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Artigos de revistas sobre o tema "Post-transcriptional RNA processing"

Autor: Grafiati

Publicado: 4 de junho de 2021

Última modificação: 18 de fevereiro de 2022

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1

Akker, SA, PJ Smith, and SL Chew. "Nuclear post-transcriptional control of gene expression." Journal of Molecular Endocrinology 27, no. 2 (2001): 123–31. http://dx.doi.org/10.1677/jme.0.0270123.

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The mammalian nucleus has considerable control over nascent transcripts. The basic mechanisms of post-transcriptional processing are well understood and recently some of the principles underlying the regulation of nuclear processing events have been elucidated. Here we review the recent progress in identification of signalling pathways that modulate the action of key RNA-binding proteins which regulate splicing, and the mechanisms of action of the C-terminal domain of RNA polymerase II that co-ordinate transcription with nuclear mRNA processing events.

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Binder, Stefan, and Axel Brennicke. "Gene expression in plant mitochondria: transcriptional and post–transcriptional control." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1429 (2003): 181–89. http://dx.doi.org/10.1098/rstb.2002.1179.

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The informational content of the mitochondrial genome in plants is, although small, essential for each cell. Gene expression in these organelles involves a number of distinct transcriptional and post–transcriptional steps. The complex post–transcriptional processes of plant mitochondria such as 5′ and 3′ RNA processing, intron splicing, RNA editing and controlled RNA stability extensively modify individual steady–state RNA levels and influence the mRNA quantities available for translation. In this overview of the processes in mitochondrial gene expression, we focus on confirmed and potential s

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3

Louloupi, Annita, Evgenia Ntini, Julia Liz, and Ulf Andersson Ørom. "Microprocessor dynamics shows co- and post-transcriptional processing of pri-miRNAs." RNA 23, no. 6 (2017): 892–98. http://dx.doi.org/10.1261/rna.060715.117.

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4

Si, Fuyan, Xiaofeng Cao, Xianwei Song, and Xian Deng. "Processing of coding and non-coding RNAs in plant development and environmental responses." Essays in Biochemistry 64, no. 6 (2020): 931–45. http://dx.doi.org/10.1042/ebc20200029.

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Abstract Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in t

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DECUYPERE, S., J. VANDESOMPELE, V. YARDLEY, et al. "Differential polyadenylation of ribosomal RNA during post-transcriptional processing inLeishmania." Parasitology 131, no. 3 (2005): 321–29. http://dx.doi.org/10.1017/s0031182005007808.

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The protozoan parasiteLeishmaniabelongs to the most ancient eukaryotic lineages and this is reflected in several distinctive biological features, such as eukaryotic polycistronic transcription and RNA trans-splicing. The disclosure of this organism's unusual characteristics leads to a better understanding of the origin and nature of fundamental biological processes in eukaryotes. Here we report another unusual phenomenon as we demonstrate that precursor ribosomal RNA can be extensively polyadenylated during post-transcriptional processing[dagger]. Furthermore, we demonstrate that the degree of

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6

Rorbach, Joanna, and Michal Minczuk. "The post-transcriptional life of mammalian mitochondrial RNA." Biochemical Journal 444, no. 3 (2012): 357–73. http://dx.doi.org/10.1042/bj20112208.

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Mammalian mitochondria contain their own genome that encodes mRNAs for thirteen essential subunits of the complexes performing oxidative phosporylation as well as the RNA components (two rRNAs and 22 tRNAs) needed for their translation in mitochondria. All RNA species are produced from single polycistronic precursor RNAs, yet the relative concentrations of various RNAs differ significantly. This underscores the essential role of post-transcriptional mechanisms that control the maturation, stability and translation of mitochondrial RNAs. The present review provides a detailed summary on the rol

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Ferguson, Matthew L., Antoine Coulon, Valeria de Turris, Murali Palangat, Carson C. Chow, and Daniel R. Larson. "Single Molecule Imaging In Vivo Determines Post-Transcriptional RNA Processing Dynamics." Biophysical Journal 106, no. 2 (2014): 223a. http://dx.doi.org/10.1016/j.bpj.2013.11.1305.

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M, Hitit. "Putative Role of Micro - RNA s i n Female Reproductive Tract." Open Access Journal of Veterinary Science & Research 2, no. 2 (2017): 1–5. http://dx.doi.org/10.23880/oajvsr-16000131.

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Female reproductive tract is composed of ovarium, oviduct, cervix and uterus. Development and function of reproductive tract is dispens a ble for maintenance and achievement of reproduction. Reproductive tract responses to cyclic changes and ovarium hormones which provide optimum conditions for gam e t e movement and development. While the potential influence of pitu i tary and gonadal hormones on reproductive function is clearly understood, the molecular mechanism regulating reproductive tract remains elusive. Although, post - transcriptional gene regulation has critical role in cell differ e

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Sanford, J. R., J. Ellis, and J. F. Cáceres. "Multiple roles of arginine/serine-rich splicing factors in RNA processing." Biochemical Society Transactions 33, no. 3 (2005): 443–46. http://dx.doi.org/10.1042/bst0330443.

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SR proteins (serine- and arginine-rich proteins) are an evolutionarily conserved family consisting of essential pre-mRNA splicing factors. Since their discovery and initial characterization, roles of SR proteins in pre-mRNA splicing and in subsequent steps of post-transcriptional gene expression have expanded significantly. The current hypotheses suggest that SR proteins are multifunctional adaptor molecules that may couple distinct steps of RNA metabolism. In the present study, we will provide an overview of the roles of SR proteins in different steps of post-transcriptional gene expression.

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Simpson, G. G., V. Quesada, I. R. Henderson, P. P. Dijkwel, R. Macknight, and C. Dean. "RNA processing and Arabidopsis flowering time control." Biochemical Society Transactions 32, no. 4 (2004): 565–66. http://dx.doi.org/10.1042/bst0320565.

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Plants control their flowering time in order to ensure that they reproduce under favourable conditions. The components involved in this complex process have been identified using a molecular genetic approach in Arabidopsis and classified into genetically separable pathways. The autonomous pathway controls the level of mRNA encoding a floral repressor, FLC, and comprises three RNA-binding proteins, FCA, FPA and FLK. FCA interacts with the 3′-end RNA-processing factor FY to autoregulate its own expression post-transcriptionally and to control FLC. Other components of the autonomous pathway, FVE

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11

Lui, Lauren, and Todd Lowe. "Small nucleolar RNAs and RNA-guided post-transcriptional modification." Essays in Biochemistry 54 (April 30, 2013): 53–77. http://dx.doi.org/10.1042/bse0540053.

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snoRNAs (small nucleolar RNAs) constitute one of the largest and best-studied classes of non-coding RNAs that confer enzymatic specificity. With associated proteins, these snoRNAs form ribonucleoprotein complexes that can direct 2′-O-methylation or pseudouridylation of target non-coding RNAs. Aided by computational methods and high-throughput sequencing, new studies have expanded the diversity of known snoRNA functions. Complexes incorporating snoRNAs have dynamic specificity, and include diverse roles in RNA silencing, telomerase maintenance and regulation of alternative splicing. Evidence th

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Harrison, Andrew P., Joanna Rowsell, Renata da Silva Camargo, et al. "The use of Affymetrix GeneChips as a tool for studying alternative forms of RNA." Biochemical Society Transactions 36, no. 3 (2008): 511–13. http://dx.doi.org/10.1042/bst0360511.

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We are developing a computational pipeline to use surveys of Affymetrix GeneChips as a discovery tool for unravelling some of the biology associated with post-transcriptional processing of RNA. This work involves the integration of a number of bioinformatics resources, from comparing annotations to processing images to determining the structure of transcripts. The rapidly growing datasets of GeneChips available to the community puts us in a strong position to discover novel biology about post-transcriptional processing, and should enable us to determine the mechanisms by which some groups of g

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Desi, Ng, and Yvonne Tay. "The Butterfly Effect of RNA Alterations on Transcriptomic Equilibrium." Cells 8, no. 12 (2019): 1634. http://dx.doi.org/10.3390/cells8121634.

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Post-transcriptional regulation plays a key role in modulating gene expression, and the perturbation of transcriptomic equilibrium has been shown to drive the development of multiple diseases including cancer. Recent studies have revealed the existence of multiple post-transcriptional processes that coordinatively regulate the expression and function of each RNA transcript. In this review, we summarize the latest research describing various mechanisms by which small alterations in RNA processing or function can potentially reshape the transcriptomic landscape, and the impact that this may have

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Jamonnak, N., T. J. Creamer, M. M. Darby, P. Schaughency, S. J. Wheelan, and J. L. Corden. "Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing." RNA 17, no. 11 (2011): 2011–25. http://dx.doi.org/10.1261/rna.2840711.

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Ibrahim, Amr Galal Abd El-Raheem, Ricardo Z. N. Vêncio, Alan P. R. Lorenzetti, and Tie Koide. "Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites." Genes 12, no. 7 (2021): 1018. http://dx.doi.org/10.3390/genes12071018.

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Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly availa

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16

Gao, Chen, and Yibin Wang. "mRNA Metabolism in Cardiac Development and Disease: Life After Transcription." Physiological Reviews 100, no. 2 (2020): 673–94. http://dx.doi.org/10.1152/physrev.00007.2019.

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The central dogma of molecular biology illustrates the importance of mRNAs as critical mediators between genetic information encoded at the DNA level and proteomes/metabolomes that determine the diverse functional outcome at the cellular and organ levels. Although the total number of protein-producing (coding) genes in the mammalian genome is ~20,000, it is evident that the intricate processes of cardiac development and the highly regulated physiological regulation in the normal heart, as well as the complex manifestation of pathological remodeling in a diseased heart, would require a much hig

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17

Hopper, Anita K. "Transfer RNA Post-Transcriptional Processing, Turnover, and Subcellular Dynamics in the Yeast Saccharomyces cerevisiae." Genetics 194, no. 1 (2013): 43–67. http://dx.doi.org/10.1534/genetics.112.147470.

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Pasternak, Alexander O., and Ben Berkhout. "The Splice of Life: Does RNA Processing Have a Role in HIV-1 Persistence?" Viruses 13, no. 9 (2021): 1751. http://dx.doi.org/10.3390/v13091751.

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Antiretroviral therapy (ART) suppresses HIV-1 replication but does not eradicate the virus. Persistence of HIV-1 latent reservoirs in ART-treated individuals is considered the main obstacle to achieving an HIV-1 cure. However, these HIV-1 reservoirs are not transcriptionally silent, and viral transcripts can be detected in most ART-treated individuals. HIV-1 latency is regulated at the transcriptional and at multiple post-transcriptional levels. Here, we review recent insights into the possible contribution of viral RNA processing to the persistence of HIV-1 reservoirs, and discuss the clinica

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19

Dvinge, Heidi, Rhonda E. Ries, Janine O. Ilagan, Derek L. Stirewalt, Soheil Meshinchi, and Robert K. Bradley. "Sample Processing Obscures Cancer-Specific Alterations in Leukemic Transcriptomes." Blood 124, no. 21 (2014): 2201. http://dx.doi.org/10.1182/blood.v124.21.2201.2201.

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Abstract Substantial effort is currently devoted to identifying cancer-associated alterations using genomics technologies. While the genome is inherently stable over short time frames, the transcriptome is dynamic and potentially susceptible to alteration as samples move from the patient to the lab bench. Here, we show that standard blood collection procedures rapidly change the transcriptional and post-transcriptional landscapes of hematopoietic cells, resulting in biased activation of specific biological pathways, up-regulation of pseudogenes, antisense RNAs, and unannotated coding isoforms,

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20

Zhang, Hui, R. Dale Brown, Kurt R. Stenmark, and Cheng-Jun Hu. "RNA-Binding Proteins in Pulmonary Hypertension." International Journal of Molecular Sciences 21, no. 11 (2020): 3757. http://dx.doi.org/10.3390/ijms21113757.

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Pulmonary hypertension (PH) is a life-threatening disease characterized by significant vascular remodeling and aberrant expression of genes involved in inflammation, apoptosis resistance, proliferation, and metabolism. Effective therapeutic strategies are limited, as mechanisms underlying PH pathophysiology, especially abnormal expression of genes, remain unclear. Most PH studies on gene expression have focused on gene transcription. However, post-transcriptional alterations have been shown to play a critical role in inflammation and metabolic changes in diseases such as cancer and systemic ca

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21

Olesnicky, Eugenia, and Ethan Wright. "Drosophila as a Model for Assessing the Function of RNA-Binding Proteins during Neurogenesis and Neurological Disease." Journal of Developmental Biology 6, no. 3 (2018): 21. http://dx.doi.org/10.3390/jdb6030021.

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An outstanding question in developmental neurobiology is how RNA processing events contribute to the regulation of neurogenesis. RNA processing events are increasingly recognized as playing fundamental roles in regulating multiple developmental events during neurogenesis, from the asymmetric divisions of neural stem cells, to the generation of complex and diverse neurite morphologies. Indeed, both asymmetric cell division and neurite morphogenesis are often achieved by mechanisms that generate asymmetric protein distributions, including post-transcriptional gene regulatory mechanisms such as t

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22

Witzel, Ini-Isabée, Li Fang Koh, and Neil D. Perkins. "Regulation of cyclin D1 gene expression." Biochemical Society Transactions 38, no. 1 (2010): 217–22. http://dx.doi.org/10.1042/bst0380217.

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Cyclin D1 is a key regulator of cell proliferation and its expression is subject to both transcriptional and post-transcriptional regulation. In different cellular contexts, different pathways assume a dominant role in regulating its expression, whereas their disregulation can contribute to overexpression of cyclin D1 in tumorigenesis. Here, we discuss the ability of the NF-κB (nuclear factor κB)/IKK [IκB (inhibitor of NF-κB) kinase] pathways to regulate cyclin D1 gene transcription and also consider the newly discovered role of the SNARP (SNIP1/SkIP-associated RNA processing) complex as a co-

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23

Nakayama, Koh, and Naoyuki Kataoka. "Regulation of Gene Expression under Hypoxic Conditions." International Journal of Molecular Sciences 20, no. 13 (2019): 3278. http://dx.doi.org/10.3390/ijms20133278.

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Eukaryotes are often subjected to different kinds of stress. In order to adjust to such circumstances, eukaryotes activate stress–response pathways and regulate gene expression. Eukaryotic gene expression consists of many different steps, including transcription, RNA processing, RNA transport, and translation. In this review article, we focus on both transcriptional and post-transcriptional regulations of gene expression under hypoxic conditions. In the first part of the review, transcriptional regulations mediated by various transcription factors including Hypoxia-Inducible Factors (HIFs) are

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24

Lee, Kwanuk, and Hunseung Kang. "Roles of Organellar RNA-Binding Proteins in Plant Growth, Development, and Abiotic Stress Responses." International Journal of Molecular Sciences 21, no. 12 (2020): 4548. http://dx.doi.org/10.3390/ijms21124548.

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Organellar gene expression (OGE) in chloroplasts and mitochondria is primarily modulated at post-transcriptional levels, including RNA processing, intron splicing, RNA stability, editing, and translational control. Nucleus-encoded Chloroplast or Mitochondrial RNA-Binding Proteins (nCMRBPs) are key regulatory factors that are crucial for the fine-tuned regulation of post-transcriptional RNA metabolism in organelles. Although the functional roles of nCMRBPs have been studied in plants, their cellular and physiological functions remain largely unknown. Nevertheless, existing studies that have cha

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25

Wang, Jinkai. "Integrative analyses of transcriptome data reveal the mechanisms of post-transcriptional regulation." Briefings in Functional Genomics 20, no. 4 (2021): 207–12. http://dx.doi.org/10.1093/bfgp/elab004.

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Abstract Post-transcriptional processing of RNAs plays important roles in a variety of physiological and pathological processes. These processes can be precisely controlled by a series of RNA binding proteins and cotranscriptionally regulated by transcription factors as well as histone modifications. With the rapid development of high-throughput sequencing techniques, multiomics data have been broadly used to study the mechanisms underlying the important biological processes. However, how to use these high-throughput sequencing data to elucidate the fundamental regulatory roles of post-transcr

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Zhang, Xiaopei, Wei Wang, Weidong Zhu, et al. "Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels." International Journal of Molecular Sciences 20, no. 22 (2019): 5573. http://dx.doi.org/10.3390/ijms20225573.

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Long non-coding (lnc) RNAs are non-coding RNAs longer than 200 nt. lncRNAs primarily interact with mRNA, DNA, protein, and miRNA and consequently regulate gene expression at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels in a variety of ways. They play important roles in biological processes such as chromatin remodeling, transcriptional activation, transcriptional interference, RNA processing, and mRNA translation. lncRNAs have important functions in plant growth and development; biotic and abiotic stress responses; and in regulation of cell

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Reyes-Herrera, Paula H., and Elisa Ficarra. "Computational Methods for CLIP-Seq Data Processing." Bioinformatics and Biology Insights 8 (January 2014): BBI.S16803. http://dx.doi.org/10.4137/bbi.s16803.

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RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level. One of the principal challenges in the field of gene expression regulation is to understand RBPs mechanism of action. As a result of recent evolution of experimental techniques, it is now possible to obtain the RNA regions recognized by RBPs on a transcriptome-wide scale. In fact, CLIP-seq protocols use the joint action of CLIP, crosslinking immunoprecipitation, and high-throughput sequencing to recover the transcriptome-wide set of interaction regions for a part

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Sengupta, Sibani. "Bringing RNA Interference (RNAi) into the High School Classroom." American Biology Teacher 75, no. 9 (2013): 698–703. http://dx.doi.org/10.1525/abt.2013.75.9.12.

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RNA interference (abbreviated RNAi) is a relatively new discovery in the field of mechanisms that serve to regulate gene expression (a.k.a. protein synthesis). Gene expression can be regulated at the transcriptional level (mRNA production, processing, or stability) and at the translational level (protein synthesis). RNAi acts in a gene-specific manner and degrades the specific message (mRNA) to lower mRNA stability and, in the process, decreases protein production. The RNAi mechanism thus acts as a negative regulator of gene expression and undoubtedly has been one of the most significant devel

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Dou, Yuhui, Svetlana Kalmykova, Maria Pashkova, et al. "Affinity proteomic dissection of the human nuclear cap-binding complex interactome." Nucleic Acids Research 48, no. 18 (2020): 10456–69. http://dx.doi.org/10.1093/nar/gkaa743.

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Abstract A 5′,7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative CBC together with NCBP1, and to interact

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Delannoy, E., W. A. Stanley, C. S. Bond, and I. D. Small. "Pentatricopeptide repeat (PPR) proteins as sequence-specificity factors in post-transcriptional processes in organelles." Biochemical Society Transactions 35, no. 6 (2007): 1643–47. http://dx.doi.org/10.1042/bst0351643.

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PPR (pentatricopeptide repeat) genes form a large family particularly prevalent in higher plants and targeted to organelles. They are involved in many post-transcriptional processes such as splicing, editing, processing and translation. Current data suggest that PPR proteins are involved in targeting effectors to the correct sites on the correct transcripts but the molecular mechanisms for RNA binding and effector recruitment by PPR proteins are not understood yet.

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31

Satoh, Jun-Ichi, Yoji Yamamoto, Shouta Kitano, Mika Takitani, Naohiro Asahina, and Yoshihiro Kino. "Molecular Network Analysis Suggests a Logical Hypothesis for the Pathological Role of C9orf72 in Amyotrophic Lateral Sclerosis/Frontotemporal Dementia." Journal of Central Nervous System Disease 6 (January 2014): JCNSD.S18103. http://dx.doi.org/10.4137/jcnsd.s18103.

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Background Expanded GGGGCC hexanucleotide repeats, ranging from hundreds to thousands in number, located in the noncoding region of the chromosome 9 open reading frame 72 ( C9orf72) gene represent the most common genetic abnormality for familial and sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) (abbreviated as C9ALS). Currently, three pathological mechanisms, such as haplo insufficiency of C9orf72, formation of nuclear RNA foci composed of sense and antisense repeats, and accumulation of unconventionally transcribed dipeptide-repeat (DPR) proteins, are proposed

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Holcakova, Jitka, Petr Muller, Peter Tomasec, et al. "Inhibition of Post-Transcriptional RNA Processing by CDK Inhibitors and Its Implication in Anti-Viral Therapy." PLoS ONE 9, no. 2 (2014): e89228. http://dx.doi.org/10.1371/journal.pone.0089228.

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Durand, Sylvain, Adam Callan-Sidat, Josie McKeown, et al. "Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis." Nucleic Acids Research 49, no. 11 (2021): 6399–419. http://dx.doi.org/10.1093/nar/gkab444.

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Abstract sRNAs are a taxonomically-restricted but transcriptomically-abundant class of post-transcriptional regulators. While of major importance for adaption to the environment, we currently lack global-scale methodology enabling target identification, especially in species without known RNA hub proteins (e.g. Hfq). Using psoralen RNA cross-linking and Illumina-sequencing we identify RNA–RNA interacting pairs in vivo in Bacillus subtilis, resolving previously well-described interactants. Although sRNA–sRNA pairings are rare (compared with sRNA–mRNA), we identify a robust example involving the

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Lirussi, Lisa, Özlem Demir, Panpan You, Antonio Sarno, Rommie E. Amaro, and Hilde Nilsen. "RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control." Biomolecules 11, no. 1 (2021): 76. http://dx.doi.org/10.3390/biom11010076.

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RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essentia

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Lirussi, Lisa, Özlem Demir, Panpan You, Antonio Sarno, Rommie E. Amaro, and Hilde Nilsen. "RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control." Biomolecules 11, no. 1 (2021): 76. http://dx.doi.org/10.3390/biom11010076.

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RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essentia

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Ademokun, Alexander, and Martin Turner. "Regulation of B-cell differentiation by microRNAs and RNA-binding proteins." Biochemical Society Transactions 36, no. 6 (2008): 1191–93. http://dx.doi.org/10.1042/bst0361191.

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Post-transcriptional control of gene expression is an important mechanism for maintaining cellular homoeostasis and regulating the immune response to infection. It allows control of mRNA abundance, translation and localization. Mechanisms for post-transcriptional control involve RNA-binding proteins and miRNAs (microRNAs). The TTP(tristetraprolin) family of proteins recognize and bind AU-rich elements. Deletion of TTP led to a systemic autoimmune syndrome with excess circulating TNFα (tumour necrosis factor α) and GM-CSF (granulocyte/macrophage colony-stimulating factor) due to aberrantly stab

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Panigrahi*, Gagan Kumar, Annapurna Sahoo, and Sasmita Panda. "A complex network of molecular events triggered upon environmental cues which decide the fate of gene expression: a review." International Journal of Bioassays 5, no. 12 (2016): 5185. http://dx.doi.org/10.21746/ijbio.2016.12.0013.

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Gene expression in eukaryotes depends on a web of events which are inter-related and tightly regulated. These key events can be broadly classified into post-transcriptional and post-translational processes. In general, the post-transcriptional events include pre-mRNA processing (capping, splicing, polyadenylation), RNA stability, and translation as well as chromatin modifications through regulatory RNAs (miRNA, siRNAs and long non-coding RNAs). Protein phosphorylation, ubiquitination and sumoylation are a few post-translational events. These events are constitutive as well as provoked by speci

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Walsh, Matthew J., Guillaume M. Hautbergue, and Stuart A. Wilson. "Structure and function of mRNA export adaptors." Biochemical Society Transactions 38, no. 1 (2010): 232–36. http://dx.doi.org/10.1042/bst0380232.

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The mRNA export adaptors provide an important link between multiple nuclear mRNA processing events and the mRNA export receptor TAP/NXF1/Mex67p. They are recruited to mRNA through transcriptional and post-transcriptional events, integrating this information to licence mRNA for export. Subsequently they hand mRNA over to TAP and switch TAP to a higher-affinity RNA-binding state, ensuring its stable association with mRNA destined for export. Here we discuss the structure and function of adaptors and how they are recruited to mRNA.

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Adachi, Hironori, Martin Hengesbach, Yi-Tao Yu, and Pedro Morais. "From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies." Biomedicines 9, no. 5 (2021): 550. http://dx.doi.org/10.3390/biomedicines9050550.

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Therapeutic oligonucleotides interact with a target RNA via Watson-Crick complementarity, affecting RNA-processing reactions such as mRNA degradation, pre-mRNA splicing, or mRNA translation. Since they were proposed decades ago, several have been approved for clinical use to correct genetic mutations. Three types of mechanisms of action (MoA) have emerged: RNase H-dependent degradation of mRNA directed by short chimeric antisense oligonucleotides (gapmers), correction of splicing defects via splice-modulation oligonucleotides, and interference of gene expression via short interfering RNAs (siR

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Lenzen, Benjamin, Thilo Rühle, Marie-Kristin Lehniger, et al. "The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation." International Journal of Molecular Sciences 21, no. 16 (2020): 5633. http://dx.doi.org/10.3390/ijms21165633.

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Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main

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Chatterjee, Sumantra, Lin Min, R. Krishna Murthy Karuturi, and Thomas Lufkin. "The role of post-transcriptional RNA processing and plasmid vector sequences on transient transgene expression in zebrafish." Transgenic Research 19, no. 2 (2009): 299–304. http://dx.doi.org/10.1007/s11248-009-9312-x.

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Willbanks, Amber, Shaun Wood, and Jason X. Cheng. "RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases." Genes 12, no. 5 (2021): 627. http://dx.doi.org/10.3390/genes12050627.

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Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcr

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Manavski, Nikolay, Lisa-Marie Schmid, and Jörg Meurer. "RNA-stabilization factors in chloroplasts of vascular plants." Essays in Biochemistry 62, no. 1 (2018): 51–64. http://dx.doi.org/10.1042/ebc20170061.

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In contrast to the cyanobacterial ancestor, chloroplast gene expression is predominantly governed on the post-transcriptional level such as modifications of the RNA sequence, decay rates, exo- and endonucleolytic processing as well as translational events. The concerted function of numerous chloroplast RNA-binding proteins plays a fundamental and often essential role in all these processes but our understanding of their impact in regulation of RNA degradation is only at the beginning. Moreover, metabolic processes and post-translational modifications are thought to affect the function of RNA p

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Sleiman, Sophie, and Francois Dragon. "Recent Advances on the Structure and Function of RNA Acetyltransferase Kre33/NAT10." Cells 8, no. 9 (2019): 1035. http://dx.doi.org/10.3390/cells8091035.

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Ribosome biogenesis is one of the most energy demanding processes in the cell. In eukaryotes, the main steps of this process occur in the nucleolus and include pre-ribosomal RNA (pre-rRNA) processing, post-transcriptional modifications, and assembly of many non-ribosomal factors and ribosomal proteins in order to form mature and functional ribosomes. In yeast and humans, the nucleolar RNA acetyltransferase Kre33/NAT10 participates in different maturation events, such as acetylation and processing of 18S rRNA, and assembly of the 40S ribosomal subunit. Here, we review the structural and functio

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Nguyen-Chi, Mai, and Dominique Morello. "RNA-binding proteins, RNA granules, and gametes: is unity strength?" REPRODUCTION 142, no. 6 (2011): 803–17. http://dx.doi.org/10.1530/rep-11-0257.

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Changes in mRNA translation and degradation represent post-transcriptional processes operating during gametogenesis and early embryogenesis to ensure regulated protein synthesis. Numerous mRNA-binding proteins (RBPs) have been described in multiple animal models that contribute to the control of mRNA translation and decay during oogenesis and spermatogenesis. An emerging view from studies performed in germ cells and somatic cells is that RBPs associate with their target mRNAs in RNA–protein (or ribonucleoprotein) complexes (mRNPs) that assemble in various cytoplasmic RNA granules that communic

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D’Souza, Aaron R., Lindsey Van Haute, Christopher A. Powell, et al. "YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria." Nucleic Acids Research 49, no. 10 (2021): 5798–812. http://dx.doi.org/10.1093/nar/gkab404.

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Abstract Mitochondria contain their own translation apparatus which enables them to produce the polypeptides encoded in their genome. The mitochondrially-encoded RNA components of the mitochondrial ribosome require various post-transcriptional processing steps. Additional protein factors are required to facilitate the biogenesis of the functional mitoribosome. We have characterized a mitochondrially-localized protein, YbeY, which interacts with the assembling mitoribosome through the small subunit. Loss of YbeY leads to a severe reduction in mitochondrial translation and a loss of cell viabili

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Matsui, Akihiro, Kentaro Nakaminami, and Motoaki Seki. "Biological Function of Changes in RNA Metabolism in Plant Adaptation to Abiotic Stress." Plant and Cell Physiology 60, no. 9 (2019): 1897–905. http://dx.doi.org/10.1093/pcp/pcz068.

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Abstract Plant growth and productivity are greatly impacted by environmental stresses. Therefore, plants have evolved various sophisticated mechanisms for adaptation to nonoptimal environments. Recent studies using RNA metabolism-related mutants have revealed that RNA processing, RNA decay and RNA stability play an important role in regulating gene expression at a post-transcriptional level in response to abiotic stresses. Studies indicate that RNA metabolism is a unified network, and modification of stress adaptation-related transcripts at multiple steps of RNA metabolism is necessary to cont

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Drider, D., J. M. Santos, C. M. Arraiano, and P. López. "RNA processing is involved in the post-transcriptional control of the citQRP operon from Lactococcus lactis biovar diacetylactis." Molecular and General Genetics MGG 258, no. 1-2 (1998): 9–15. http://dx.doi.org/10.1007/s004380050701.

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Smialek, Maciej J., Erkut Ilaslan, Marcin P. Sajek, et al. "Characterization of RNP Networks of PUM1 and PUM2 Post-Transcriptional Regulators in TCam-2 Cells, a Human Male Germ Cell Model." Cells 9, no. 4 (2020): 984. http://dx.doi.org/10.3390/cells9040984.

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Mammalian Pumilio (PUM) proteins are sequence-specific, RNA-binding proteins (RBPs) with wide-ranging roles. They are involved in germ cell development, which has functional implications in development and fertility. Although human PUM1 and PUM2 are closely related to each other and recognize the same RNA binding motif, there is some evidence for functional diversity. To address that problem, first we used RIP-Seq and RNA-Seq approaches, and identified mRNA pools regulated by PUM1 and PUM2 proteins in the TCam-2 cell line, a human male germ cell model. Second, applying global mass spectrometry

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Marini, Federico, Denise Scherzinger, and Sven Danckwardt. "TREND-DB—a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation." Nucleic Acids Research 49, no. D1 (2020): D243—D253. http://dx.doi.org/10.1093/nar/gkaa722.

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Abstract Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3′ end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3′ end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modificat

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