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Research: A CRISPR knockout screen identifies SETDB1-target retroelement silencing factors in embryonic stem cells
- Kei Fukuda,
- Akihiko Okuda,
- Kosuke Yusa,
- and Yoichi Shinkai
Genome Res. June 2018 28: 846-858; Published in Advance May 4, 2018, doi:10.1101/gr.227280.117
...) performed a -wide siRNA screen and identified multiple known and previously uncharacterized silencing factors. Since siRNA generally cannot completely down-regulate gene expression, it is possible that there are further unidentified retroelement silencing factors. Gene perturbation by editing using...
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Method: Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
- Arshad H. Khan,
- Andy Lin,
- Richard T. Wang,
- Joshua S. Bloom,
- Kenneth Lange,
- and Desmond J. Smith
Genome Res. October 2020 30: 1458-1467; Published in Advance September 2, 2020, doi:10.1101/gr.262204.120
...RNAs (siRNAs) to specifically degrade transcripts. These reagents have given insights into multiple phenotypes (Root et al. 2006; Blakely et al. 2011; Mohr et al. 2014; Boettcher and McManus 2015). More recently, CRISPR-Cas9 gene editing approaches that introduce targeted mutations into DNA have...
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Research: A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells
- Keren Imberg-Kazdan,
- Susan Ha,
- Alex Greenfield,
- Christopher S. Poultney,
- Richard Bonneau,
- Susan K. Logan,
- and Michael J. Garabedian
Genome Res. April 2013 23: 581-591; Published in Advance February 12, 2013, doi:10.1101/gr.144774.112
...PCR and normalized to RPL19. Each assay was performed in duplicate, with error bars representing the range of the mean. (C–F ) MED19 selectively regulates AR transcriptional activity. LNCaP-abl cells were transfected with control siRNA (siControl) or siRNA against MED19 (siMED19) togetherwith (C ) a plasmid...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...was performed with human antisense probe 3. For all above tissue sections, negligible signal was observed with sense sequence probes in adjacent sections (Supplemental Fig. 3D), confirming specificity of the antisense probe staining. Evrony et al. 1330 Genome Research www..org qPCR after siRNA knockdown...
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Method: Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases
- Julia Ritzerfeld,
- Steffen Remmele,
- Tao Wang,
- Koen Temmerman,
- Britta Brügger,
- Sabine Wegehingel,
- Stella Tournaviti,
- Jeroen R.P.M. Strating,
- Felix T. Wieland,
- Beate Neumann,
- Jan Ellenberg,
- Chris Lawerenz,
- Jürgen Hesser,
- Holger Erfle,
- Rainer Pepperkok,
- and Walter Nickel
Genome Res. November 2011 21: 1955-1968; Published in Advance July 27, 2011, doi:10.1101/gr.116087.110
...partition upon palmitoylation. In the present study, we established a live-cell imaging screening system to identify gene products involved in plasma membrane targeting of SRC kinases. Based on siRNA arrays and a human model cell line expressing two kinds of SH4 reporter molecules, we conducted a genome...
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Research: A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity
- Bing Zhang,
- Daniel S. Day,
- Joshua W. Ho,
- Lingyun Song,
- Jingjing Cao,
- Danos Christodoulou,
- Jonathan G. Seidman,
- Gregory E. Crawford,
- Peter J. Park,
- and William T. Pu
Genome Res. June 2013 23: 917-927; Published in Advance April 1, 2013, doi:10.1101/gr.149674.112
...measured the effect of EP300 knockdown on H3K27ac chromatin occupancy. siRNA EP300 knockdown (Supplemental Fig. 4) blocked VEGFA-stimulated deposition of H3K27ac at NR4A1, HLX, and KDR (Fig. 2B; Supplemental Fig. 5A). To determine if EP300 histone acetyltransferase catalytic activity, as opposed to other...
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Research: Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs
- Adrian A. Valli,
- Bruno A.C.M. Santos,
- Silvia Hnatova,
- Andrew R. Bassett,
- Attila Molnar,
- Betty Y. Chung,
- and David C. Baulcombe
Genome Res. April 2016 26: 519-529; Published in Advance March 11, 2016, doi:10.1101/gr.199703.115
...RNA-mediated RNA silencing in the model algal species, Chlamydomonas reinhardtii . Among the mutants from this screen, there were three at Dicer-like 3 that failed to produce both miRNAs and siRNAs and others affecting diverse post-biogenesis stages of miRNA-mediated silencing. The DCL3-dependent siRNAs fell...
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Method: AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
...the unique coding sequence of FGFR1-238 (Supplemental Table S4). Then we studied the dependence of tumor cell growth on the expression of FGFR1-238 by conducting a long-term (10 days) cell proliferation assay in the presence or absence (control) of siRNA knockdown. Our experimental results show...
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Research: Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity
- Stacia K. Wyman,
- Emily C. Knouf,
- Rachael K. Parkin,
- Brian R. Fritz,
- Daniel W. Lin,
- Lucas M. Dennis,
- Michael A. Krouse,
- Philippa J. Webster,
- and Muneesh Tewari
Genome Res. September 2011 21: 1450-1461; Published in Advance August 3, 2011, doi:10.1101/gr.118059.110
...%) in the cells treated with siRNAs targeting the enzyme of interest versus those treated with the negative control, siCyclophilin, and (2) showed at least a 5% absolute decrease in fractional abundance of the variant miRNA. The letter(s) within each bar for a given miRNA identifies which 39 variant displays...
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Method: ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens
- Diane D. Shao,
- Aviad Tsherniak,
- Shuba Gopal,
- Barbara A. Weir,
- Pablo Tamayo,
- Nicolas Stransky,
- Steven E. Schumacher,
- Travis I. Zack,
- Rameen Beroukhim,
- Levi A. Garraway,
- Adam A. Margolin,
- David E. Root,
- William C. Hahn,
- and Jill P. Mesirov
Genome Res. April 2013 23: 665-678; Published in Advance December 26, 2012, doi:10.1101/gr.143586.112
...further opportunities for the application and interpretation of functional screens. For screens in mammalian cells, a short interfering RNA (siRNA) is introduced into cells either directly as a duplex or by expression of a short hairpin RNA (shRNA) that is processed into active siRNA. This siRNA...

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