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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...heterochromatin dissociation during meiotic diplotene. PLoS Genet 17: e1009778. doi:10.1371/journal.pgen.1009778 ↵Cowley M, Wood AJ, Böhm S, Schulz R, Oakey RJ. 2012. Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res 40: 8917–8926. doi:10.1093/nar/gks654...
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Research: A compendium of conserved cleavage and polyadenylation events in mammalian genes
- Ruijia Wang,
- Dinghai Zheng,
- Ghassan Yehia,
- and Bin Tian
Genome Res. October 2018 28: 1427-1441; Published in Advance August 24, 2018, doi:10.1101/gr.237826.118
..., Rutgers University, New Brunswick, New Jersey 08901, USA Corresponding author: btian@rutgers.eduAbstractCleavage and polyadenylation is essential for 3′ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA...
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Research: RNA editing in nascent RNA affects pre-mRNA splicing
- Yun-Hua Esther Hsiao,
- Jae Hoon Bahn,
- Yun Yang,
- Xianzhi Lin,
- Stephen Tran,
- Ei-Wen Yang,
- Giovanni Quinones-Valdez,
- and Xinshu Xiao
Genome Res. June 2018 28: 812-823; Published in Advance May 3, 2018, doi:10.1101/gr.231209.117
..., revealed remarkable interplay between RNA editing and splicing and expanded the repertoire of functional RNA editing sites.The maturation of eukaryotic mRNAs involves an intricate series of molecular processes that modify newly synthesized RNA molecules, such as 5′ capping, splicing, RNA editing...
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Method: Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data
- Zhaozhao Zhao,
- Qiushi Xu,
- Ran Wei,
- Weixu Wang,
- Dong Ding,
- Yu Yang,
- Jun Yao,
- Liye Zhang,
- Yue-Qing Hu,
- Gang Wei,
- and Ting Ni
Genome Res. November 2021 31: 2095-2106; Published in Advance September 2, 2021, doi:10.1101/gr.271627.120
...discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes.Alternative polyadenylation (APA) of mRNA is a widespread phenomenon in diverse species, serving as an important contributor to transcriptome...
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Research: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- Jonathan Neve,
- Kaspar Burger,
- Wencheng Li,
- Mainul Hoque,
- Radhika Patel,
- Bin Tian,
- Monika Gullerova,
- and Andre Furger
Genome Res. January 2016 26: 24-35; Published in Advance November 6, 2015, doi:10.1101/gr.193995.115
...premRNA processing reaction that matures primary transcripts into functional mRNA molecules. In humans, more than half of all genes containmultiple CPA sites (Tian et al. 2005), and their alternative usage is widespread. Alternative cleavage and polyadenylation (APA) can lead to regulated synthesis...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...–Inserm U 1258, 67404 Illkirch CEDEX, France; 6OncoDNA Group, IntegraGen, 91000 Evry, France; 7Scipio Bioscience, 92120 Montrouge, France Corresponding authors: sandra.duharcourt@ijm.fr; chunlong.chen@curie.frAbstractEukaryotic genes are interrupted by introns that must be accurately spliced from mRNA...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...RNA occurrence (Methods) (Fig. 5A). Unlike the coding mRNA component, these long noncoding fractions (median size = 346 nucleotides) are not spliced and are not polyadenylated (Andersson et al. 2014). With the recent advancement in high-throughput sequencing, the occurrence of eRNA along with H3K27ac histone...
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Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
...no detectable RBFOX1 or RBFOX3 mRNA (data not shown) but do express moderate levels of RBFOX2 mRNA and protein (see below), consistent with restricted expression of RBFOX1 (muscle, heart, and brain) and RBFOX3 (brain) but more widespread expression of RBFOX2 (Conboy 2016). Therefore, we analyzed the splicing...
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Research: Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
- Xiaochuan Liu,
- Mainul Hoque,
- Marc Larochelle,
- Jean-François Lemay,
- Nathan Yurko,
- James L. Manley,
- François Bachand,
- and Bin Tian
Genome Res. October 2017 27: 1685-1695; Published in Advance September 15, 2017, doi:10.1101/gr.222331.117
...of Biochemistry, Université de Sherbrooke, Sherbrooke, Quebec J1E 4K8, Canada; 3Department of Biological Sciences, Columbia University, New York, New York 10027, USA Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically...
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Research: Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
- Danny A. Bitton,
- Sophie R. Atkinson,
- Charalampos Rallis,
- Graeme C. Smith,
- David A. Ellis,
- Yuan Y.C. Chen,
- Michal Malecki,
- Sandra Codlin,
- Jean-François Lemay,
- Cristina Cotobal,
- François Bachand,
- Samuel Marguerat,
- Juan Mata,
- and Jürg Bähler
Genome Res. June 2015 25: 884-896; Published in Advance April 16, 2015, doi:10.1101/gr.185371.114
...-skipping events using RNA-seq. (A) Scheme showing pre-mRNA (top) along with all possible normally spliced mRNAs and exon-skipping isoforms. The colored lines below the junctions represent diagnostic reads for normal exon–exon junctions (5′-3′; green, orange, cyan), and for exon-skipping junctions (5′-3′; blue...
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