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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
...transgene, here designed with a large intron context. We define the trapped exons as “autonomous.” We obtained ∼1.25 million trapped exons, including most known mRNA and well-annotated lncRNA internal exons, demonstrating that human exons are predominantly autonomous. mRNA exons are trapped with the highest...
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RESOURCE: Large-scale gene trapping in C57BL/6N mouse embryonic stem cells
- Gwenn M. Hansen,
- Diane C. Markesich,
- Michael B. Burnett,
- Qichao Zhu,
- Karen M. Dionne,
- Lizabeth J. Richter,
- Richard H. Finnell,
- Arthur T. Sands,
- Brian P. Zambrowicz,
- and Alejandro Abuin
Genome Res. October 2008 18: 1670-1679; Published in Advance September 17, 2008, doi:10.1101/gr.078352.108
...by the splice acceptor element within the trapping construct, or alternatively, by direct gene disruption as a result of insertion within an exon. Gene trapping is inherently amenable to high-throughput, cost-effective mutant clone production and mutation identification. A single gene trapping vector can...
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ARTICLE: Identification of 3'-terminal exons from yeast artificial chromosomes.
- D B Krizman,
- T A Hofmann,
- U DeSilva,
- E D Green,
- P S Meltzer,
- and J M Trent
Genome Res. June 1995 4: 322-326
...) Two distinct approaches to exon trap- ping have been developed: Internal exon trapping and 3'-terminal exon trapping. 3'-Terminal exon trapping was reported as a method that offers several advan- tages over internal exon trapping, such as (1) a positive selection scheme, (2) the isolation of larger...
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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
...of pathogenic D4Z4 contractions. High resolution analysis of individual D4Z4 repeat methylation revealed areas of low methylation near the CTCF/insulator region and areas of high methylation immediately preceding the DUX4 transcriptional start site. Within the DUX4 exons, we observed a waxing/waning methylation...
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Method: Efficient and flexible tagging of endogenous genes by homology-independent intron targeting
- Yevgeniy V. Serebrenik,
- Stephanie E. Sansbury,
- Saranya Santhosh Kumar,
- Jorge Henao-Mejia,
- and Ophir Shalem
Genome Res. August 2019 29: 1322-1328; Published in Advance June 25, 2019, doi:10.1101/gr.246413.118
...utilizing a generic donor (Suzuki et al. 2016).An alternative approach for generating endogenous fusions is by random integration of synthetic exons delivered by transposons or retroviral particles (Trinh le and Fraser 2013). This approach, known as “protein trapping” or “CD-tagging” (Jarvik et al. 1996...
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Perspective: Parlez-vous VUS?
- Gregory M. Cooper
Genome Res. October 2015 25: 1423-1426; doi:10.1101/gr.190116.115
...variants. In this perspective, I discuss the challenge of “variant interpretation” and the value of comparative and functional genomic information in meeting that challenge. Although already essential, genomic annotations will become even more important as our analytical focus widens beyond coding exons...
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ARTICLE: Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
- Timothy Ravasi,
- Harukazu Suzuki,
- Ken C. Pang,
- Shintaro Katayama,
- Masaaki Furuno,
- Rie Okunishi,
- Shiro Fukuda,
- Kelin Ru,
- Martin C. Frith,
- M. Milena Gongora,
- Sean M. Grimmond,
- David A. Hume,
- Yoshihide Hayashizaki,
- and John S. Mattick
Genome Res. January 2006 16: 11-19; Published in Advance December 12, 2005, doi:10.1101/gr.4200206
...terminal poly(A) tracts but internal priming sites within longer transcripts, only a minority of which is encompassed by known genes. A significant proportion of these transcripts exhibit tissue-specific expression patterns, as well as dynamic changes in their expression in macrophages following...
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Methods: Post-entrapment genome engineering: First exon size does not affect the expression of fusion transcripts generated by gene entrapment
- Anna B. Osipovich,
- Aparna Singh,
- and H. Earl Ruley
Genome Res. March 2005 15: 428-435; doi:10.1101/gr.3258105
...of first exons than has been reported for internal exons. Finally, a retroviral poly(A) trap (consisting of a RNA polymerase II promoter, a neomycin-resistance gene, and 5′-splice site) typically produced mutagenized clones in which vector sequences spliced to the 3′-terminal exons of cellular...
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Research: Saturation mutagenesis reveals manifold determinants of exon definition
- Shengdong Ke,
- Vincent Anquetil,
- Jorge Rojas Zamalloa,
- Alisha Maity,
- Anthony Yang,
- Mauricio A. Arias,
- Sergey Kalachikov,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. January 2018 28: 11-24; Published in Advance December 14, 2017, doi:10.1101/gr.219683.116
....eduAbstractTo illuminate the extent and roles of exonic sequences in the splicing of human RNA transcripts, we conducted saturation mutagenesis of a 51-nt internal exon in a three-exon minigene. All possible single and tandem dinucleotide substitutions were surveyed. Using high-throughput genetics, 5560 minigene molecules...
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Research: Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
- Milana Frenkel-Morgenstern,
- Vincent Lacroix,
- Iakes Ezkurdia,
- Yishai Levin,
- Alexandra Gabashvili,
- Jaime Prilusky,
- Angela del Pozo,
- Michael Tress,
- Rory Johnson,
- Roderic Guigo,
- and Alfonso Valencia
Genome Res. July 2012 22: 1231-1242; Published in Advance May 15, 2012, doi:10.1101/gr.130062.111
...in the , we performed the following mapping protocol. First, we mapped the RNA-seq reads to the reference , in order to identify which reads can be assigned to exons, i.e., exonic reads. In order to identify junction reads, we constructed, for each gene, the combination of all pairs of exons, yielding...
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