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Journal articles on the topic 'Independent 3'UTR RNA'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Newburn, Laura R., Baodong Wu, and K. Andrew White. "Investigation of Novel RNA Elements in the 3′UTR of Tobacco Necrosis Virus-D." Viruses 12, no. 8 (2020): 856. http://dx.doi.org/10.3390/v12080856.

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RNA elements in the untranslated regions of plus-strand RNA viruses can control a variety of viral processes including translation, replication, packaging, and subgenomic mRNA production. The 3′ untranslated region (3′UTR) of Tobacco necrosis virus strain D (TNV-D; genus Betanecrovirus, family Tombusviridae) contains several well studied regulatory RNA elements. Here, we explore a previously unexamined region of the viral 3′UTR, the sequence located upstream of the 3′-cap independent translation enhancer (3′CITE). Our results indicate that (i) a long-range RNA–RNA interaction between an intern

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2

Serrano, Paula, Miguel Rodriguez Pulido, Margarita Sáiz, and Encarnacion Martínez-Salas. "The 3′ end of the foot-and-mouth disease virus genome establishes two distinct long-range RNA–RNA interactions with the 5′ end region." Journal of General Virology 87, no. 10 (2006): 3013–22. http://dx.doi.org/10.1099/vir.0.82059-0.

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The untranslated regions (UTRs) of the foot-and-mouth disease virus (FMDV) genome contain multiple functional elements. In the 5′ UTR, the internal ribosome entry site (IRES) element governs cap-independent translation initiation, whereas the S region is presumably involved in RNA replication. The 3′ UTR, composed of two stem–loops and a poly(A) tract, is required for viral infectivity and stimulates IRES activity. Here, it was found that the 3′ end established two distinct strand-specific, long-range RNA–RNA interactions, one with the S region and another with the IRES element. These interact

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3

Huang, Cheng-Yen, Yih-Leh Huang, Menghsiao Meng, Yau-Heiu Hsu, and Ching-Hsiu Tsai. "Sequences at the 3′ Untranslated Region of Bamboo Mosaic Potexvirus RNA Interact with the Viral RNA-Dependent RNA Polymerase." Journal of Virology 75, no. 6 (2001): 2818–24. http://dx.doi.org/10.1128/jvi.75.6.2818-2824.2001.

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ABSTRACT The 3′ untranslated region (UTR) of bamboo mosaic potexvirus (BaMV) genomic RNA was found to fold into a series of stem-loop structures including a pseudoknot structure. These structures were demonstrated to be important for viral RNA replication and were believed to be recognized by the replicase (C.-P. Cheng and C.-H. Tsai, J. Mol. Biol. 288:555–565, 1999). Electrophoretic mobility shift and competition assays have now been used to demonstrate that theEscherichia coli-expressed RNA-dependent RNA polymerase domain (Δ893) derived from BaMV open reading frame 1 could specifically bind

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4

Berzal-Herranz, Alfredo, Beatriz Berzal-Herranz, Sara Esther Ramos-Lorente, and Cristina Romero-López. "The Genomic 3′ UTR of Flaviviruses Is a Translation Initiation Enhancer." International Journal of Molecular Sciences 23, no. 15 (2022): 8604. http://dx.doi.org/10.3390/ijms23158604.

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Viruses rely on the cellular machinery of host cells to synthesize their proteins, and have developed different mechanisms enabling them to compete with cellular mRNAs for access to it. The genus Flavivirus is a large group of positive, single-stranded RNA viruses that includes several important human pathogens, such as West Nile, Dengue and Zika virus. The genome of flaviviruses bears a type 1 cap structure at its 5′ end, needed for the main translation initiation mechanism. Several members of the genus also use a cap-independent translation mechanism. The present work provides evidence that

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5

Liu, D., and P. Xue. "Existence of independent C/EBP 3'-UTR RNA in human tissues." Acta Biochimica et Biophysica Sinica 46, no. 1 (2013): 76–77. http://dx.doi.org/10.1093/abbs/gmt120.

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6

Wang, Sai, Kitti Wing Ki Chan, Min Jie Alvin Tan, et al. "A conserved arginine in NS5 binds genomic 3′ stem–loop RNA for primer-independent initiation of flavivirus RNA replication." RNA 28, no. 2 (2021): 177–93. http://dx.doi.org/10.1261/rna.078949.121.

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The commitment to replicate the RNA genome of flaviviruses without a primer involves RNA–protein interactions that have been shown to include the recognition of the stem–loop A (SLA) in the 5′ untranslated region (UTR) by the nonstructural protein NS5. We show that DENV2 NS5 arginine 888, located within the carboxy-terminal 18 residues, is completely conserved in all flaviviruses and interacts specifically with the top-loop of 3′SL in the 3′UTR which contains the pentanucleotide 5′-CACAG-3′ previously shown to be critical for flavivirus RNA replication. We present virological and biochemical d

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7

Shen, Ruizhong, Aurélie M. Rakotondrafara, and W. Allen Miller. "trans Regulation of Cap-Independent Translation by a Viral Subgenomic RNA." Journal of Virology 80, no. 20 (2006): 10045–54. http://dx.doi.org/10.1128/jvi.00991-06.

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ABSTRACT Many positive-strand RNA viruses generate 3′-coterminal subgenomic mRNAs to allow translation of 5′-distal open reading frames. It is unclear how viral genomic and subgenomic mRNAs compete with each other for the cellular translation machinery. Translation of the uncapped Barley yellow dwarf virus genomic RNA (gRNA) and subgenomic RNA1 (sgRNA1) is driven by the powerful cap-independent translation element (BTE) in their 3′ untranslated regions (UTRs). The BTE forms a kissing stem-loop interaction with the 5′ UTR to mediate translation initiation at the 5′ end. Here, using reporter mRN

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8

Ji, Xinjun, Jian Kong, Russ P. Carstens та Stephen A. Liebhaber. "The 3′ Untranslated Region Complex Involved in Stabilization of Human α-globin mRNA Assembles in the Nucleus and Serves an Independent Role as a Splice Enhancer". Molecular and Cellular Biology 27, № 9 (2007): 3290–302. http://dx.doi.org/10.1128/mcb.02289-05.

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ABSTRACT Posttranscriptional controls, mediated primarily by RNA-protein complexes, have the potential to alter multiple steps in RNA processing and function. Human α-globin mRNA is bound at a C-rich motif in the 3′ untranslated region (3′UTR) by the KH domain protein α-globin poly(C)-binding protein (αCP). This “α-complex” is essential to cytoplasmic stability of α-globin mRNA in erythroid cells. Here we report that the 3′UTR α-complex also serves an independent nuclear role as a splice enhancer. Consistent with this role, we find that αCP binds α-globin transcripts prior to splicing. Surpris

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Bhardwaj, Usha, Paul Powell, and Dixie J. Goss. "Eukaryotic initiation factor (eIF) 3 mediates Barley Yellow Dwarf Viral mRNA 3′–5′ UTR interactions and 40S ribosomal subunit binding to facilitate cap-independent translation." Nucleic Acids Research 47, no. 12 (2019): 6225–35. http://dx.doi.org/10.1093/nar/gkz448.

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Abstract Barley Yellow Dwarf Virus (BYDV) is a positive strand RNA virus that lacks the canonical 5′ 7-methylguanosine cap and a 3′ poly-A tail. Instead, BYDV utilizes a cruciform cap independent translation element (CITE) in its 3′UTR RNA (BYDV-like CITE or BTE) that binds eukaryotic translation initiation factor (eIF) 4F and recruits 40S ribosomal subunits in the presence of active helicase factors (eIF4A, eIF4B, eIF4F and ATP). A long-range, 5-nucleotide, base-pairing kissing loop interaction between the 3′BTE and a 5′UTR stem-loop is necessary for translation to initiate. The 40S–eIF compl

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10

Qu, Feng, and T. Jack Morris. "Cap-Independent Translational Enhancement of Turnip Crinkle Virus Genomic and Subgenomic RNAs." Journal of Virology 74, no. 3 (2000): 1085–93. http://dx.doi.org/10.1128/jvi.74.3.1085-1093.2000.

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ABSTRACT The presence of translational control elements and cap structures has not been carefully investigated for members of theCarmovirus genus, a group of small icosahedral plant viruses with positive-sense RNA genomes. In this study, we examined both the 5′ and 3′ untranslated regions (UTRs) of the turnip crinkle carmovirus (TCV) genomic RNA (4 kb) as well as the 5′ UTR of the coat protein subgenomic RNA (1.45 kb) for their roles in translational regulation. All three UTRs enhanced translation of the firefly luciferase reporter gene to different extents. Optimal translational efficiency wa

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11

Paudel, Dinesh Babu, and Hélène Sanfaçon. "Mapping of sequences in the 5’ region and 3’ UTR of tomato ringspot virus RNA2 that facilitate cap-independent translation of reporter transcripts in vitro." PLOS ONE 16, no. 4 (2021): e0249928. http://dx.doi.org/10.1371/journal.pone.0249928.

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Tomato ringspot virus (ToRSV, genus Nepovirus, family Secoviridae, order Picornavirales) is a bipartite positive-strand RNA virus, with each RNA encoding one large polyprotein. ToRSV RNAs are linked to a 5’-viral genome-linked protein (VPg) and have a 3’ polyA tail, suggesting a non-canonical cap-independent translation initiation mechanism. The 3’ untranslated regions (UTRs) of RNA1 and RNA2 are unusually long (~1.5 kb) and share several large stretches of sequence identities. Several putative in-frame start codons are present in the 5’ regions of the viral RNAs, which are also highly conserv

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12

Wang, Zhaowei, Di Wu, Yongxiang Liu, et al. "Drosophila Dicer-2 has an RNA interference–independent function that modulates Toll immune signaling." Science Advances 1, no. 9 (2015): e1500228. http://dx.doi.org/10.1126/sciadv.1500228.

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Dicer-2 is the central player for small interfering RNA biogenesis in the Drosophila RNA interference (RNAi) pathway. Intriguingly, we found that Dicer-2 has an unconventional RNAi-independent function that positively modulates Toll immune signaling, which defends against Gram-positive bacteria, fungi, and some viruses, in both cells and adult flies. The loss of Dicer-2 expression makes fruit flies more susceptible to fungal infection. We further revealed that Dicer-2 posttranscriptionally modulates Toll signaling because Dicer-2 is required for the proper expression of Toll protein but not fo

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13

Ander, Stephanie E., Kathryn S. Carpentier, Wes Sanders, et al. "A 44-Nucleotide Region in the Chikungunya Virus 3′ UTR Dictates Viral Fitness in Disparate Host Cells." Viruses 16, no. 6 (2024): 861. http://dx.doi.org/10.3390/v16060861.

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We previously reported that deletion of a 44-nucleotide element in the 3′ untranslated region (UTR) of the Chikungunya virus (CHIKV) genome enhances the virulence of CHIKV infection in mice. Here, we find that while this 44-nucleotide deletion enhances CHIKV fitness in murine embryonic fibroblasts in a manner independent of the type I interferon response, the same mutation decreases viral fitness in C6/36 mosquito cells. Further, the fitness advantage conferred by the UTR deletion in mammalian cells is maintained in vivo in a mouse model of CHIKV dissemination. Finally, SHAPE-MaP analysis of t

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14

Shen, Ruizhong, and W. Allen Miller. "The 3′ Untranslated Region of Tobacco Necrosis Virus RNA Contains a Barley Yellow Dwarf Virus-Like Cap-Independent Translation Element." Journal of Virology 78, no. 9 (2004): 4655–64. http://dx.doi.org/10.1128/jvi.78.9.4655-4664.2004.

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ABSTRACT RNAs of many viruses are translated efficiently in the absence of a 5′ cap structure. The tobacco necrosis virus (TNV) genome is an uncapped, nonpolyadenylated RNA whose translation mechanism has not been well investigated. Computational analysis predicted a cap-independent translation element (TE) within the 3′ untranslated region (3′ UTR) of TNV RNA that resembles the TE of barley yellow dwarf virus (BYDV), a luteovirus. Here we report that such a TE does indeed exist in the 3′ UTR of TNV strain D. Like the BYDV TE, the TNV TE (i) functions both in vitro and in vivo, (ii) requires a

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15

Truniger, Verónica, Giuliano Sting Pechar, and Miguel A. Aranda. "Advances in Understanding the Mechanism of Cap-Independent Cucurbit Aphid-Borne Yellows Virus Protein Synthesis." International Journal of Molecular Sciences 24, no. 24 (2023): 17598. http://dx.doi.org/10.3390/ijms242417598.

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Non-canonical translation mechanisms have been described for many viral RNAs. In the case of several plant viruses, their protein synthesis is controlled by RNA elements in their genomic 3′-ends that are able to enhance cap-independent translation (3′-CITE). The proposed general mechanism of 3′-CITEs includes their binding to eukaryotic translation initiation factors (eIFs) that reach the 5′-end and AUG start codon through 5′-3′-UTR-interactions. It was previously shown that cucurbit aphid-borne yellows virus (CABYV) has a 3′-CITE, which varies in sequence and structure depending on the phylog

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16

Iwakawa, Hiro-oki, Hiroyuki Mizumoto, Hideaki Nagano, et al. "A Viral Noncoding RNA Generated by cis-Element-Mediated Protection against 5′→3′ RNA Decay Represses both Cap-Independent and Cap-Dependent Translation." Journal of Virology 82, no. 20 (2008): 10162–74. http://dx.doi.org/10.1128/jvi.01027-08.

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ABSTRACT Positive-strand RNA viruses use diverse mechanisms to regulate viral and host gene expression for ensuring their efficient proliferation or persistence in the host. We found that a small viral noncoding RNA (0.4 kb), named SR1f, accumulated in Red clover necrotic mosaic virus (RCNMV)-infected plants and protoplasts and was packaged into virions. The genome of RCNMV consists of two positive-strand RNAs, RNA1 and RNA2. SR1f was generated from the 3′ untranslated region (UTR) of RNA1, which contains RNA elements essential for both cap-independent translation and negative-strand RNA synth

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Singh, Irtisha, Mehmet K. Samur, Lee Shih-Han, et al. "Global 3' UTR Sequencing in Multiple Myeloma (MM)." Blood 126, no. 23 (2015): 2994. http://dx.doi.org/10.1182/blood.v126.23.2994.2994.

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Abstract The 3' untranslated region (3'UTR) of mRNA contains elements that play regulatory roles in polyadenylation, localization, translation efficiency, and mRNA stability. Although relative contributions of different regulatory mechanisms remain poorly understood, several recent studies showed that alterations in 3'UTRs may affect protein localization as well as their interactions with other proteins. Here, we obtained global measurements of 3'UTR sequencing and RNA-seq in MM and normal plasma cells to study the effects of 3'UTR alterations in MM. The transcriptomes of 15 MM samples and two

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18

Mizumoto, Hiroyuki, Hiro-oki Iwakawa, Masanori Kaido, Kazuyuki Mise, and Tetsuro Okuno. "Cap-Independent Translation Mechanism of Red Clover Necrotic Mosaic Virus RNA2 Differs from That of RNA1 and Is Linked to RNA Replication." Journal of Virology 80, no. 8 (2006): 3781–91. http://dx.doi.org/10.1128/jvi.80.8.3781-3791.2006.

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ABSTRACT The genome of Red clover necrotic mosaic virus (RCNMV) in the genus Dianthovirus is divided into two RNA molecules of RNA1 and RNA2, which have no cap structure at the 5′ end and no poly(A) tail at the 3′ end. The 3′ untranslated region (3′ UTR) of RCNMV RNA1 contains an essential RNA element (3′TE-DR1), which is required for cap-independent translation. In this study, we investigated a cap-independent translational mechanism of RNA2 using a firefly luciferase (Luc) gene expression assay system in cowpea protoplasts and a cell-free lysate (BYL) prepared from evacuolated tobacco BY2 pr

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Kong, Jian, Xinjun Ji та Stephen A. Liebhaber. "The KH-Domain Protein αCP Has a Direct Role in mRNA Stabilization Independent of Its Cognate Binding Site". Molecular and Cellular Biology 23, № 4 (2003): 1125–34. http://dx.doi.org/10.1128/mcb.23.4.1125-1134.2003.

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ABSTRACT Previous studies suggest that high-level stability of a subset of mammalian mRNAs is linked to a C-rich motif in the 3′ untranslated region (3′UTR). High-level expression of human α-globin mRNA (hα-globin mRNA) in erythroid cells has been specifically attributed to formation of an RNA-protein complex comprised of a 3′UTR C-rich motif and an associated 39-kDa poly(C) binding protein, αCP. Documentation of this RNA-protein α-complex has been limited to in vitro binding studies, and its impact has been monitored by alterations in steady-state mRNA. Here we demonstrate that αCP is stably

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Reichard, N., A. Kerstein-Staehle, A. Müller, G. Riemekasten, P. Lamprecht, and S. Schinke. "THU0025 MICRO-RNA DIFFERENTIALLY REGULATE THE ALTERNATIVE PRTN3-MRNA IN GRANULOMATOSIS WITH POLYANGIITIS." Annals of the Rheumatic Diseases 79, Suppl 1 (2020): 225.2–226. http://dx.doi.org/10.1136/annrheumdis-2020-eular.4700.

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Background:Micro-RNAs (miRNA) are short non-coding RNAs that regulate inflammation mostly by translational repression. Previously, we screened 847 miRNAs in nasal tissue from GPA patients and found a disease associated alteration of miRNA expression compared to healthy controls and chronic rhinosinusitis. MiR-184 was most over expressed in nasal tissue from GPA (13.4x). The dual-luciferase reporter assay confirmed a significant reduction of Proteinase-3 (PRTN3) expression by miR-184 (1).PRTN3 transcripts with an alternative 3’ untranslated region (UTR) have been described in GPA (2). The patho

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Miras, Manuel, Miguel A. Aranda, and Verónica Truniger. "Different RNA Elements Control Viral Protein Synthesis in Polerovirus Isolates Evolved in Separate Geographical Regions." International Journal of Molecular Sciences 23, no. 20 (2022): 12503. http://dx.doi.org/10.3390/ijms232012503.

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Most plant viruses lack the 5′-cap and 3′-poly(A) structures, which are common in their host mRNAs, and are crucial for translation initiation. Thus, alternative translation initiation mechanisms were identified for viral mRNAs, one of these being controlled by an RNA element in their 3′-ends that is able to enhance mRNA cap-independent translation (3′-CITE). The 3′-CITEs are modular and transferable RNA elements. In the case of poleroviruses, the mechanism of translation initiation of their RNAs in the host cell is still unclear; thus, it was studied for one of its members, cucurbit aphid-bor

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Matsuda, Daiki, Lisa Bauer, Kathryn Tinnesand, and Theo W. Dreher. "Expression of the Two Nested Overlapping Reading Frames of Turnip Yellow Mosaic Virus RNA Is Enhanced by a 5′ Cap and by 5′ and 3′ Viral Sequences." Journal of Virology 78, no. 17 (2004): 9325–35. http://dx.doi.org/10.1128/jvi.78.17.9325-9335.2004.

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ABSTRACT The translation efficiency of an mRNA molecule is typically determined by its 5′- and/or 3′-untranslated regions (UTRs). Previously, we have found that the 3′-UTR of Turnip yellow mosaic virus (TYMV) RNA enhances translation synergistically with a 5′ cap. Here, we use a luciferase reporter system in cowpea protoplasts to show that the 5′ 217 nucleotides from TYMV genomic RNA enhance expression relative to a vector-derived 17-nucleotide 5′-UTR. Maximum expression was observed from RNAs with a cap and both 5′ and 3′ TYMV sequences. In paired reporter constructs, the 5′ 217 nucleotides h

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23

Zhang, Long-Bin, Ting-Ting Qiu, and Wu-Wei-Jie Yang. "Bioinformatic Analysis Reveals the Distinct Role of 5′UTR-Specific m6A RNA Modification in Mice Developing Cerebral Cortices." Developmental Neuroscience 44, no. 2 (2021): 67–79. http://dx.doi.org/10.1159/000521620.

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N6-methyladenosine (m6A) abundantly exists in the cerebral cortex and is emerging as an essential factor in cortical development and function. As the m6A-binding site appears to be dynamically methylated in different RNA regions at the temporal-specific developing stage, it is of value to distinguish the unique character of region- and temporal-specific m6A. Herein, we analyzed the status of temporal-specific m6A within RNA 5′ untranslated region (5′UTR) using m6A-methylated sequencing data and transcriptomic sequencing data from 12.5- to 13-day embryonic cerebral cortices and 14-day postnatal

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Spicher, Albert, Oivin M. Guicherit, Laurent Duret, et al. "Highly Conserved RNA Sequences That Are Sensors of Environmental Stress." Molecular and Cellular Biology 18, no. 12 (1998): 7371–82. http://dx.doi.org/10.1128/mcb.18.12.7371.

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ABSTRACTThe putative function of highly conserved regions (HCRs) within 3′ untranslated regions (3′UTRs) as regulatory RNA sequences was efficiently and quantitatively assessed by using modular retroviral vectors. This strategy led to the identification of HCRs that alter gene expression in response to oxidative or mitogenic stress. Databases were screened for UTR sequences of >100 nucleotides that had retained 70% identity over more than 300 million years of evolution. The effects of 10 such HCRs on a standard reporter mRNA or protein were studied. To this end, we developed a modular retro

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Schumacher, J. M., K. Lee, S. Edelhoff, and R. E. Braun. "Spnr, a murine RNA-binding protein that is localized to cytoplasmic microtubules." Journal of Cell Biology 129, no. 4 (1995): 1023–32. http://dx.doi.org/10.1083/jcb.129.4.1023.

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Previous studies in transgenic mice have established the importance of the 3' untranslated region (UTR) of the spermatid-specific protamine-1 (Prm-1) mRNA in its translational control during male germ cell development. To clone genes that mediate the translational repression or activation of the Prm-1 mRNA, we screened cDNA expression libraries made with RNA from pachytene spermatocytes and round spermatids, with an RNA probe corresponding to the 3' UTR of Prm-1. We obtained six independent clones that encode Spnr, a spermatid perinuclear RNA-binding protein. Spnr is a 71-kD protein that conta

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Wang, Aikun, Paul K. M. Cheung, Huifang Zhang, et al. "Specific Inhibition of Coxsackievirus B3 Translation and Replication by Phosphorothioate Antisense Oligodeoxynucleotides." Antimicrobial Agents and Chemotherapy 45, no. 4 (2001): 1043–52. http://dx.doi.org/10.1128/aac.45.4.1043-1052.2001.

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ABSTRACT The 5′ and 3′ untranslated regions (UTRs) of coxsackievirus B3 (CVB3) RNA form highly ordered secondary structures that have been confirmed to play important regulatory roles in viral cap-independent internal translation initiation and RNA replication. We previously demonstrated that deletions in different regions of the 5′ UTR significantly reduced viral RNA translation and infectivity. Such observations suggested strongly that viral RNA translation and replication could be blocked if highly specific antisense oligodeoxynucleotides (AS-ODNs) were applied to target crucial sites withi

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Gu, Tongjun, Audrey Q. Fu, Michael J. Bolt, and Kevin P. White. "Clinical Relevance of Noncoding Adenosine-to-Inosine RNA Editing in Multiple Human Cancers." JCO Clinical Cancer Informatics, no. 3 (December 2019): 1–8. http://dx.doi.org/10.1200/cci.18.00151.

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PURPOSE RNA editing is a post-transcriptional process that alters the nucleotide sequences of certain transcripts, in vertebrate most often converting adenosines to inosines. Multiple studies have recently implicated RNA editing in cancer development; however, most studies have focused on recoding RNA editing events. The function and clinical relevance of noncoding RNA (ncRNA) editing events in cancers have not been systematically examined. PATIENTS AND METHODS We improved our previously published pipeline to identify ncRNA editing sites from four human cancers: liver hepatocellular carcinoma,

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Vera-Otarola, Jorge, Estefania Castillo-Vargas, Jenniffer Angulo, Francisco M. Barriga, Eduard Batlle, and Marcelo Lopez-Lastra. "The viral nucleocapsid protein and the human RNA-binding protein Mex3A promote translation of the Andes orthohantavirus small mRNA." PLOS Pathogens 17, no. 9 (2021): e1009931. http://dx.doi.org/10.1371/journal.ppat.1009931.

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The capped Small segment mRNA (SmRNA) of the Andes orthohantavirus (ANDV) lacks a poly(A) tail. In this study, we characterize the mechanism driving ANDV-SmRNA translation. Results show that the ANDV-nucleocapsid protein (ANDV-N) promotes in vitro translation from capped mRNAs without replacing eukaryotic initiation factor (eIF) 4G. Using an RNA affinity chromatography approach followed by mass spectrometry, we identify the human RNA chaperone Mex3A (hMex3A) as a SmRNA-3’UTR binding protein. Results show that hMex3A enhances SmRNA translation in a 3’UTR dependent manner, either alone or when c

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Roy, Gourgopal, Mysore R. Sudarshana, Diane E. Ullman, Shou-Wei Ding, Abhaya M. Dandekar, and Bryce W. Falk. "Chimeric cDNA Sequences from Citrus tristeza virus Confer RNA Silencing-Mediated Resistance in Transgenic Nicotiana benthamiana Plants." Phytopathology® 96, no. 8 (2006): 819–27. http://dx.doi.org/10.1094/phyto-96-0819.

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RNA silencing has been shown to be an important mechanism for conferring resistance in transgenic, virus-resistant plants. We used this approach to evaluate resistance in Nicotiana benthamiana plants transformed with chimeric coding and noncoding sequences from Citrus tristeza virus (CTV). Several independent transgenic plant lines were generated, using two constructs (pCTV1 and pCTV2) designed to produce self-complementary transcripts. The pCTV1 contained cDNA sequences from the CTV capsid protein (CP), p20, and 3′ untranslated region (UTR); and pCTV2 contained CP, p23, and 3′ UTR sequences.

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Uzri, Dina, and Lee Gehrke. "Nucleotide Sequences and Modifications That Determine RIG-I/RNA Binding and Signaling Activities." Journal of Virology 83, no. 9 (2009): 4174–84. http://dx.doi.org/10.1128/jvi.02449-08.

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ABSTRACT Cytoplasmic viral RNAs with 5′ triphosphates (5′ppp) are detected by the RNA helicase RIG-I, initiating downstream signaling and alpha/beta interferon (IFN-α/β) expression that establish an antiviral state. We demonstrate here that the hepatitis C virus (HCV) 3′ untranslated region (UTR) RNA has greater activity as an immune stimulator than several flavivirus UTR RNAs. We confirmed that the HCV 3′-UTR poly(U/UC) region is the determinant for robust activation of RIG-I-mediated innate immune signaling and that its antisense sequence, poly(AG/A), is an equivalent RIG-I activator. The po

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WANG, LIZHONG, RUNHUA LIU, XINCHENG ZHENG, SHILI LIN, PAN ZHENG, and YANG LIU. "A Destabilizing Di-nucleotide Deletion in 3’-Untranslated Region of Human CD24 mRNA Confers Protection against Multiple Sclerosis (129.1)." Journal of Immunology 178, no. 1_Supplement (2007): S217. http://dx.doi.org/10.4049/jimmunol.178.supp.129.1.

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Abstract Single-nucleodie polymorphism (SNP) has a profound impact upon one’s susceptibility to autoimmune diseases such as multiple sclerosis (MS). Although it is well established that 3’UTR play a major role in regulating RNA stability, the contribution of SNP in the 3’UTR to the risk of autoimmune diseases has not well characterized. We have proviously reported the contribution of mouse CD24 3’UTR to its mRNA stability, so we investigated the significance of SNPs in the hCD24 3’UTR to MS susceptibility. Our analysis of the 316 MS patients and 342 controls revealed that a di-nucleotide delet

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Hel, Z., E. Skamene, and D. Radzioch. "Two distinct regions in the 3' untranslated region of tumor necrosis factor alpha mRNA form complexes with macrophage proteins." Molecular and Cellular Biology 16, no. 10 (1996): 5579–90. http://dx.doi.org/10.1128/mcb.16.10.5579.

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The production of tumor necrosis factor alpha (TNF-alpha), a key proinflammatory cytokine essential for the function of the immune system, is regulated at both the transcriptional and posttranscriptional levels. In this report, we focus on the interaction of TNF-alpha mRNA with macrophage proteins, likely mediators of its post-transcriptional control. Mapping of murine TNF-alpha mRNA by using a combination of RNase protection and RNA gel shift assays revealed that two distinct sites within the 3' untranslated region (3'-UTR) engage in the formation of four major RNA-protein complexes, while no

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Wilson, Gerald M., Yue Sun, Jeremy Sellers, et al. "Regulation of AUF1 Expression via Conserved Alternatively Spliced Elements in the 3′ Untranslated Region." Molecular and Cellular Biology 19, no. 6 (1999): 4056–64. http://dx.doi.org/10.1128/mcb.19.6.4056.

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ABSTRACT The A+U-rich RNA-binding factor AUF1 exhibits characteristics of atrans-acting factor contributing to the rapid turnover of many cellular mRNAs. Structural mapping of the AUF1 gene and its transcribed mRNA has revealed alternative splicing events within the 3′ untranslated region (3′-UTR). In K562 erythroleukemia cells, we have identified four alternatively spliced AUF1 3′-UTR variants, including a population of AUF1 mRNA containing a highly conserved 107-nucleotide (nt) 3′-UTR exon (exon 9) and the adjacent downstream intron (intron 9). Functional analyses using luciferase–AUF1 3′-UT

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Ferrari, A. C., L. Wang, E. M. Johnson, et al. "A novel androgen receptor (AR) suppressor complex (ARS)—An essential factor in androgen-independent progression of prostate cancer (PC)." Journal of Clinical Oncology 25, no. 18_suppl (2007): 5145. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.5145.

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5145 Background: Increased AR level, characteristic of advanced PC, has been linked to AI growth while its down-regulation to restored androgen-dependence (AD). However, the mechanisms of AR overexpression remain in dispute. The objectives were to study the proteins comprising a novel ARS that binds to 5’-UTR of AR gene, which is partially lost in AI LNCaP cells; the status of ARS proteins in AD and AI human specimens and therapeutic modulation of ARS proteins. Methods: Parental AD LNCaP cells and its AI- derivative expressing 4 fold more AR-mRNA and protein than parental AD LNCaP were used to

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Sugimoto, Misaki, Akiyo Suda, Shiroh Futaki, and Miki Imanishi. "Effective RNA Regulation by Combination of Multiple Programmable RNA-Binding Proteins." Applied Sciences 10, no. 19 (2020): 6803. http://dx.doi.org/10.3390/app10196803.

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RNAs play important roles in gene expression through translation and RNA splicing. Regulation of specific RNAs is useful to understand and manipulate specific transcripts. Pumilio and fem-3 mRNA-binding factor (PUF) proteins, programmable RNA-binding proteins, are promising tools for regulating specific RNAs by fusing them with various functional domains. The key question is: How can PUF-based molecular tools efficiently regulate RNA functions? Here, we show that the combination of multiple PUF proteins, compared to using a single PUF protein, targeting independent RNA sequences at the 3′ untr

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Züst, Roland, Timothy B. Miller, Scott J. Goebel, Volker Thiel, and Paul S. Masters. "Genetic Interactions between an Essential 3′ cis-Acting RNA Pseudoknot, Replicase Gene Products, and the Extreme 3′ End of the Mouse Coronavirus Genome." Journal of Virology 82, no. 3 (2007): 1214–28. http://dx.doi.org/10.1128/jvi.01690-07.

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ABSTRACT The upstream end of the 3′ untranslated region (UTR) of the mouse hepatitis virus genome contains two essential and overlapping RNA secondary structures, a bulged stem-loop and a pseudoknot, which have been proposed to be elements of a molecular switch that is critical for viral RNA synthesis. It has previously been shown that a particular six-base insertion in loop 1 of the pseudoknot is extremely deleterious to the virus. We have now isolated multiple independent second-site revertants of the loop 1 insertion mutant, and we used reverse-genetics methods to confirm the identities of

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Chen, Min-Hsin, and Teryl K. Frey. "Mutagenic Analysis of the 3′ cis-Acting Elements of the Rubella Virus Genome." Journal of Virology 73, no. 4 (1999): 3386–403. http://dx.doi.org/10.1128/jvi.73.4.3386-3403.1999.

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ABSTRACT Thermodynamically predicted secondary structure analysis of the 3′-terminal 305 nucleotides (nt) of the rubella virus (RUB) genome, a region conserved in all RUB defective interfering RNAs, revealed four stem-loop (SL) structures; SL1 and SL2 are both located in the E1 coding region, while SL3 and SL4 are within the 59-nt 3′ untranslated region (UTR) preceding the poly(A) tract. SL2 is a structure shown to interact with human calreticulin (CAL), an autoantigen potentially involved in RUB RNA replication and pathogenesis. RNase mapping indicated that SL2 and SL3 are in equilibrium betw

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Wu, Ligang, and Joel G. Belasco. "Micro-RNA Regulation of the Mammalian lin-28 Gene during Neuronal Differentiation of Embryonal Carcinoma Cells." Molecular and Cellular Biology 25, no. 21 (2005): 9198–208. http://dx.doi.org/10.1128/mcb.25.21.9198-9208.2005.

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ABSTRACT Vertebrate genomes each encode hundreds of micro-RNAs (miRNAs), yet for few of these miRNAs is there empirical evidence as to which mRNA(s) they regulate. Here we report the identification of human lin-28 mRNA as a regulatory target of human miR-125b and its homolog miR-125a. Studies of miR-125b function in mouse P19 embryonal carcinoma cells induced to develop into neurons suggest a role for this regulatory miRNA in mammalian neuronal differentiation, since its increased concentration in these cells contributes to lin-28 downregulation. Within the lin-28 3′ untranslated region (UTR)

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Duan, Haichuan, Nadia Cherradi, Jean-Jacques Feige, and Colin Jefcoate. "cAMP-Dependent Posttranscriptional Regulation of Steroidogenic Acute Regulatory (STAR) Protein by the Zinc Finger Protein ZFP36L1/TIS11b." Molecular Endocrinology 23, no. 4 (2009): 497–509. http://dx.doi.org/10.1210/me.2008-0296.

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Abstract Star is expressed in steroidogenic cells as 3.5- and 1.6-kb transcripts that differ only in their 3′-untranslated regions (3′-UTR). In mouse MA10 testis and Y-1 adrenal lines, Br-cAMP preferentially stimulates 3.5-kb mRNA. ACTH is similarly selective in primary bovine adrenocortical cells. The 3.5-kb form harbors AU-rich elements (AURE) in the extended 3′-UTR, which enhance turnover. After peak stimulation of 3.5-kb mRNA, degradation is seen. Star mRNA turnover is enhanced by the zinc finger protein ZFP36L1/TIS11b, which binds to UAUUUAUU repeats in the extended 3′-UTR. TIS11b is rapi

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Ainger, Kevin, Daniela Avossa, Amy S. Diana, Christopher Barry, Elisa Barbarese, and John H. Carson. "Transport and Localization Elements in Myelin Basic Protein mRNA." Journal of Cell Biology 138, no. 5 (1997): 1077–87. http://dx.doi.org/10.1083/jcb.138.5.1077.

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Myelin basic protein (MBP) mRNA is localized to myelin produced by oligodendrocytes of the central nervous system. MBP mRNA microinjected into oligodendrocytes in primary culture is assembled into granules in the perikaryon, transported along the processes, and localized to the myelin compartment. In this work, microinjection of various deleted and chimeric RNAs was used to delineate regions in MBP mRNA that are required for transport and localization in oligodendrocytes. The results indicate that transport requires a 21-nucleotide sequence, termed the RNA transport signal (RTS), in the 3′ UTR

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Schneider, Brian D., and Elizabeth A. Leibold. "Effects of iron regulatory protein regulation on iron homeostasis during hypoxia." Blood 102, no. 9 (2003): 3404–11. http://dx.doi.org/10.1182/blood-2003-02-0433.

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AbstractIron regulatory proteins (IRP1 and IRP2) are RNA-binding proteins that affect the translation and stabilization of specific mRNAs by binding to stem-loop structures known as iron responsive elements (IREs). IREs are found in the 5′-untranslated region (UTR) of ferritin (Ft) and mitochondrial aconitase (m-Aco) mRNAs, and in the 3′-UTR of transferrin receptor (TfR) and divalent metal transporter-1 (DMT1) mRNAs. Our previous studies show that besides iron, IRPs are regulated by hypoxia. Here we describe the consequences of IRP regulation and show that iron homeostasis is regulated in 2 ph

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Nanbu, R., P. A. Menoud, and Y. Nagamine. "Multiple instability-regulating sites in the 3' untranslated region of the urokinase-type plasminogen activator mRNA." Molecular and Cellular Biology 14, no. 7 (1994): 4920–28. http://dx.doi.org/10.1128/mcb.14.7.4920-4928.1994.

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In LLC-PK1 cells urokinase-type plasminogen activator (uPA) mRNA has a short half-life. It is stabilized by inhibition of protein synthesis and by downregulation of protein kinase C (PKC). In the present study on uPA mRNA metabolism, we focused our attention on the 3' untranslated region (3'UTR) of the uPA mRNA, as this region is long and highly conserved among several mammalian species, including mice and humans. To investigate the possible role of the 3'UTR of uPA mRNA in mRNA metabolism, we inserted this region into the 3'UTR of the rabbit beta-globin gene that is linked to the cytomegalovi

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Nanbu, R., P. A. Menoud, and Y. Nagamine. "Multiple instability-regulating sites in the 3' untranslated region of the urokinase-type plasminogen activator mRNA." Molecular and Cellular Biology 14, no. 7 (1994): 4920–28. http://dx.doi.org/10.1128/mcb.14.7.4920.

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In LLC-PK1 cells urokinase-type plasminogen activator (uPA) mRNA has a short half-life. It is stabilized by inhibition of protein synthesis and by downregulation of protein kinase C (PKC). In the present study on uPA mRNA metabolism, we focused our attention on the 3' untranslated region (3'UTR) of the uPA mRNA, as this region is long and highly conserved among several mammalian species, including mice and humans. To investigate the possible role of the 3'UTR of uPA mRNA in mRNA metabolism, we inserted this region into the 3'UTR of the rabbit beta-globin gene that is linked to the cytomegalovi

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Panigrahi, Mamata, Michael A. Palmer, and Joyce A. Wilson. "MicroRNA-122 Regulation of HCV Infections: Insights from Studies of miR-122-Independent Replication." Pathogens 11, no. 9 (2022): 1005. http://dx.doi.org/10.3390/pathogens11091005.

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Despite the advancement in antiviral therapy, Hepatitis C remains a global health challenge and one of the leading causes of hepatitis related deaths worldwide. Hepatitis C virus, the causative agent, is a positive strand RNA virus that requires a liver specific microRNA called miR-122 for its replication. Unconventional to the canonical role of miRNAs in translation suppression by binding to 3′Untranslated Region (UTR) of messenger RNAs, miR-122 binds to two sites on the 5′UTR of viral genome and promotes viral propagation. In this review, we describe the unique relationship between the liver

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Mizumoto, Hiroyuki, Masahiro Tatsuta, Masanori Kaido, Kazuyuki Mise, and Tetsuro Okuno. "Cap-Independent Translational Enhancement by the 3′ Untranslated Region of Red Clover Necrotic Mosaic Virus RNA1." Journal of Virology 77, no. 22 (2003): 12113–21. http://dx.doi.org/10.1128/jvi.77.22.12113-12121.2003.

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ABSTRACT Red clover necrotic mosaic virus (RCNMV) is a member of the genus Dianthovirus and has a bipartite positive-sense genomic RNA with 3′ ends that are not polyadenylated. In this study, we show that both genomic RNA1 and RNA2 lack a 5′ cap structure and that uncapped in vitro transcripts of RCNMV RNA1 replicated to a level comparable to that for capped transcripts in cowpea protoplasts. Because the 5′ cap and 3′ poly(A) tail play important roles in the translation of many eukaryotic mRNAs, genomic RNAs of RCNMV should contain an element(s) responsible for 5′ cap- and poly(A) tail-indepen

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Paek, Ki Young, Ka Young Hong, Incheol Ryu, et al. "Translation initiation mediated by RNA looping." Proceedings of the National Academy of Sciences 112, no. 4 (2015): 1041–46. http://dx.doi.org/10.1073/pnas.1416883112.

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Eukaryotic translation initiation commences at the initiation codon near the 5′ end of mRNA by a 40S ribosomal subunit, and the recruitment of a 40S ribosome to an mRNA is facilitated by translation initiation factors interacting with the m7G cap and/or poly(A) tail. The 40S ribosome recruited to an mRNA is then transferred to the AUG initiation codon with the help of translation initiation factors. To understand the mechanism by which the ribosome finds an initiation codon, we investigated the role of eIF4G in finding the translational initiation codon. An artificial polypeptide eIF4G fused w

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Furger, A., N. Schürch, U. Kurath, and I. Roditi. "Elements in the 3' untranslated region of procyclin mRNA regulate expression in insect forms of Trypanosoma brucei by modulating RNA stability and translation." Molecular and Cellular Biology 17, no. 8 (1997): 4372–80. http://dx.doi.org/10.1128/mcb.17.8.4372.

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Procyclins are the major surface glycoproteins of insect forms of Trypanosoma brucei. We have previously shown that a conserved 16-mer in the 3' untranslated region (UTR) of procyclin transcripts functions as a positive element in procyclic-form trypanosomes. A systematic analysis of the entire 297-base 3' UTR has now revealed additional elements which are involved in posttranscriptional regulation: a positive element which requires the first 40 bases of the 3' UTR and at least one negative element between nucleotides 101 and 173 (the LII domain). Deletion of either positive element resulted i

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Cherradi, Nadia, Cyrille Lejczak, Agnes Desroches-Castan, and Jean-Jacques Feige. "Antagonistic Functions of Tetradecanoyl Phorbol Acetate-Inducible-Sequence 11b and HuR in the Hormonal Regulation of Vascular Endothelial Growth Factor Messenger Ribonucleic Acid Stability by Adrenocorticotropin." Molecular Endocrinology 20, no. 4 (2006): 916–30. http://dx.doi.org/10.1210/me.2005-0121.

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Abstract Expression of vascular endothelial growth factor (VEGF), an endothelial cell-specific mitogen and a potent angiogenic factor, is up-regulated by a variety of factors including hypoxia, growth factors, and hormones. In the adrenal cortex, regulation of VEGF expression by the pituitary hormone ACTH ensures the maintenance of the organ vasculature. We have previously shown that ACTH evokes a rapid and transient increase in VEGF mRNA levels in primary adrenocortical cells through transcription-independent mechanisms. We further demonstrated that the zinc finger RNA-binding protein Tis11b

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Lacey, Derek, Peter Hickey, Benedicta D. Arhatari, et al. "Spontaneous retrotransposon insertion into TNF 3′UTR causes heart valve disease and chronic polyarthritis." Proceedings of the National Academy of Sciences 112, no. 31 (2015): 9698–703. http://dx.doi.org/10.1073/pnas.1508399112.

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Rheumatoid arthritis (RA) and ankylosing spondylitis (AS) are chronic inflammatory diseases that together affect 2–3% of the population. RA and AS predominantly involve joints, but heart disease is also a common feature in RA and AS patients. Here we have studied a new spontaneous mutation that causes severe polyarthritis in bone phenotype spontaneous mutation 1 (BPSM1) mice. In addition to joint destruction, mutant mice also develop aortic root aneurism and aorto-mitral valve disease that can be fatal depending on the genetic background. The cause of the disease is the spontaneous insertion o

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Sarawaneeyaruk, Siriruk, Hiro-oki Iwakawa, Hiroyuki Mizumoto, et al. "Host-dependent roles of the viral 5′ untranslated region (UTR) in RNA stabilization and cap-independent translational enhancement mediated by the 3′ UTR of Red clover necrotic mosaic virus RNA1." Virology 391, no. 1 (2009): 107–18. http://dx.doi.org/10.1016/j.virol.2009.05.037.

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