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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...effects of mRNA half-life, we pulse-labeled ESCs with 5-ethynyl uridine (EU) to label and purify nascent mRNA, followed by RT–quantitative polymerase chain reaction (qPCR). In the presence of LBH589, nascent Pou5f1 and Nanog transcripts decreased within 1 h of treatment and showed a progressive reduction...
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Research: Enhancers with tissue-specific activity are enriched in intronic regions
- Beatrice Borsari,
- Pablo Villegas-Mirón,
- Sílvia Pérez-Lluch,
- Isabel Turpin,
- Hafid Laayouni,
- Alba Segarra-Casas,
- Jaume Bertranpetit,
- Roderic Guigó,
- and Sandra Acosta
Genome Res. August 2021 31: 1325-1336; Published in Advance July 21, 2021, doi:10.1101/gr.270371.120
...-sense mediated decay (Lewis et al. 2003), and to the control of transcription initiation via recruitment of RNA Polymerase II, likely as alternative promoters (Bieberstein et al. 2012; Kowalczyk et al. 2012). However, here we found that, in most tissues, about half of the ELSs located in introns do not regulate...
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Method: Accurate and efficient detection of gene fusions from RNA sequencing data
- Sebastian Uhrig,
- Julia Ellermann,
- Tatjana Walther,
- Pauline Burkhardt,
- Martina Fröhlich,
- Barbara Hutter,
- Umut H. Toprak,
- Olaf Neumann,
- Albrecht Stenzinger,
- Claudia Scholl,
- Stefan Fröhling,
- and Benedikt Brors
Genome Res. March 2021 31: 448-460; Published in Advance January 13, 2021, doi:10.1101/gr.257246.119
...–generated fusion transcripts from Jia et al. (2013), who simulated 150 fusion transcripts and merged them into an RNA-seq sample from benign tissue (H1 human embryonic stem cells), serving as background expression. To measure the sensitivity of a method as a function of the expression level of a fusion transcript...
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Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
- Thomas O. Auer,
- Karine Duroure,
- Anne De Cian,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
...www..org vs. 4% when using the kif5aa knock-in set) when using a less efficient sgRNA (66% of indel mutations for sgRNA eGFP 1 vs. 22% for sgRNA kif5aa 1). Combination of multiple sgRNAs to increase knock-in efficiency To overcome this reduced efficiency and demonstrate the flexibility of the CRISPR...
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Research: A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver
- Donatella Canella,
- David Bernasconi,
- Federica Gilardi,
- Gwendal LeMartelot,
- Eugenia Migliavacca,
- Viviane Praz,
- Pascal Cousin,
- Mauro Delorenzi,
- Nouria Hernandez,
- and The CycliX Consortium
Genome Res. April 2012 22: 666-680; Published in Advance January 27, 2012, doi:10.1101/gr.130286.111
...A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver Donatella Canella 1 , 5 , David Bernasconi 1 , 2 , 5 , Federica Gilardi 1 , 6 , Gwendal LeMartelot 3 , 6...
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Research: Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation
- Joanna Y. Ip,
- Dominic Schmidt,
- Qun Pan,
- Arun K. Ramani,
- Andrew G. Fraser,
- Duncan T. Odom,
- and Benjamin J. Blencowe
Genome Res. March 2011 21: 390-401; Published in Advance December 16, 2010, doi:10.1101/gr.111070.110
...Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation Joanna Y. Ip 1 , 2 , Dominic Schmidt 3 , 4 , Qun Pan 1 , Arun K. Ramani 1 , Andrew G. Fraser 1 , 2 , Duncan T. Odom 3 , 4...
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Methods: Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
- J. Douglas Freeman,
- René L. Warren,
- John R. Webb,
- Brad H. Nelson,
- and Robert A. Holt
Genome Res. October 2009 19: 1817-1824; Published in Advance June 18, 2009, doi:10.1101/gr.092924.109
...A, Hercend T, Triebel F, Pannetier C, Kourilsky P. 1995. T-cell repertoires in healthy and diseased human tissues analysed by T-cell receptor beta-chain CDR3 size determination: Evidence for oligoclonal expansions in tumours and inflammatory diseases. Res Immunol 146: 65–80. Flicek P, Aken BL, Beal...
REVIEW: The ligase chain reaction in a PCR world.
- F Barany
Genome Res. August 1991 1: 5-16; doi:10.1101/gr.1.1.5
...DNA and RNA probes with polymerase chain reaction. Anal. Biochem. 177 : 90 – 94 . 36. Sarkar, G., , Cassady, J. , Bottema, C.D. , Sommer. S.S. Sarkar, G., Cassady, J. Bottema, C.D. and Sommer. S.S. 1990 . Characterization of polymerase chain reaction amplification of specific alleles. Anal. Biochem...
ARTICLE: Effect of different laboratory techniques for guanidinium-phenol-chloroform RNA extraction on A260/A280 and on accuracy of mRNA quantitation by reverse transcriptase-PCR.
- M Yamaguchi,
- C W Dieffenbach,
- R Connolly,
- D F Cruess,
- W Baur,
- and J B Sharefkin
Genome Res. May 1992 1: 286-290; doi:10.1101/gr.1.4.286
...of the dystrophin gene in human muscle and non-muscle tissues. Nature 333 : 858 – 860 . 3. Wang, A.M., , Doyle, M.V. , Mark. D.F. Wang, A.M., Doyle, M.V. and Mark. D.F. 1989 . Quantitation of mRNA by the polymerase chain reaction. Proc. Natl. Acad. Sri. 86 : 9717 – 9721 . 4. Robinson, M.O. , Simon. M.I. Robinson, M...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
...Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance Tim Downing 1 , 10 , Hideo Imamura 2 , 10 , Saskia Decuypere 2 , Taane G. Clark 3...
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