOSE, Koji NISHIO, Naoki YAMAMOTO, Yosihiro KINOSHITA, and Shiro MITA. "Identification of S1 proteins B2, C1 and D1 as AUF1 isoforms and their major role as heterogeneous nuclear ribonucleoprotein proteins." Biochemical Journal 372, no. 3 (June 15, 2003): 775–85. http://dx.doi.org/10.1042/bj20021719.

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AUF1 (A+U-rich RNA binding factor) participates in the rapid decay of mRNAs in the cytoplasm. It is sometimes called heterogeneous nuclear ribonucleoprotein (hnRNP) D0; however, evidence for its characterization as an hnRNP protein has been scarce. S1 proteins A–D are those selectively extracted at pH 4.9 from isolated nuclei pretreated with either RNase A or DNase I. In the present study we identified S1 (‘first supernatant’) proteins B2, C1 and D1 with p45, p40 and p37 AUF1s respectively, by microsequencing and product analysis of transfected cDNAs. We found, further, that more than 96% of the S1 proteins occurred in the nucleus, and localized largely in RNase-sensitive structures. B2 was confined in the nucleus and C1 directly bound to heterogeneous nuclear RNAs (hnRNAs). These B2 and C1 proteins formed hnRNP structures responsible for the 33 S, and, to lesser extent, the 40 S particles, which were liberated upon mild nucleolytic cleavage. On the other hand, D1 and the remainder of C1 were associated with nuclease-hypersensitive sites of hnRNAs, and comprised the major cytoplasmic AUF1s that may be involved in mRNA decay. Two-dimensional immunoblotting resolved each S1 isoform into up to six spots or more, and suggested that the previous uncertain relationship of hnRNP D0 and hnRNP D is resolved in terms of charge differences and differential splicing arising from one gene. The present results thus indicate that S1 proteins B2, C1 and D1 are identical with AUF1 proteins, but largely occur as hnRNP proteins in the nucleus. That hnRNP D0 is indeed an hnRNP protein was verified.

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Shao, Ruijin, Xiaoqin Wang, Birgitta Weijdegård, Anders Norström, Julia Fernandez-Rodriguez, Mats Brännström, and Håkan Billig. "Coordinate regulation of heterogeneous nuclear ribonucleoprotein dynamics by steroid hormones in the human fallopian tube and endometrium in vivo and in vitro." American Journal of Physiology-Endocrinology and Metabolism 302, no. 10 (May 15, 2012): E1269—E1282. http://dx.doi.org/10.1152/ajpendo.00673.2011.

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Heterogeneous nuclear ribonucleoproteins (hnRNPs), which are chromatin-associated RNA-binding proteins, participate in mRNA stability, transport, intracellular localization, and translation by acting as transacting factors. Several studies have shown that steroid hormones can regulate hnRNP expression. However, to date, the regulation of hnRNPs and their interactions with steroid hormone signaling in fallopian tubes and endometrium are not fully elucidated. In the present study, we determined whether hnRNP expression is regulated during the menstrual cycle and correlates with estrogen receptor (ER) and progesterone receptor (PR) levels in human fallopian tubes in vivo. Because of the limited availability of human tubal tissues for the research, we also explored the mechanisms of hnRNP regulation in human endometrium in vitro. Fallopian tissue was obtained from patients in the early, late, and postovulatory phases and the midsecretory phase and endometrial tissue from premenopausal and postmenopausal women undergoing hysterectomy. We measured expression of hnRNPs and assessed their intracellular localization and interactions with ERs and PRs. We also determined the effects of human chorionic gonadotropin, 17β-estradiol (E2), and progesterone (P4) on hnRNP expression. In fallopian tubes, mRNA and protein levels of hnRNP A1, AB, D, G, H, and U changed dynamically during ovulation and in the midsecretory phase. In coimmunolocation and coimmunoprecipitation experiments, hnRNPs interacted with each other and with ERs and PRs in fallopian tubes. After treatment with E2 and/or P4 to activate ERs and PRs, hnRNP A1, AB, D, G, and U proteins displayed overlapping but distinct patterns of regulation in the endometrium in vitro. Our findings expand the physiological repertoire of hnRNPs in human fallopian tubes and endometrium and suggest that steroid hormones regulate different hnRNPs directly by interacting with ERs and/or PRs or indirectly by binding other hnRNPs. Both actions may contribute to regulation of gene transcription.

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Dalziel, Martin, Nuno Miguel Nunes, and Andre Furger. "Two G-Rich Regulatory Elements Located Adjacent to and 440 Nucleotides Downstream of the Core Poly(A) Site of the Intronless Melanocortin Receptor 1 Gene Are Critical for Efficient 3′ End Processing." Molecular and Cellular Biology 27, no. 5 (December 22, 2006): 1568–80. http://dx.doi.org/10.1128/mcb.01821-06.

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ABSTRACT Cleavage and polyadenylation is an essential processing reaction required for the maturation of pre-mRNAs into stable, export- and translation-competent mature mRNA molecules. This reaction requires the assembly of a multimeric protein complex onto a bipartite core sequence element consisting of an AAUAAA hexamer and a GU/U-rich downstream sequence element. In this study we have analyzed 3′ end processing of the human melanocortin 1 receptor gene (MC1R). The MC1R gene is an intron-free transcription unit, and its poly(A) site lacks a defined U/GU-rich element. We describe two G-rich sequence elements that are critical for efficient cleavage at the MC1R poly(A) site. The first element is located 30 nucleotides downstream of the cleavage site and acts as an essential closely positioned enhancer. The second G-rich region is positioned more than 440 nucleotides downstream of the MC1R processing site and is instrumental for optimal processing efficiency. Both G-rich sequences contain clusters of heterogeneous nuclear ribonucleoprotein binding motifs and act together to enhance cleavage at the MC1R poly(A) site.

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ARAO, Yukitomo, Atsumi KIKUCHI, Kazuhiro IKEDA, Satoshi NOMOTO, Hyogo HORIGUCHI, and Fujio KAYAMA. "A+U-rich-element RNA-binding factor 1/heterogeneous nuclear ribonucleoprotein D gene expression is regulated by oestrogen in the rat uterus." Biochemical Journal 361, no. 1 (January 1, 2002): 125. http://dx.doi.org/10.1042/0264-6021:3610125.

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34

Romero, Francisco, Francisco Ramos-Morales, Africa Domı́nguez, Rosa Marı́a Rios, Fabien Schweighoffer, Bruno Tocqué, José Antonio Pintor-Toro, Siegmund Fischer, and Marı́a Tortolero. "Grb2 and Its Apoptotic Isoform Grb3-3 Associate with Heterogeneous Nuclear Ribonucleoprotein C, and These Interactions Are Modulated by Poly(U) RNA." Journal of Biological Chemistry 273, no. 13 (March 27, 1998): 7776–81. http://dx.doi.org/10.1074/jbc.273.13.7776.

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35

Li, Siming, Lin Mi, Lei Yu, Qi Yu, Tongyu Liu, Guo-Xiao Wang, Xu-Yun Zhao, Jun Wu, and Jiandie D. Lin. "Zbtb7b engages the long noncoding RNA Blnc1 to drive brown and beige fat development and thermogenesis." Proceedings of the National Academy of Sciences 114, no. 34 (August 7, 2017): E7111—E7120. http://dx.doi.org/10.1073/pnas.1703494114.

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Brown and beige adipocytes convert chemical energy into heat through uncoupled respiration to defend against cold stress. Beyond thermogenesis, brown and beige fats engage other metabolic tissues via secreted factors to influence systemic energy metabolism. How the protein and long noncoding RNA (lncRNA) regulatory networks act in concert to regulate key aspects of thermogenic adipocyte biology remains largely unknown. Here we developed a genome-wide functional screen to interrogate the transcription factors and cofactors in thermogenic gene activation and identified zinc finger and BTB domain-containing 7b (Zbtb7b) as a potent driver of brown fat development and thermogenesis and cold-induced beige fat formation. Zbtb7b is required for activation of the thermogenic gene program in brown and beige adipocytes. Genetic ablation of Zbtb7b impaired cold-induced transcriptional remodeling in brown fat, rendering mice sensitive to cold temperature, and diminished browning of inguinal white fat. Proteomic analysis revealed a mechanistic link between Zbtb7b and the lncRNA regulatory pathway through which Zbtb7b recruits the brown fat lncRNA 1 (Blnc1)/heterogeneous nuclear ribonucleoprotein U (hnRNPU) ribonucleoprotein complex to activate thermogenic gene expression in adipocytes. These findings illustrate the emerging concept of a protein–lncRNA regulatory network in the control of adipose tissue biology and energy metabolism.

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Wilusz, J., and T. Shenk. "A uridylate tract mediates efficient heterogeneous nuclear ribonucleoprotein C protein-RNA cross-linking and functionally substitutes for the downstream element of the polyadenylation signal." Molecular and Cellular Biology 10, no. 12 (December 1990): 6397–407. http://dx.doi.org/10.1128/mcb.10.12.6397.

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Every RNA added to an in vitro polyadenylation extract became stably associated with both the heterogeneous nuclear ribonucleoprotein (hnRNP) A and C proteins, as assayed by immunoprecipitation analysis using specific monoclonal antibodies. UV-cross-linking analysis, however, which assays the specific spatial relationship of certain amino acids and RNA bases, indicated that the hnRNP C proteins, but not the A proteins, were associated with downstream sequences of the simian virus 40 late polyadenylation signal in a sequence-mediated manner. A tract of five consecutive uridylate residues was required for this interaction. The insertion of a five-base U tract into a pGEM4 polylinker-derived transcript was sufficient to direct sequence-specific cross-linking of the C proteins to RNA. Finally, the five-base uridylate tract restored efficient in vitro processing to several independent poly(A) signals in which it substituted for downstream element sequences. The role of the downstream element in polyadenylation efficiency, therefore, may be mediated by sequence-directed alignment or phasing of an hnRNP complex.

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37

Wilusz, J., and T. Shenk. "A uridylate tract mediates efficient heterogeneous nuclear ribonucleoprotein C protein-RNA cross-linking and functionally substitutes for the downstream element of the polyadenylation signal." Molecular and Cellular Biology 10, no. 12 (December 1990): 6397–407. http://dx.doi.org/10.1128/mcb.10.12.6397-6407.1990.

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Every RNA added to an in vitro polyadenylation extract became stably associated with both the heterogeneous nuclear ribonucleoprotein (hnRNP) A and C proteins, as assayed by immunoprecipitation analysis using specific monoclonal antibodies. UV-cross-linking analysis, however, which assays the specific spatial relationship of certain amino acids and RNA bases, indicated that the hnRNP C proteins, but not the A proteins, were associated with downstream sequences of the simian virus 40 late polyadenylation signal in a sequence-mediated manner. A tract of five consecutive uridylate residues was required for this interaction. The insertion of a five-base U tract into a pGEM4 polylinker-derived transcript was sufficient to direct sequence-specific cross-linking of the C proteins to RNA. Finally, the five-base uridylate tract restored efficient in vitro processing to several independent poly(A) signals in which it substituted for downstream element sequences. The role of the downstream element in polyadenylation efficiency, therefore, may be mediated by sequence-directed alignment or phasing of an hnRNP complex.

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Xu, Ting, Qing Zou, Jing Wu, Bin Yu, Zicheng Xu, Hongzhou Cai, and Wei Zhang. "Heterogeneous nuclear ribonucleoprotein U-like 1 and Poly (ADP-ribose) polymerase 1 are downregulated in renal cell carcinoma and connected with the prognosis." Cancer Biomarkers 13, no. 6 (December 27, 2013): 411–15. http://dx.doi.org/10.3233/cbm-140390.

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39

Gasperini, Lisa, Annalisa Rossi, Nicola Cornella, Daniele Peroni, Paola Zuccotti, Valentina Potrich, Alessandro Quattrone, and Paolo Macchi. "The hnRNP RALY regulates PRMT1 expression and interacts with the ALS-linked protein FUS: implication for reciprocal cellular localization." Molecular Biology of the Cell 29, no. 26 (December 15, 2018): 3067–81. http://dx.doi.org/10.1091/mbc.e18-02-0108.

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The RBP associated with lethal yellow mutation (RALY) is a member of the heterogeneous nuclear ribonucleoprotein family whose transcriptome and interactome have been recently characterized. RALY binds poly-U rich elements within several RNAs and regulates the expression as well as the stability of specific transcripts. Here we show that RALY binds PRMT1 mRNA and regulates its expression. PRMT1 catalyzes the arginine methylation of Fused in Sarcoma (FUS), an RNA-binding protein that interacts with RALY. We demonstrate that RALY down-regulation decreases protein arginine N-methyltransferase 1 levels, thus reducing FUS methylation. It is known that mutations in the FUS nuclear localization signal (NLS) retain the protein to the cytosol, promote aggregate formation, and are associated with amyotrophic lateral sclerosis. Confirming that inhibiting FUS methylation increases its nuclear import, we report that RALY knockout enhances FUS NLS mutants’ nuclear translocation, hence decreasing aggregate formation. Furthermore, we characterize the RNA-dependent interaction of RALY with FUS in motor neurons. We show that mutations in FUS NLS as well as in RALY NLS reciprocally alter their localization and interaction with target mRNAs. These data indicate that RALY’s activity is impaired in FUS pathology models, raising the possibility that RALY might modulate disease onset and/or progression.

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Gabler, Stefan, Holger Schütt, Peter Groitl, Hans Wolf, Thomas Shenk, and Thomas Dobner. "E1B 55-Kilodalton-Associated Protein: a Cellular Protein with RNA-Binding Activity Implicated in Nucleocytoplasmic Transport of Adenovirus and Cellular mRNAs." Journal of Virology 72, no. 10 (October 1, 1998): 7960–71. http://dx.doi.org/10.1128/jvi.72.10.7960-7971.1998.

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ABSTRACT The adenovirus type 5 (Ad5) early 1B 55-kDa protein (E1B-55kDa) is a multifunctional phosphoprotein that regulates viral DNA replication and nucleocytoplasmic RNA transport in lytically infected cells. In addition, E1B-55kDa provides functions required for complete oncogenic transformation of rodent cells in cooperation with the E1A proteins. Using the far-Western technique, we have isolated human genes encoding E1B-55kDa-associated proteins (E1B-APs). The E1B-AP5 gene encodes a novel nuclear RNA-binding protein of the heterogeneous nuclear ribonucleoprotein (hnRNP) family that is highly related to hnRNP-U/SAF-A. Immunoprecipitation experiments indicate that two distinct segments in the 55-kDa polypeptide which partly overlap regions responsible for p53 binding are required for complex formation with E1B-AP5 in Ad-infected cells and that this protein interaction is modulated by the adenovirus E4orf6 protein. Expression of E1B-AP5 efficiently interferes with Ad5 E1A/E1B-mediated transformation of primary rat cells. Furthermore, stable expression of E1B-AP5 in Ad-infected cells overcomes the E1B-dependent inhibition of cytoplasmic host mRNA accumulation. These data suggest that E1B-AP5 might play a role in RNA transport and that this function is modulated by E1B-55kDa in Ad-infected cells.

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Stolow, D. T., and S. M. Berget. "UV cross-linking of polypeptides associated with 3'-terminal exons." Molecular and Cellular Biology 10, no. 11 (November 1990): 5937–44. http://dx.doi.org/10.1128/mcb.10.11.5937.

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Association of nuclear proteins with chimeric vertebrate precursor RNAs containing both polyadenylation signals and an intron was examined by UV cross-linking. One major difference in cross-linking pattern was observed between this chimeric precursor RNA and precursors containing only polyadenylation or splicing signals. The heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptide C cross-linked strongly to sequences downstream of the A addition site in polyadenylation precursor RNA containing only the polyadenylation signal from the simian virus 40 (SV40) late transcription unit. In contrast, the hnRNP C polypeptide cross-linked to chimeric RNA containing the same SV40 late poly(A) cassette very poorly, at a level less than 5% of that observed with the precursor RNA containing just the poly(A) site. Observation that cross-linking of the hnRNP C polypeptide to elements within the SV40 late poly(A) site was altered by the presence of an upstream intron suggests differences in the way nuclear factors associate with poly(A) sites in the presence and absence of an upstream intron. Cross-linking of C polypeptide to chimeric RNA increased with RNAs mutated for splicing or polyadenylation consensus sequences and under reaction conditions (high magnesium) that inhibited polyadenylation. Furthermore, cross-linking of hnRNP C polypeptide to precursors containing just the SV40 late poly(A) site was eliminated in the presence of competing poly(U); polyadenylation, however, was unaffected. Correlation of loss of activity with high levels of hnRNP C polypeptide cross-linking raises questions about the specificity of the interaction between the hnRNP C polypeptide and polyadenylation precursor RNAs in vitro.

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42

Stolow, D. T., and S. M. Berget. "UV cross-linking of polypeptides associated with 3'-terminal exons." Molecular and Cellular Biology 10, no. 11 (November 1990): 5937–44. http://dx.doi.org/10.1128/mcb.10.11.5937-5944.1990.

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Association of nuclear proteins with chimeric vertebrate precursor RNAs containing both polyadenylation signals and an intron was examined by UV cross-linking. One major difference in cross-linking pattern was observed between this chimeric precursor RNA and precursors containing only polyadenylation or splicing signals. The heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptide C cross-linked strongly to sequences downstream of the A addition site in polyadenylation precursor RNA containing only the polyadenylation signal from the simian virus 40 (SV40) late transcription unit. In contrast, the hnRNP C polypeptide cross-linked to chimeric RNA containing the same SV40 late poly(A) cassette very poorly, at a level less than 5% of that observed with the precursor RNA containing just the poly(A) site. Observation that cross-linking of the hnRNP C polypeptide to elements within the SV40 late poly(A) site was altered by the presence of an upstream intron suggests differences in the way nuclear factors associate with poly(A) sites in the presence and absence of an upstream intron. Cross-linking of C polypeptide to chimeric RNA increased with RNAs mutated for splicing or polyadenylation consensus sequences and under reaction conditions (high magnesium) that inhibited polyadenylation. Furthermore, cross-linking of hnRNP C polypeptide to precursors containing just the SV40 late poly(A) site was eliminated in the presence of competing poly(U); polyadenylation, however, was unaffected. Correlation of loss of activity with high levels of hnRNP C polypeptide cross-linking raises questions about the specificity of the interaction between the hnRNP C polypeptide and polyadenylation precursor RNAs in vitro.

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Cok, Steven J., Stephen J. Acton, and Aubrey R. Morrison. "The Proximal Region of the 3′-Untranslated Region of Cyclooxygenase-2 is Recognized by a Multimeric Protein Complex Containing HuR, TIA-1, TIAR, and the Heterogeneous Nuclear Ribonucleoprotein U." Journal of Biological Chemistry 278, no. 38 (July 9, 2003): 36157–62. http://dx.doi.org/10.1074/jbc.m302547200.

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Zhang, Xuan, Chenyi Xue, Jennie Lin, Jane F. Ferguson, Amber Weiner, Wen Liu, Yumiao Han, et al. "Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism." Science Translational Medicine 10, no. 446 (June 20, 2018): eaar5987. http://dx.doi.org/10.1126/scitranslmed.aar5987.

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Long intergenic noncoding RNAs (lincRNAs) have emerged as important modulators of cellular functions. Most lincRNAs are not conserved among mammals, raising the fundamental question of whether nonconserved adipose-expressed lincRNAs are functional. To address this, we performed deep RNA sequencing of gluteal subcutaneous adipose tissue from 25 healthy humans. We identified 1001 putative lincRNAs expressed in all samples through de novo reconstruction of noncoding transcriptomes and integration with existing lincRNA annotations. One hundred twenty lincRNAs had adipose-enriched expression, and 54 of these exhibited peroxisome proliferator–activated receptor γ (PPARγ) or CCAAT/enhancer binding protein α (C/EBPα) binding at their loci. Most of these adipose-enriched lincRNAs (~85%) were not conserved in mice, yet on average, they showed degrees of expression and binding of PPARγ and C/EBPα similar to those displayed by conserved lincRNAs. Most adipose lincRNAs differentially expressed (n = 53) in patients after bariatric surgery were nonconserved. The most abundant adipose-enriched lincRNA in our subcutaneous adipose data set, linc-ADAL, was nonconserved, up-regulated in adipose depots of obese individuals, and markedly induced during in vitro human adipocyte differentiation. We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.

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Spagnoli, Carlotta, Susanna Rizzi, Grazia Gabriella Salerno, Daniele Frattini, Juha Koskenvuo, and Carlo Fusco. "Pharmacological Treatment of Severe Breathing Abnormalities in a Case of HNRNPU Epileptic Encephalopathy." Molecular Syndromology 12, no. 2 (2021): 101–5. http://dx.doi.org/10.1159/000512566.

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Abnormal breathing patterns are a typical feature of Rett and Pitt-Hopkins syndrome and their variants. Their treatment can be challenging, with a risk of long-term detrimental consequences. Early infantile epileptic encephalopathy (EIEE) type 54 is a rare epileptic encephalopathy caused by pathogenic variants in the heterogeneous nuclear ribonucleoprotein U (HNRNPU) gene. Only one case has been described in the literature with episodes of hyperventilation and apnea, but treatment was not discussed. We describe the clinical and genetic features and treatment strategies in a case of EIEE type 54 and severely abnormal breathing pattern. A novel and likely pathogenic c.2277dup, p.(Pro760Serfs*5) variant in the HNRNPU gene was found in a male patient with severe episodes of hyperventilation and apnea, leading to syncope. Combination therapy with acetazolamide, alprazolam and aripiprazole led to significant clinical improvement. Although HNRNPU has not been implicated in breathing control, pathogenic variants in this gene can be associated with the development of abnormal breathing patterns reminiscent of Rett and Pitt-Hopkins syndrome. Its function as a gene expression regulator and its interaction with transcription factors offers a potential pathogenetic link between these 3 disorders. Based on our experience, treatment strategies can be similar to those already applied for patients with Pitt-Hopkins and Rett syndrome.

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Ing, Nancy H., Dana A. Massuto, and Laurie A. Jaeger. "Estradiol Up-regulates AUF1p45 Binding to Stabilizing Regions within the 3′-Untranslated Region of Estrogen Receptor α mRNA." Journal of Biological Chemistry 283, no. 3 (November 19, 2007): 1764–72. http://dx.doi.org/10.1074/jbc.m704745200.

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Estradiol up-regulates expression of the estrogen receptor α gene in the uterus by stabilizing estrogen receptor α mRNA. Previously, we defined two discrete minimal estradiol-modulated stability sequences (MEMSS) within the extensive 3′-untranslated region of estrogen receptor α mRNA with an in vitro stability assay using cytosolic extracts from sheep uterus. We report here that excess MEMSS RNA inhibited the enhanced stability of estrogen receptor α mRNA in extracts from estradiol-treated ewes compared with those from control ewes. Several estradiol-induced MEMSS-binding proteins were characterized by UV cross-linking in uterine extracts from ewes in a time course study (0, 8, 16, and 24 h after estradiol injection). The pattern of binding proteins changed at 16 h post-injection, concurrent with enhanced estrogen receptor α mRNA stability and the highest rate of accumulation of estrogen receptor α mRNA. The predominant MEMSS-binding protein induced by estradiol treatment was identified as AUF1 (A + U-rich RNA-binding factor 1) protein isoform p45 (a product of the heterogeneous nuclear ribonucleoprotein D gene). Immunoblot analysis indicated that only two of four AUF1 protein isoforms were present in the uterine cytosolic extracts and that estradiol treatment strongly increased the ratio of AUF1 isoforms p45 to p37. Nonphosphorylated recombinant AUF1p45 protected estrogen receptor α mRNA in vitro in a dose-dependent manner. These studies describe estrogenic induction of AUF1p45 binding to the estrogen receptor α mRNA as a molecular mechanism for post-transcriptional up-regulation of gene expression.

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Watson, Gregory, Daniel Lester, Hui Ren, Connor M. Forsyth, Elliot Medina, David Gonzalez Perez, Lancia Darville, et al. "Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3." Cells 10, no. 6 (May 25, 2021): 1310. http://dx.doi.org/10.3390/cells10061310.

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Alterations in genes encoding for proteins that control fucosylation are known to play causative roles in several developmental disorders, such as Dowling-Degos disease 2 and congenital disorder of glycosylation type IIc (CDGIIc). Recent studies have provided evidence that changes in fucosylation can contribute to the development and progression of several different types of cancers. It is therefore important to gain a detailed understanding of how fucosylation is altered in disease states so that interventions may be developed for therapeutic purposes. In this report, we find that fucosylation occurs on many intracellular proteins. This is an interesting finding, as the fucosylation machinery is restricted to the secretory pathway and is thought to predominately affect cell-membrane-bound and secreted proteins. We find that Ribosomal protein S3 (RPS3) is fucosylated in normal tissues and in cancer cells, and that the extent of its fucosylation appears to respond to stress, including MAPK inhibitors, suggesting a new role in posttranslational protein function. Our data identify a new ribosome-independent species of fucosylated RPS3 that interacts with proteins involved in posttranscriptional regulation of RNA, such as Heterogeneous nuclear ribonucleoprotein U (HNRNPU), as well as with a predominance of non-coding RNAs. These data highlight a novel role for RPS3, which, given previously reported oncogenic roles for RPS3, might represent functions that are perturbed in pathologies such as cancer. Together, our findings suggest a previously unrecognized role for fucosylation in directly influencing intracellular protein functions.

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Prescott, J., and E. Falck-Pedersen. "Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites." Molecular and Cellular Biology 14, no. 7 (July 1994): 4682–93. http://dx.doi.org/10.1128/mcb.14.7.4682.

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The adenovirus major late transcription unit is a well-characterized transcription unit which relies heavily on alternative pre-mRNA processing to generate distinct populations of mRNA during the early and late stages of viral infection. In the early stage of infection, two major late transcription unit mRNA transcripts are generated through use of the first (L1) of five available poly(A) sites (L1 through L5). This contrasts with the late stage of infection when as many as 45 distinct mRNAs are generated, with each of the five poly(A) sites being used. In previous work characterizing elements involved in alternative poly(A) site use, we showed that the L1 poly(A) site is processed less efficiently than the L3 poly(A) site both in vitro and in vivo. Because of the dramatic difference in processing efficiency and the role processing efficiency plays in production of steady-state levels of mRNA, we have identified the sequence elements that account for the differences in L1 and L3 poly(A) site processing efficiency. We have found that the element most likely to be responsible for poly(A) site strength, the GU/U-rich downstream element, plays a minor role in the different processing efficiencies observed for the L1 and L3 poly(A) sites. The sequence element most responsible for inefficient processing of the L1 poly(A) site includes the L1 AAUAAA consensus sequence and those sequences which immediately surround the consensus hexanucleotide. This region of the L1 poly(A) site contributes to an inability to form a stable processing complex with the downstream GU/U-rich element. In contrast to the L1 element, the L3 poly(A) site has a consensus hexanucleotide and surrounding sequences which can form a stable processing complex in cooperation with the downstream GU/U-rich element. The L3 poly(A) site is also aided by the presence of sequences upstream of the hexanucleotide which facilitate processing efficiency. The sequence UUCUUUUU, present in the L3 upstream region, is shown to enhance processing efficiency as well as stable complex formation (shown by increased binding of the 64-kDa cleavage stimulatory factor subunit) and acts as a binding site for heterogeneous nuclear ribonucleoprotein C proteins.

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Prescott, J., and E. Falck-Pedersen. "Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites." Molecular and Cellular Biology 14, no. 7 (July 1994): 4682–93. http://dx.doi.org/10.1128/mcb.14.7.4682-4693.1994.

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The adenovirus major late transcription unit is a well-characterized transcription unit which relies heavily on alternative pre-mRNA processing to generate distinct populations of mRNA during the early and late stages of viral infection. In the early stage of infection, two major late transcription unit mRNA transcripts are generated through use of the first (L1) of five available poly(A) sites (L1 through L5). This contrasts with the late stage of infection when as many as 45 distinct mRNAs are generated, with each of the five poly(A) sites being used. In previous work characterizing elements involved in alternative poly(A) site use, we showed that the L1 poly(A) site is processed less efficiently than the L3 poly(A) site both in vitro and in vivo. Because of the dramatic difference in processing efficiency and the role processing efficiency plays in production of steady-state levels of mRNA, we have identified the sequence elements that account for the differences in L1 and L3 poly(A) site processing efficiency. We have found that the element most likely to be responsible for poly(A) site strength, the GU/U-rich downstream element, plays a minor role in the different processing efficiencies observed for the L1 and L3 poly(A) sites. The sequence element most responsible for inefficient processing of the L1 poly(A) site includes the L1 AAUAAA consensus sequence and those sequences which immediately surround the consensus hexanucleotide. This region of the L1 poly(A) site contributes to an inability to form a stable processing complex with the downstream GU/U-rich element. In contrast to the L1 element, the L3 poly(A) site has a consensus hexanucleotide and surrounding sequences which can form a stable processing complex in cooperation with the downstream GU/U-rich element. The L3 poly(A) site is also aided by the presence of sequences upstream of the hexanucleotide which facilitate processing efficiency. The sequence UUCUUUUU, present in the L3 upstream region, is shown to enhance processing efficiency as well as stable complex formation (shown by increased binding of the 64-kDa cleavage stimulatory factor subunit) and acts as a binding site for heterogeneous nuclear ribonucleoprotein C proteins.

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Xiao, Suhong, Ying-Sheng Tang, Rehana A. Khan, Yonghua Zhang, Praveen Kusumanchi, Sally P. Stabler, Hiremagalur N. Jayaram, and Aśok C. Antony. "Influence of Physiologic Folate Deficiency on Human Papillomavirus Type 16 (HPV16)-harboring Human Keratinocytes in Vitro and in Vivo." Journal of Biological Chemistry 287, no. 15 (February 17, 2012): 12559–77. http://dx.doi.org/10.1074/jbc.m111.317040.

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Although HPV16 transforms infected epithelial tissues to cancer in the presence of several co-factors, there is insufficient molecular evidence that poor nutrition has any such role. Because physiological folate deficiency led to the intracellular homocysteinylation of heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) and activated a nutrition-sensitive (homocysteine-responsive) posttranscriptional RNA operon that included interaction with HPV16 L2 mRNA, we investigated the functional consequences of folate deficiency on HPV16 in immortalized HPV16-harboring human (BC-1-Ep/SL) keratinocytes and HPV16-organotypic rafts. Although homocysteinylated hnRNP-E1 interacted with HPV16 L2 mRNA cis-element, it also specifically bound another HPV16 57-nucleotide poly(U)-rich cis-element in the early polyadenylation element (upstream of L2̂L1 genes) with greater affinity. Together, these interactions led to a profound reduction of both L1 and L2 mRNA and proteins without effects on HPV16 E6 and E7 in vitro, and in cultured keratinocyte monolayers and HPV16-low folate-organotypic rafts developed in physiological low folate medium. In addition, HPV16-low folate-organotypic rafts contained fewer HPV16 viral particles, a similar HPV16 DNA viral load, and a much greater extent of integration of HPV16 DNA into genomic DNA when compared with HPV16-high folate-organotypic rafts. Subcutaneous implantation of 18-day old HPV16-low folate-organotypic rafts into folate-replete immunodeficient mice transformed this benign keratinocyte-derived raft tissue into an aggressive HPV16-induced cancer within 12 weeks. Collectively, these studies establish a likely molecular linkage between poor folate nutrition and HPV16 and predict that nutritional folate and/or vitamin-B12 deficiency, which are both common worldwide, will alter the natural history of HPV16 infections and also warrant serious consideration as reversible co-factors in oncogenic transformation of HPV16-infected tissues to cancer.

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Journal articles on the topic 'Heterogeneous-Nuclear Ribonucleoprotein U'

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