Genomes and Genes
post transcriptional rna processing
Summary: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
- Ely A, Naidoo T, Arbuthnot P. Efficient silencing of gene expression with modular trimeric Pol II expression cassettes comprising microRNA shuttles. Nucleic Acids Res. 2009;37:e91 pubmed publisher..The modular nature of the cassettes together with compatibility with expression from Pol II promoters should be advantageous for gene silencing applications requiring simultaneous targeting of different sites. ..
- Suzuki H, Yamagata K, Sugimoto K, Iwamoto T, Kato S, Miyazono K. Modulation of microRNA processing by p53. Nature. 2009;460:529-33 pubmed publisher..Our study reveals a previously unrecognized function of p53 in miRNA processing, which may underlie key aspects of cancer biology. ..
- Moore M, Proudfoot N. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell. 2009;136:688-700 pubmed publisher..The connections of pre-mRNA processing to upstream events in transcription and downstream events, including translation and mRNA decay, are elaborate, extensive, and remarkably interwoven. ..
- Ceppi M, Pereira P, Dunand Sauthier I, Barras E, Reith W, Santos M, et al. MicroRNA-155 modulates the interleukin-1 signaling pathway in activated human monocyte-derived dendritic cells. Proc Natl Acad Sci U S A. 2009;106:2735-40 pubmed publisher..Our observations suggest, therefore, that in mature human DCs, miR-155 is part of a negative feedback loop, which down-modulates inflammatory cytokine production in response to microbial stimuli. ..
- Oeffinger M, Zenklusen D, Ferguson A, Wei K, El Hage A, Tollervey D, et al. Rrp17p is a eukaryotic exonuclease required for 5' end processing of Pre-60S ribosomal RNA. Mol Cell. 2009;36:768-81 pubmed publisher..We show that Rrp17p binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery, and provide evidence for physical and functional links between late 60S subunit processing and export. ..
- Tran D, Satou K, Ho T. Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinformatics. 2008;9 Suppl 12:S5 pubmed publisher..Moreover, review of the literature reveals that miRNAs in a module are involved in several types of human cancer. ..
- Kim S, Yang J, Xu J, Jang I, Prigge M, Chua N. Two cap-binding proteins CBP20 and CBP80 are involved in processing primary MicroRNAs. Plant Cell Physiol. 2008;49:1634-44 pubmed publisher..Genetic and molecular analyses show that CBP20 and 80 have overlapping function in the same developmental pathway as SE and HYL1. Our results identify new components in miRNA biogenesis. ..
- Heo I, Joo C, Cho J, Ha M, Han J, Kim V. Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell. 2008;32:276-84 pubmed publisher..The Lin28-mediated downregulation of let-7 may play a key role in development, stem cell programming, and tumorigenesis. ..
- Soifer H, Sano M, Sakurai K, Chomchan P, Saetrom P, Sherman M, et al. A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs. Nucleic Acids Res. 2008;36:6511-22 pubmed publisher..These results suggest an important function for the Dicer helicase domain in the processing of thermodynamically unstable hairpin structures. ..
- Pedrioli D, Karpanen T, Dabouras V, Jurisic G, van de Hoek G, Shin J, et al. miR-31 functions as a negative regulator of lymphatic vascular lineage-specific differentiation in vitro and vascular development in vivo. Mol Cell Biol. 2010;30:3620-34 pubmed publisher..Collectively, our findings identify miR-31 is a potent regulator of vascular lineage-specific differentiation and development in vertebrates. ..
- Taylor J, Ghorbel S, Nicot C. Genome wide analysis of human genes transcriptionally and post-transcriptionally regulated by the HTLV-I protein p30. BMC Genomics. 2009;10:311 pubmed publisher..In addition, these alterations in gene expression may play a role in cell transformation and the onset of leukemia. ..
- Pfalz J, Bayraktar O, Prikryl J, Barkan A. Site-specific binding of a PPR protein defines and stabilizes 5' and 3' mRNA termini in chloroplasts. EMBO J. 2009;28:2042-52 pubmed publisher..These results, together with recent insights into bacterial RNA decay, suggest a unifying model for the biogenesis of chloroplast transcript populations and for the determinants of chloroplast mRNA stability. ..
- Kerr T, Davidson N. Therapeutic RNA manipulation in liver disease. Hepatology. 2010;51:1055-61 pubmed publisher..We will highlight developments in vector development and validation for therapeutic manipulation of mRNA expression with a focus on potential applications in metabolic and immunomediated liver disease. ..
- Yuan Z, Sanders A, Ye L, Jiang W. HuR, a key post-transcriptional regulator, and its implication in progression of breast cancer. Histol Histopathol. 2010;25:1331-40 pubmed publisher..The review also covers the current knowledge of HuR's role in carcinogenesis, particularly its involvement in breast cancer, and the feasibility of using HuR as a therapeutic target for the treatment of breast cancer. ..
- Sarras H, Alizadeh Azami S, McPherson J. In search of a function for BCLAF1. ScientificWorldJournal. 2010;10:1450-61 pubmed publisher..We also present recent findings from our laboratory and others indicating a role for BCLAF1 in post-transcriptional processes that impact mRNA metabolism, instead of a direct role for this protein in apoptosis or transcription. ..
- ..Owing to the loop-to-base processing and the unusual length of the stem, several additional small RNA species are produced before the cognate miRNA is excised, a phenomenon that might shed light on the origin of MIRNA genes. ..
- Moser J, Fritzler M. Cytoplasmic ribonucleoprotein (RNP) bodies and their relationship to GW/P bodies. Int J Biochem Cell Biol. 2010;42:828-43 pubmed publisher..This review will focus on the similarities and differences of the various cytoplasmic RNP granules as an approach to understanding their functional relationships to GW/P bodies. ..
- Shetty S, Velusamy T, Shetty R, Marudamuthu A, Shetty S, Florova G, et al. Post-transcriptional regulation of plasminogen activator inhibitor type-1 expression in human pleural mesothelial cells. Am J Respir Cell Mol Biol. 2010;43:358-67 pubmed publisher..This newly recognized pathway could influence expression of PAI-1 by mesothelial or mesothelioma cells at the level of mRNA stability in the context of pleural inflammation or malignancy. ..
- Fong N, Ohman M, Bentley D. Fast ribozyme cleavage releases transcripts from RNA polymerase II and aborts co-transcriptional pre-mRNA processing. Nat Struct Mol Biol. 2009;16:916-22 pubmed publisher..We propose that damaging the nascent transcript aborts pre-mRNA processing and that this mechanism may help to prevent association of processing factors with Pol II that is not productively engaged in transcription. ..
- Kim H, Mahato R, Lee M. Hypoxia-specific gene expression for ischemic disease gene therapy. Adv Drug Deliv Rev. 2009;61:614-22 pubmed publisher..This review examines the current status and future challenges of hypoxia-specific systems for safe and effective gene therapy of ischemic diseases. ..
- Blencowe B, Ahmad S, Lee L. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes Dev. 2009;23:1379-86 pubmed publisher..We also consider how future advances in HTS technology are likely to transform our understanding of integrated cellular networks operating at the RNA level. ..
- Muto M, Henry R, Mayfield S. Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast. BMC Biotechnol. 2009;9:26 pubmed publisher..Since Rubisco is ubiquitous to land plants and green algae, this strategy may also be applied to higher plant transgenic expression systems. ..
- Saikia M, Fu Y, PAVON ETERNOD M, He C, Pan T. Genome-wide analysis of N1-methyl-adenosine modification in human tRNAs. RNA. 2010;16:1317-27 pubmed publisher..Our results show a distinct pattern for m(1)A58 hypomodification in human tRNAs, and are consistent with the notion that this modification fine tunes tRNA functions in different contexts. ..
- Amadio M, Scapagnini G, Laforenza U, Intrieri M, Romeo L, Govoni S, et al. Post-transcriptional regulation of HSP70 expression following oxidative stress in SH-SY5Y cells: the potential involvement of the RNA-binding protein HuR. Curr Pharm Des. 2008;14:2651-8 pubmed
- Hirayama T, Shinozaki K. Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant J. 2010;61:1041-52 pubmed publisher..In this review, we summarize recent progress in abiotic stress studies, especially in the post-genomic era, and offer new perspectives on research directions for the next decade. ..
- Cha S, Chen P, Johansson G, Chu C, Wang M, Jeng Y, et al. MicroRNA-519c suppresses hypoxia-inducible factor-1alpha expression and tumor angiogenesis. Cancer Res. 2010;70:2675-85 pubmed publisher..Taken together, our findings provide the first evidence that miR-519c is a pivotal regulator of tumor angiogenesis and that microenvironmental HGF contributes to regulating miR-519c biogenesis in cancer cells. ..
- Werner S, Wollmann H, Schneeberger K, Weigel D. Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Curr Biol. 2010;20:42-8 pubmed publisher..Our ability to engineer de novo a functional minimal miRNA precursor highlights that we have discovered several elements both necessary and sufficient for accurate miRNA processing. ..
- Shenouda S, Alahari S. MicroRNA function in cancer: oncogene or a tumor suppressor?. Cancer Metastasis Rev. 2009;28:369-78 pubmed publisher..Similarly, miRNAs can down-regulate different proteins with oncogenic activity; i.e., they act as tumor suppressors. This review will highlight the recent discoveries regarding miRNAs and their importance in cancer. ..
- Salvail H, Lanthier Bourbonnais P, Sobota J, Caza M, Benjamin J, Mendieta M, et al. A small RNA promotes siderophore production through transcriptional and metabolic remodeling. Proc Natl Acad Sci U S A. 2010;107:15223-8 pubmed publisher..Thus, RyhB plays an essential role in siderophore production and may modulate bacterial virulence through optimization of siderophore production. ..
- Guo W, Wu S, Wang L, Wang R, Wei X, Liu J, et al. Interruption of RNA processing machinery by a small compound, 1-[(4-chlorophenyl)methyl]-1H-indole-3-carboxaldehyde (oncrasin-1). Mol Cancer Ther. 2009;8:441-8 pubmed publisher..Together, our results suggest that oncrasin-1 suppresses the function of RNA processing machinery and that PKCiota might be involved in the biological function of RNA processing complexes. ..
- Deutscher M. Maturation and degradation of ribosomal RNA in bacteria. Prog Mol Biol Transl Sci. 2009;85:369-91 pubmed publisher..The second focus of this review is to describe these degradative reactions, the RNases that carry them out, and the conditions that initiate the turnover process. ..
- Valkov V, Scotti N, Kahlau S, Maclean D, Grillo S, Gray J, et al. Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control. Plant Physiol. 2009;150:2030-44 pubmed publisher..Candidate regulatory sequences that potentially can improve plastid (trans)gene expression in amyloplasts have been identified. ..
- Heinemann I, Soll D, Randau L. Transfer RNA processing in archaea: unusual pathways and enzymes. FEBS Lett. 2010;584:303-9 pubmed publisher..Here, we give an overview of recently discovered tRNA maturation pathways that require intricate processing steps to finally generate the standard tRNA from these unusual tRNA genes. ..
- Keshamouni V, Jagtap P, Michailidis G, Strahler J, Kuick R, Reka A, et al. Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition. J Proteome Res. 2009;8:35-47 pubmed publisher..These results are the first demonstration of post-transcriptional regulation of cytoskeletal remodelling and a key role for cofilin1 during TGF-beta-induced EMT. ..
- Romanova L, Grand A, Zhang L, Rayner S, Katoku Kikyo N, Kellner S, et al. Critical role of nucleostemin in pre-rRNA processing. J Biol Chem. 2009;284:4968-77 pubmed publisher..Collectively, these biochemical and functional studies demonstrate a novel role of nucleostemin in ribosome biogenesis. This is a key aspect of the role of nucleostemin in regulating cell proliferation. ..
- Tang X, Zhang Y, Tucker L, Ramratnam B. Phosphorylation of the RNase III enzyme Drosha at Serine300 or Serine302 is required for its nuclear localization. Nucleic Acids Res. 2010;38:6610-9 pubmed publisher..Furthermore, mimicking phosphorylation status by mutating S?E at S300 and/or S?D at S302 restored nuclear localization. Our findings add a further layer of complexity to the molecular anatomy of Drosha as it relates to miRNA biogenesis. ..
- Pelosi E, Labbaye C, Testa U. MicroRNAs in normal and malignant myelopoiesis. Leuk Res. 2009;33:1584-93 pubmed publisher..Extensive miRNA deregulation has been observed in leukemia and functional studies support a role for miRNAs in the pathogenesis of these disorders. ..
- Lonka Nevalaita L, Lume M, Leppänen S, Jokitalo E, Peranen J, Saarma M. Characterization of the intracellular localization, processing, and secretion of two glial cell line-derived neurotrophic factor splice isoforms. J Neurosci. 2010;30:11403-13 pubmed publisher..Thus, the processing and secretion mechanisms of GDNF are different from those of BDNF and NGF. ..
- Wong D, Tai T, Wong Faull D, Claycomb R, Kvetnansky R. Adrenergic responses to stress: transcriptional and post-transcriptional changes. Ann N Y Acad Sci. 2008;1148:249-56 pubmed publisher..Together, findings suggest that stress increases PNMT gene transcriptional activity but post-transcriptional regulatory mechanisms limit the biological end-point of functional PNMT enzyme and, thereby, Epi. ..
- Riehl W, Segrè D. Optimal metabolic regulation using a constraint-based model. Genome Inform. 2008;20:159-70 pubmed..We explore the ability of the model to predict optimal regulatory responses in both a simple toy network and in a fragment of the well-described glycolysis pathway. ..
- Ouellet D, Plante I, Boissonneault V, Ayari C, Provost P. Refractoriness of hepatitis C virus internal ribosome entry site to processing by Dicer in vivo. J Negat Results Biomed. 2009;8:8 pubmed publisher..Our results suggest that the HCV IRES may have evolved to adopt a structure or a cellular context that is refractory to Dicer processing, which may contribute to viral escape of the host RNA silencing machinery. ..