Genomes and Genes
Summary: RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
- Segerstolpe Ã, Granneman S, BjÃ¶rk P, de Lima Alves F, Rappsilber J, Andersson C, et al. Multiple RNA interactions position Mrd1 at the site of the small subunit pseudoknot within the 90S pre-ribosome. Nucleic Acids Res. 2013;41:1178-90 pubmed publisher..We speculate that the modular structure of Mrd1 coordinates pseudoknot formation with pre-rRNA processing and subunit assembly. ..
- Turunen J, Verma B, Nyman T, Frilander M. HnRNPH1/H2, U1 snRNP, and U11 snRNP cooperate to regulate the stability of the U11-48K pre-mRNA. RNA. 2013;19:380-9 pubmed publisher..Thus, our results elucidate the mechanism in which snRNPs from both spliceosomes together with hnRNPH1/H2 proteins regulate the recognition and activation of the highly conserved alternative splice sites within the U11-48K pre-mRNA. ..
- Gudys A, Szcześniak M, Sikora M, Makałowska I. HuntMi: an efficient and taxon-specific approach in pre-miRNA identification. BMC Bioinformatics. 2013;14:83 pubmed publisher..The HuntMi software as well as datasets used in the research are freely available at http://lemur.amu.edu.pl/share/HuntMi/. ..
- Feng Y, Zhang X, Graves P, Zeng Y. A comprehensive analysis of precursor microRNA cleavage by human Dicer. RNA. 2012;18:2083-92 pubmed publisher..Dicer binding protects the terminal loop from digestion by S1 nuclease, suggesting that Dicer interacts directly with the terminal loop region. ..
- Schneider C, Kudla G, Wlotzka W, Tuck A, Tollervey D. Transcriptome-wide analysis of exosome targets. Mol Cell. 2012;48:422-33 pubmed publisher..Rrp6 was preferentially associated with structured targets, which frequently did not associate with the core exosome indicating that substrates follow multiple pathways to the nucleases. ..
- Ameyar Zazoua M, Rachez C, Souidi M, Robin P, Fritsch L, Young R, et al. Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol. 2012;19:998-1004 pubmed publisher..Our data thus uncover a new model for the regulation of alternative splicing, in which Argonaute proteins couple RNA polymerase II elongation to chromatin modification. ..
- Arslan A, He X, Wang M, Rumschlag Booms E, Rong L, Beck W. A high-throughput assay to identify small-molecule modulators of alternative pre-mRNA splicing. J Biomol Screen. 2013;18:180-90 pubmed publisher..Based on these findings and the role that upregulated PTB has on cell proliferation and malignant properties of tumors, targeting PTB for inhibition with small molecules offers a promising strategy for cancer therapy. ..
- ..This review focuses on recent advances in the characterization of the splicing helicases and their interactions, and highlights the deep integration of splicing helicases in global mRNP biogenesis pathways...
- Gamalinda M, Jakovljevic J, Babiano R, Talkish J, de la Cruz J, Woolford J. Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing. Nucleic Acids Res. 2013;41:1965-83 pubmed publisher..Altogether, these data support that L17, L35 and L37 are specifically required for a recruiting step immediately preceding removal of ITS2. ..
- Sardana R, White J, Johnson A. The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP. RNA. 2013;19:828-40 pubmed publisher..The genetic interaction with the SSU processome suggests that Bud23 could be involved in triggering disassembly of the SSU processome, or of particular subcomplexes of the processome. ..
- Khodor Y, Menet J, Tolan M, Rosbash M. Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse. RNA. 2012;18:2174-86 pubmed publisher..The gene length and distance effects indicate that more "nascent time" gives rise to greater cotranscriptional splicing efficiency in both systems. ..
- Arikit S, Zhai J, Meyers B. Biogenesis and function of rice small RNAs from non-coding RNA precursors. Curr Opin Plant Biol. 2013;16:170-9 pubmed publisher..Although many small RNAs have been identified by deep sequencing in rice, their precise regulatory functions and cell-type specificity are in many cases still unknown. ..
- Graf R, Munschauer M, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, et al. Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation. RNA Biol. 2013;10:1146-59 pubmed publisher..Computational analyses provided evidence that the strength of protein synthesis reduction correlated with the location of LIN28B binding sites within target transcripts. ..
- Woolford J, Baserga S. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics. 2013;195:643-81 pubmed publisher..Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes. ..
- Wang Y, Ma M, Xiao X, Wang Z. Intronic splicing enhancers, cognate splicing factors and context-dependent regulation rules. Nat Struct Mol Biol. 2012;19:1044-52 pubmed publisher..We provide a comprehensive picture of general ISE activities and suggest new models of how single elements can function oppositely, depending on locations and binding factors. ..
- Ben Chaabane S, Liu R, Chinnusamy V, Kwon Y, Park J, Kim S, et al. STA1, an Arabidopsis pre-mRNA processing factor 6 homolog, is a new player involved in miRNA biogenesis. Nucleic Acids Res. 2013;41:1984-97 pubmed publisher..These results suggest that STA1 is involved in miRNA biogenesis directly by functioning in pri-miRNA splicing and indirectly by modulating the DCL1 transcript level. ..
- Pastor T, Pagani F. Interaction of hnRNPA1/A2 and DAZAP1 with an Alu-derived intronic splicing enhancer regulates ATM aberrant splicing. PLoS ONE. 2011;6:e23349 pubmed publisher..On the contrary, HuR and DHX36 have no effect on ATM splicing pattern. These data suggest that splicing factors with both negative and positive effect can assemble on the intronic Alu repeats and regulate pre-mRNA splicing. ..
- Westholm J, Lai E. Mirtrons: microRNA biogenesis via splicing. Biochimie. 2011;93:1897-904 pubmed publisher..Altogether, the features of mirtron pathways illustrate unexpected flexibility in combining RNA processing pathways, and highlight how multiple functions can be encoded by individual transcripts. ..
- Fan L, Wang Z, Liu J, Guo W, Yan J, Huang Y. A survey of green plant tRNA 3'-end processing enzyme tRNase Zs, homologs of the candidate prostate cancer susceptibility protein ELAC2. BMC Evol Biol. 2011;11:219 pubmed publisher..Our results also support the coevolution of tRNase Zs and tRNA 3'-trailer sequences in plants. ..
- Horn D, Mason S, Karbstein K. Rcl1 protein, a novel nuclease for 18 S ribosomal RNA production. J Biol Chem. 2011;286:34082-7 pubmed publisher..Furthermore, because Rcl1 has no homology to other known endonucleases, these data also establish a novel class of nucleases. ..
- Sebbag Sznajder N, Raitskin O, Angenitzki M, Sato T, Sperling J, Sperling R. Regulation of alternative splicing within the supraspliceosome. J Struct Biol. 2012;177:152-9 pubmed publisher..These observations support the proposed role of the supraspliceosome in splicing regulation and alternative splicing...
- Nag A, Steitz J. Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing. RNA Biol. 2012;9:334-42 pubmed publisher..Together our results suggest recruitment of the nuclear decay machinery to the spliceosome to ensure production of properly spliced mRNA. ..
- Salman V, Amann R, Shub D, Schulz Vogt H. Multiple self-splicing introns in the 16S rRNA genes of giant sulfur bacteria. Proc Natl Acad Sci U S A. 2012;109:4203-8 pubmed publisher..Accordingly, the introns do not inhibit the formation of functional ribosomes. ..
- Talkish J, Zhang J, Jakovljevic J, Horsey E, Woolford J. Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res. 2012;40:8646-61 pubmed..Inhibition of TOR kinase decreases association of Rpf2, Spb4, Nog1 and Nog2 with pre-ribosomes. ..
- Peacey E, Rodriguez L, Liu Y, Wolfe M. Targeting a pre-mRNA structure with bipartite antisense molecules modulates tau alternative splicing. Nucleic Acids Res. 2012;40:9836-49 pubmed publisher..This general bipartite antisense strategy could be employed to modulate other splicing events that are regulated by RNA secondary structure. ..
- Adamson B, Smogorzewska A, Sigoillot F, King R, Elledge S. A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol. 2012;14:318-28 pubmed publisher..Our screen also revealed that off-target depletion of RAD51 is a common source of RNAi false positives, raising a cautionary note for siRNA screens and RNAi-based studies of HR. ..
- Mullineux S, Lafontaine D. Mapping the cleavage sites on mammalian pre-rRNAs: where do we stand?. Biochimie. 2012;94:1521-32 pubmed publisher..These features might have been selected because they increase the robustness of pre-rRNA processing by acting as "back-up" mechanisms to ensure the proper maturation of rRNA. ..
- Warzecha C, Hovhannisyan R, Carstens R. Dynamic fluorescent and luminescent reporters for cell-based splicing screens. Methods Mol Biol. 2012;867:273-87 pubmed publisher..These reporters also have a dynamic range that is suitable for small molecule screening for compounds that can regulate splicing. ..
- Albulescu L, Sabet N, Gudipati M, Stepankiw N, Bergman Z, Huffaker T, et al. A quantitative, high-throughput reverse genetic screen reveals novel connections between Pre-mRNA splicing and 5' and 3' end transcript determinants. PLoS Genet. 2012;8:e1002530 pubmed publisher..cerevisiae may more closely resemble mammalian models of exon-definition. More broadly, our work demonstrates the capacity of this approach to identify novel regulators of various cellular RNAs. ..
- Hoskins A, Moore M. The spliceosome: a flexible, reversible macromolecular machine. Trends Biochem Sci. 2012;37:179-88 pubmed publisher..These experiments are rewriting the textbooks, with a new picture emerging of a dynamic, malleable machine heavily influenced by the identity of its pre-mRNA substrate. ..
- Xue Z, Yuan H, Guo J, Liu Y. Reconstitution of an Argonaute-dependent small RNA biogenesis pathway reveals a handover mechanism involving the RNA exosome and the exonuclease QIP. Mol Cell. 2012;46:299-310 pubmed publisher..In addition, exosome is also important for the decay of sRNAs. Together, our results establish a biochemical mechanism of an Argonaute-dependent sRNA biogenesis pathway and critical roles of exosome in sRNA processing. ..
- Zong X, Tripathi V, Prasanth K. RNA splicing control: yet another gene regulatory role for long nuclear noncoding RNAs. RNA Biol. 2011;8:968-77 pubmed publisher..It will therefore be crucial to unravel the functions for the vast number of long nrRNAs, buried within the complex mine of the human genome. ..
- Berg M, Singh L, Younis I, Liu Q, Pinto A, Kaida D, et al. U1 snRNP determines mRNA length and regulates isoform expression. Cell. 2012;150:53-64 pubmed publisher..Additional experiments suggest cotranscriptional PCPA counteracted by U1 association with nascent transcripts, a process we term telescripting, ensuring transcriptome integrity and regulating mRNA length. ..
- Wu S, Chen Y, Lindell M, Mao G, Kirsebom L. Functional coupling between a distal interaction and the cleavage site in bacterial RNase-P-RNA-mediated cleavage. J Mol Biol. 2011;411:384-96 pubmed publisher..These new data provide support for an induced-fit mechanism in bacterial RPR-mediated cleavage at the correct site +1. ..
- Khan D, Jahan S, Davie J. Pre-mRNA splicing: role of epigenetics and implications in disease. Adv Biol Regul. 2012;52:377-88 pubmed publisher..In this review we present the interplay between epigenetic mechanisms and splicing regulation, as well as discuss recent studies on the role of histone deacetylases in splicing activities. ..
- Marmier Gourrier N, Cléry A, Schlotter F, Senty Ségault V, Branlant C. A second base pair interaction between U3 small nucleolar RNA and the 5'-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Res. 2011;39:9731-45 pubmed publisher..Accordingly, we got strong evidences for a role of segment VI in the association of proteins Mpp10, Imp4 and Imp3. ..
- Jakob S, Ohmayer U, Neueder A, Hierlmeier T, Pérez Fernández J, Hochmuth E, et al. Interrelationships between yeast ribosomal protein assembly events and transient ribosome biogenesis factors interactions in early pre-ribosomes. PLoS ONE. 2012;7:e32552 pubmed publisher..They point towards some of these components being transient primary pre-rRNA in vivo binders and towards a role for others in coordinating the assembly of major SSU domains. ..