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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...). The resulting sequences were aligned and manually checked to retrieve the intact exon L meeting the following criteria: (1) aligning with the previously identified L1 ORF1-derived exons, (2) including the splice site in frame, and (3) retaining more than 200 codons after trimming of putative introns. Taxonomic...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
...that they are used in their genomic context (Fig. 3D, left). In addition, a subset of the “intronic” exons displays primary sequence conservation (Fig. 3D, right). Figure 3E shows an unannotated region from the ITSN1 gene which is both conserved and trapped at high levels (10,917 read counts).Known alternative...
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Research: A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma
- Kuan-Ting Lin,
- Wai Kit Ma,
- Juergen Scharner,
- Yun-Ru Liu,
- and Adrian R. Krainer
Genome Res. March 2018 28: 275-284; Published in Advance February 15, 2018, doi:10.1101/gr.227181.117
...) report PSI values and exon coordinates of individual exons in a multiple-exon skipping event, (2) amend the GC-content and 3′-end biases from RNA-seq by using the junction reads from both ends, and (3) detect the splicing changes from alternative exons that share the same upstream intron. Thus, the new...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...additional splicing-regulatory elements embedded in the exon and flanking intronic sequences (Black 2003; Chen and Manley 2009). These cis-regulatory signals, which individually contain limited information owing to their size and degeneracy, must be recognized and integrated by hundreds of RNA...
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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
.... IPAFinder could recover ∼80% and ∼90% IPA sites at a sequencing coverage of 40× and 60×, respectively (Supplemental Fig. S3A). Furthermore, IPAFinder could exclude the interference of alternative splicing events such as alternative 5′ splice site and intron retention (Supplemental Fig. S3B). Next, we...
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Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
- Fiorella C. Grandi,
- James M. Rosser,
- Simon J. Newkirk,
- Jun Yin,
- Xiaoling Jiang,
- Zhuo Xing,
- Leanne Whitmore,
- Sanum Bashir,
- Zoltán Ivics,
- Zsuzsanna Izsvák,
- Ping Ye,
- Y. Eugene Yu,
- and Wenfeng An
Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
...and An 2012). To examine the methylation status of each insertion launched from the ORFeus transgene, we performed bisulfite-sequencing analysis of the retrotransposed GFP sequence in heart and liver. The primer pair flanked the first GFP exon and specifically amplified the intronless insertion (Fig. 1A...
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Research: Interplay between coding and exonic splicing regulatory sequences
- Nicolas Fontrodona,
- Fabien Aubé,
- Jean-Baptiste Claude,
- Hélène Polvèche,
- Sébastien Lemaire,
- Léon-Charles Tranchevent,
- Laurent Modolo,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. May 2019 29: 711-722; Published in Advance April 8, 2019, doi:10.1101/gr.241315.118
...selection process relies on RNA binding proteins or splicing factors that enhance or repress exon inclusion following two main principles. First, splicing factors bind to short intronic or exonic motifs (or splicing regulatory sequences) that are often low-complexity sequences composed of the repetition...
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Research: Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
- Yamile Marquez,
- Markus Höpfler,
- Zahra Ayatollahi,
- Andrea Barta,
- and Maria Kalyna
Genome Res. July 2015 25: 995-1007; Published in Advance May 1, 2015, doi:10.1101/gr.186585.114
...information of exons is interrupted by intervening sequences, introns. Differential inclusion of exons and introns or their parts inmature mRNAs, so-called alternative splicing (AS), results inmultiple transcript and protein variants with different fates and functions from a single gene. About 95% of human...
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Research: Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
- Arttu Jolma,
- Jilin Zhang,
- Estefania Mondragón,
- Ekaterina Morgunova,
- Teemu Kivioja,
- Kaitlin U. Laverty,
- Yimeng Yin,
- Fangjie Zhu,
- Gleb Bourenkov,
- Quaid Morris,
- Timothy R. Hughes,
- Louis James Maher III,
- and Jussi Taipale
Genome Res. July 2020 30: 962-973; Published in Advance July 23, 2020, doi:10.1101/gr.258848.119
...sequence ag|GU[g/a]agu (Fig. 6A) that is recognized by the spliceosome, suggesting that these proteins may act by binding to a subset of splice donor sites.View larger version: In this window In a new window Figure 6. RBP motif matches are conserved and enriched in distinct sequence features and classes...
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Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
- Yang I. Li,
- Luis Sanchez-Pulido,
- Wilfried Haerty,
- and Chris P. Ponting
Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
...sequences are highly conserved. Mean vertebrate phastCons scores and 95% confidence interval in the intronic flanks of symmetric (multiples of three nucleotides) alternatively spliced (AS) micro-exons, constitutively spliced (CS) micro-exons, all AS exons, and all CS exons. (B) A large proportion...
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