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Method: CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins
- Daniel Savic,
- E. Christopher Partridge,
- Kimberly M. Newberry,
- Sophia B. Smith,
- Sarah K. Meadows,
- Brian S. Roberts,
- Mark Mackiewicz,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. October 2015 25: 1581-1589; Published in Advance September 9, 2015, doi:10.1101/gr.193540.115
...palindromic repeats (CRISPR)/Cas9-based editing technology to develop CRISPR epitope tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several DNA-binding proteins spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell...
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LETTER: Novel patterns of genome rearrangement and their association with survival in breast cancer
- James Hicks,
- Alexander Krasnitz,
- B. Lakshmi,
- Nicholas E. Navin,
- Michael Riggs,
- Evan Leibu,
- Diane Esposito,
- Joan Alexander,
- Jen Troge,
- Vladimir Grubor,
- Seungtai Yoon,
- Michael Wigler,
- Kenny Ye,
- Anne-Lise Børresen-Dale,
- Bjørn Naume,
- Ellen Schlicting,
- Larry Norton,
- Torsten Hägerström,
- Lambert Skoog,
- Gert Auer,
- Susanne Månér,
- Pär Lundin,
- and Anders Zetterberg
Genome Res. December 2006 16: 1465-1479; doi:10.1101/gr.5460106
...) ( Lucito et al. 2003 ). ROMA is based on the principle that noise in microarray hybridization can be significantly reduced by reducing the complexity of the labeled DNA target in the hybridization mix. In its present configuration, ROMA uses a “representation” of the created by PCR amplification...
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Method: Read clouds uncover variation in complex regions of the human genome
- Alex Bishara,
- Yuling Liu,
- Ziming Weng,
- Dorna Kashef-Haghighi,
- Daniel E. Newburger,
- Robert West,
- Arend Sidow,
- and Serafim Batzoglou
Genome Res. October 2015 25: 1570-1580; Published in Advance August 18, 2015, doi:10.1101/gr.191189.115
...been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA...
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Research: Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
- Sarah K. Sasse,
- Margaret Gruca,
- Mary A. Allen,
- Vineela Kadiyala,
- Tengyao Song,
- Fabienne Gally,
- Arnav Gupta,
- Miles A. Pufall,
- Robin D. Dowell,
- and Anthony N. Gerber
Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
...-mediated anti-inflammatory effects (Clark and Belvisi 2012; Chinenov et al. 2013).Pregenomics and deep sequencing-based approaches have established that inductive gene regulation by the GR is typically nucleated through protein-DNA interactions between homodimeric GR and high-affinity palindromic or semi-palindromic...
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Research: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?
- Arkarachai Fungtammasan,
- Erin Walsh,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- and Kateryna D. Makova
Genome Res. June 2012 22: 993-1005; Published in Advance March 28, 2012, doi:10.1101/gr.134395.111
...microsatellites may be the factor that actually contributes to aCFS fragility, due to a high correlation in occurrence of alu repeats and mononucleotide microsatellites. AT sequence content and DNA flexibility Experimental studies have shown that long AT/TA palindromes and AT-rich sequences are associated...
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Commentary: An emerging toolkit for targeted cancer therapies
- Gordon B. Mills
Genome Res. February 2012 22: 177-182; doi:10.1101/gr.136044.111
...for cancer s. Genome Res (this issue). doi: 10.1101/gr.118414.110. ↵ Guenthoer J, Diede SJ, Tanaka H, Chai X, Hsu L, Tapscott SJ, Porter PL Guenthoer J, Diede SJ, Tanaka H, Chai X, Hsu L, Tapscott SJ, Porter PL. 2012. Assessment of palindromes as platforms for DNA amplification in breast cancer. Genome Res...
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Method: An extended set of yeast-based functional assays accurately identifies human disease mutations
- Song Sun,
- Fan Yang,
- Guihong Tan,
- Michael Costanzo,
- Rose Oughtred,
- Jodi Hirschman,
- Chandra L. Theesfeld,
- Pritpal Bansal,
- Nidhi Sahni,
- Song Yi,
- Analyn Yu,
- Tanya Tyagi,
- Cathy Tie,
- David E. Hill,
- Marc Vidal,
- Brenda J. Andrews,
- Charles Boone,
- Kara Dolinski,
- and Frederick P. Roth
Genome Res. May 2016 26: 670-680; Published in Advance March 14, 2016, doi:10.1101/gr.192526.115
...a platform for functional analysis even in the absence of orthology. Examples include yeastbased genetic assays for interaction between two human proteins or between a protein and DNA. In one study, variants of the HsABCB1 gene, encoding themajor efflux pump (also called P-glycoprotein), were functionally...
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Method: Estimation of rearrangement phylogeny for cancer genomes
- Chris D. Greenman,
- Erin D. Pleasance,
- Scott Newman,
- Fengtang Yang,
- Beiyuan Fu,
- Serena Nik-Zainal,
- David Jones,
- King Wai Lau,
- Nigel Carter,
- Paul A.W. Edwards,
- P. Andrew Futreal,
- Michael R. Stratton,
- and Peter J. Campbell
Genome Res. February 2012 22: 346-361; Published in Advance October 12, 2011, doi:10.1101/gr.118414.110
...have emerged that use information across many samples to make inferences on the order of events (Stephan-Otto Attolini et al. 2010), extracting this information from a single sample has great potential applicability. For example, identifying the earliest events in the genesis of massive DNA...
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