Searching journal content for articles similar to Ke et al. 21 (8): 1360.

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  1. Research: Exonic splice regulation imposes strong selection at synonymous sites
    • Rosina Savisaar and
    • Laurence D. Hurst
    Genome Res. October 2018 28: 1442-1454; Published in Advance August 24, 2018, doi:10.1101/gr.233999.117
    ...is the selection that maintains them? Despite a large body of research into exonic splice regulatory signals, these questions have not been answered. This is because, to our knowledge, previous investigations have not explicitly disentangled the frequency of splice regulatory elements from the strength...
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  2. Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
    ...splicing in cis, as summarized in Supplemental Figure S1 (Hui et al. 2003; Sathasivam et al. 2013; De Roeck et al. 2018; Pacheco et al. 2019). For example, a (TG)n repeat near the 3′ splice site of exon 9 of CFTR, the causative gene of cystic fibrosis, was shown to function as an intronic splicing silencer...
  3. Research: Allele-specific alternative splicing and its functional genetic variants in human tissues
    • Kofi Amoah,
    • Yun-Hua Esther Hsiao,
    • Jae Hoon Bahn,
    • Yiwei Sun,
    • Christina Burghard,
    • Boon Xin Tan,
    • Ei-Wen Yang,
    • and Xinshu Xiao
    Genome Res. March 2021 31: 359-371; Published in Advance January 15, 2021, doi:10.1101/gr.265637.120
    ...), consistent with the expectation that regulatory elements of splicing tend to locate in close proximity to splice sites. Note that because the other types of alternative exons had relatively small numbers of events, they were not included in this analysis.Experimental support of functional SNPs for GMASTo...
  4. 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
    ...-type samples. The changes in relative luciferase activity (reflected by fluorescence signal) can quantitatively evaluate the effect of a PAS variant on gene expression. Consistent with the pathogenicity of the PAS variant, for example, Mut6G in HBA2, by previous results (Higgs et al. 1983), our mpCHECK2 system...
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  5. Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
    • Joana Carlevaro-Fita,
    • Taisia Polidori,
    • Monalisa Das,
    • Carmen Navarro,
    • Tatjana I. Zoller,
    • and Rory Johnson
    Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
    ...: In this window In a new window Figure 1. Repeat insertion domains of lncRNAs (RIDLs). (A) In the RIDL model, exonically inserted fragments of transposable elements (TEs) contain pre-formed protein-binding (red), RNA-binding (green), or DNA-binding (blue) activities that contribute to the functionality...
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  6. Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
    • Marta Melé,
    • Kaia Mattioli,
    • William Mallard,
    • David M. Shechner,
    • Chiara Gerhardinger,
    • and John L. Rinn
    Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
    ...in human cells. Nature 489: 101–108. The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636–640. Fairbrother WG, Yeh R-F, Sharp PA, Burge CB. 2002. Predictive identification of exonic splicing enhancers in human genes. Science 297: 1007–1013. Goff LA, Groff...
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  7. Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
    • Charles E. Vejnar,
    • Mario Abdel Messih,
    • Carter M. Takacs,
    • Valeria Yartseva,
    • Panos Oikonomou,
    • Romain Christiano,
    • Marlon Stoeckius,
    • Stephanie Lau,
    • Miler T. Lee,
    • Jean-Denis Beaudoin,
    • Damir Musaev,
    • Hiba Darwich-Codore,
    • Tobias C. Walther,
    • Saeed Tavazoie,
    • Daniel Cifuentes,
    • and Antonio J. Giraldez
    Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
    ...), there is a paucity of quantitative models that integrate the various elements to predict mRNA deadenylation, degradation, and RBP binding. Thus, it is still poorly understood how sequence composition influences mRNA stability, how the sequence context affects the regulatory potential of each motif, what...
  8. Resource: A quantitative atlas of polyadenylation in five mammals
    • Adnan Derti,
    • Philip Garrett-Engele,
    • Kenzie D. MacIsaac,
    • Richard C. Stevens,
    • Shreedharan Sriram,
    • Ronghua Chen,
    • Carol A. Rohl,
    • Jason M. Johnson,
    • and Tomas Babak
    Genome Res. June 2012 22: 1173-1183; Published in Advance March 27, 2012, doi:10.1101/gr.132563.111
    ...sequences (Fig. 1B) and are compatible with standard cluster generation protocols.We applied PolyA-seq to 24 samples from five species, with each sample sequenced in one lane on an Illumina GAIIx sequencer. We aligned reads to the , transcripts, and exon–exon splice junctions, and retained all...
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  9. Letter: Genome-wide mapping of alternative splicing in Arabidopsis thaliana
    • Sergei A. Filichkin,
    • Henry D. Priest,
    • Scott A. Givan,
    • Rongkun Shen,
    • Douglas W. Bryant,
    • Samuel E. Fox,
    • Weng-Keen Wong,
    • and Todd C. Mockler
    Genome Res. January 2010 20: 45-58; Published in Advance October 26, 2009, doi:10.1101/gr.093302.109
    ...and deep sequencing of the transcriptome at single-base resolution, allowing accurate empirical determination of splice junctions and alternative splicing events with low false discovery rates. Our data provide an unprecedented and unbiased evaluation of alternative splicing in Arabidopsis, the premier...
  10. Research: DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure
    • Sahar Gelfman,
    • Noa Cohen,
    • Ahuvi Yearim,
    • and Gil Ast
    Genome Res. May 2013 23: 789-799; Published in Advance March 15, 2013, doi:10.1101/gr.143503.112
    .... If this is the case, could the roles of these epigenetic modifications in splicing be a side effect of the GC content of the exons? How could one isolate the measured levels of DNA methylation and nucleosome occupancy on exons and conclude a biological role unbiased by GC content? To evaluate this, we use two...
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