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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
...RNA isoforms with different 3′ UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3′ end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian m...
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Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
- Meng Chen,
- Ran Wei,
- Gang Wei,
- Mingqing Xu,
- Zhixi Su,
- Chen Zhao,
- and Ting Ni
Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
...and polyadenylation: extent, regulation and function. Nat Rev Genet 14: 496–506. doi:10.1038/nrg3482 ↵Gruber AJ, Schmidt R, Gruber AR, Martin G, Ghosh S, Belmadani M, Keller W, Zavolan M. 2016. A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role...
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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
...(A) signal AATAAA in the ±50 bp flanking sequences of IPAFinder-identified intronic pA sites (Fig. 2C) further supported the reliability of our method in discovering IpA in the pan-cancer data sets (Bailey et al. 2009).View larger version: In this window In a new window Figure 2. IPAFinder reveals the global...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...-read sequencing with Cas9-targeted enrichment of 4q and 10q D4Z4 arrays for comprehensive genetic analysis including determination of the length of the 4q and 10q D4Z4 arrays with base-pair resolution. In the same assay, we differentiate 4q from 10q telomeric sequences, determine A/B haplotype, identify...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...species within a complex pool of RNAs (Ray et al. 2013). The motifs resembled poly(C)-binding protein (PCBP), poly(A)-binding protein (PABP), and heterogeneous nuclear ribonucleoprotein (HNRNP) family binding sites (Fig. 2I; Supplemental Fig. S3B). RNA-binding proteins from these families have previously...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...), collectively corresponding to ∼50% of the human (Methods). RNA structure predictions weremade in these putatively orthologous sequence sets by CMfinder, which locally and structurally aligns a set of unaligned sequences, discarding apparently irrelevant ones (Yao et al. 2006). CMfinder is not constrained...
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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
...and translation of maternal mRNAs through sequence-specific association with 3′ UTRs before ZGA. Comparison of iCLIP data from two developmental stages revealed that Hnrnpa1 dissociates from maternal mRNAs at ZGA and instead regulates the nuclear processing of pri-mir-430 transcripts, which we validated...
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Research: Analysis of alternative splicing associated with aging and neurodegeneration in the human brain
- James R. Tollervey,
- Zhen Wang,
- Tibor Hortobágyi,
- Joshua T. Witten,
- Kathi Zarnack,
- Melis Kayikci,
- Tyson A. Clark,
- Anthony C. Schweitzer,
- Gregor Rot,
- Tomaž Curk,
- Blaž Zupan,
- Boris Rogelj,
- Christopher E. Shaw,
- and Jernej Ule
Genome Res. October 2011 21: 1572-1582; Published in Advance August 16, 2011, doi:10.1101/gr.122226.111
....3 0.8 0.7 MAGOH Protein mago nashi homolog 1.1 0.5 0.7 NUDT21 Cleavage and polyadenylation specificity factor subunit 5 1.6 1.1 0.7 PPIH Peptidyl-prolyl cis-trans isomerase H 1.2 0.6 0.6 NOVA1 RNA-binding protein Nova-1 1.2 0.5 0.6 KHDRBS3 KH-domain-containing, RNA-binding, signal transduction...

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