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Method: Structure-optimized sgRNA selection with PlatinumCRISPr for efficient Cas9 generation of knockouts
- Irmgard U. Haussmann,
- Thomas C. Dix,
- David W.J. McQuarrie,
- Veronica Dezi,
- Abdullah I. Hans,
- Roland Arnold,
- and Matthias Soller
Genome Res. December 2024 34: 2279-2292; Published in Advance December 3, 2024, doi:10.1101/gr.279479.124
...METTL3, it has been found that a functional ORF can be restored by altered splicing leaving considerable levels of m6A in mRNA (Poh et al. 2022). Likewise, compensatory responses have been observed involving upregulating genes and as a consequence causing stronger phenotypes than compared to removing...
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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
...normalized dS of ∼0.148, consistent with widespread positive selection. We considered the possibility that this signal of fast evolution could be due to sampling ESE and control sites from different parts of the exon. Alternatively, it could be driven by unusual Ke motifs that have a stronger splice enhancer...
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Resource: Genome-wide discovery of human splicing branchpoints
- Tim R. Mercer,
- Michael B. Clark,
- Stacey B. Andersen,
- Marion E. Brunck,
- Wilfried Haerty,
- Joanna Crawford,
- Ryan J. Taft,
- Lars K. Nielsen,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
...site. This is likely due to the selection against polymorphisms that can form cryptic splice sites that compete with bona fide 39 splice sites and cause aberrant splicing (Smith et al. 1993). In contrast, 40% (an ;10.4-fold enrichment over expected) of disease associFigure 5. Branchpoint motifs...
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Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
- Sahar Gelfman,
- David Burstein,
- Osnat Penn,
- Anna Savchenko,
- Maayan Amit,
- Schraga Schwartz,
- Tal Pupko,
- and Gil Ast
Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
..., with regard to ‘‘rate shifts to conservation’’ and ‘‘rate shifts to variability’’ mentioned above, are mainly due to changes in selection intensity around the splice sites. Prediction of cis-acting splicing regulatory elements To identify splicing motifs that act as major regulators of alternative splicing...
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Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
- David Thybert,
- Maša Roller,
- Fábio C.P. Navarro,
- Ian Fiddes,
- Ian Streeter,
- Christine Feig,
- David Martin-Galvez,
- Mikhail Kolmogorov,
- Václav Janoušek,
- Wasiu Akanni,
- Bronwen Aken,
- Sarah Aldridge,
- Varshith Chakrapani,
- William Chow,
- Laura Clarke,
- Carla Cummins,
- Anthony Doran,
- Matthew Dunn,
- Leo Goodstadt,
- Kerstin Howe,
- Matthew Howell,
- Ambre-Aurore Josselin,
- Robert C. Karn,
- Christina M. Laukaitis,
- Lilue Jingtao,
- Fergal Martin,
- Matthieu Muffato,
- Stefanie Nachtweide,
- Michael A. Quail,
- Cristina Sisu,
- Mario Stanke,
- Klara Stefflova,
- Cock Van Oosterhout,
- Frederic Veyrunes,
- Ben Ward,
- Fengtang Yang,
- Golbahar Yazdanifar,
- Amonida Zadissa,
- David J. Adams,
- Alvis Brazma,
- Mark Gerstein,
- Benedict Paten,
- Son Pham,
- Thomas M. Keane,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
...approach to establish how rapidly sequence changes occur in the whole as well as in specific classes of genomic elements, including ancestral repeats such as LTR, SINE, LINE, and DNA repeats, exons, and CTCF binding motifs (Fig. 2). The rate of nucleotide variation change reflects different evolutionary...
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Method: Quantitative evaluation of all hexamers as exonic splicing elements
- Shengdong Ke,
- Shulian Shang,
- Sergey M. Kalachikov,
- Irina Morozova,
- Lin Yu,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. August 2011 21: 1360-1374; Published in Advance June 9, 2011, doi:10.1101/gr.119628.110
...on short RNA stretches known as exonic and intronic splicing enhancers (ESEs and ISEs) and silencers (ESSs and ISSs). These so-called splicing regulatory motifs are manifold and, like their transcriptional counterparts, are thought to act in combination. Several different approaches have been used...
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LETTER: Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
- Schraga Schwartz,
- João Silva,
- David Burstein,
- Tal Pupko,
- Eduardo Eyras,
- and Gil Ast
Genome Res. January 2008 18: 88-103; Published in Advance November 21, 2007, doi:10.1101/gr.6818908
...splicing signals underwent extensive changes during evolution, in parallel with considerable changes in terms of exon-intron architecture and domain structure of the splicing regulators. These changes were presumably shaped by the lifestyle of the organism, selective pressure on maintaining multi...
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Letter: Complex selection on 5′ splice sites in intron-rich organisms
- Manuel Irimia,
- Scott William Roy,
- Daniel E. Neafsey,
- Josep F. Abril,
- Jordi Garcia-Fernandez,
- and Eugene V. Koonin
Genome Res. November 2009 19: 2021-2027; Published in Advance September 10, 2009, doi:10.1101/gr.089276.108
....1186/1471-2148-7-188. Jaillon O, Bouhouche K, Gout J-F, Aury J-M, Noel B, Nowacki M, Serrano V, Porcel BM, Se´gurens B, Moue¨l AL, et al. 2008. Translational control of intron splicing in eukaryotes. Nature 451: 359–362. Ke S, Zhang XHF, Chasin LA. 2008. Positive selection acting on splicing motifs reflects compensatory...
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Method: Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes
- Michael F. Lin,
- Pouya Kheradpour,
- Stefan Washietl,
- Brian J. Parker,
- Jakob S. Pedersen,
- and Manolis Kellis
Genome Res. November 2011 21: 1916-1928; Published in Advance October 12, 2011, doi:10.1101/gr.108753.110
...collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show...
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Resource: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
- Thomas Derrien,
- Rory Johnson,
- Giovanni Bussotti,
- Andrea Tanzer,
- Sarah Djebali,
- Hagen Tilgner,
- Gregory Guernec,
- David Martin,
- Angelika Merkel,
- David G. Knowles,
- Julien Lagarde,
- Lavanya Veeravalli,
- Xiaoan Ruan,
- Yijun Ruan,
- Timo Lassmann,
- Piero Carninci,
- James B. Brown,
- Leonard Lipovich,
- Jose M. Gonzalez,
- Mark Thomas,
- Carrie A. Davis,
- Ramin Shiekhattar,
- Thomas R. Gingeras,
- Tim J. Hubbard,
- Cedric Notredame,
- Jennifer Harrow,
- and Roderic Guigó
Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
...The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression Thomas Derrien 1 , 11 , Rory Johnson 1 , 11 , Giovanni Bussotti 1 , Andrea Tanzer 1 , Sarah Djebali 1 , Hagen Tilgner 1...
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