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Research: The shared genomic architecture of human nucleolar organizer regions
- Ioanna Floutsakou,
- Saumya Agrawal,
- Thong T. Nguyen,
- Cathal Seoighe,
- Austen R.D. Ganley,
- and Brian McStay
Genome Res. December 2013 23: 2003-2012; Published in Advance August 29, 2013, doi:10.1101/gr.157941.113
..., K562, MCF-7, NHEK, NHLF) from ENCODE Caltech RNA-seq. GenBank mRNAs and ESTs data were downloaded from the UCSC Genome Browser (Fujita et al. 2011) on January 1, 2012. These data were mapped to the human to which the DJ sequences had been added (Supplemental Methods).Nucleolar ChIP and FAIRECh...
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Methods: A transcription factor affinity-based code for mammalian transcription initiation
- Molly Megraw,
- Fernando Pereira,
- Shane T. Jensen,
- Uwe Ohler,
- and Artemis G. Hatzigeorgiou
Genome Res. April 2009 19: 644-656; Published in Advance January 13, 2009, doi:10.1101/gr.085449.108
...intended for high-resolution prediction in shorter regions known to contain a TSS, for example, regions preidentified by a chromatin immunoprecipitation with microarray hybridization (ChIP-chip) experiment. Results are displayed in Figure 5 for comparison with the annotation-supported model. We observe...
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ARTICLE: A code for transcription initiation in mammalian genomes
- Martin C. Frith,
- Eivind Valen,
- Anders Krogh,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Albin Sandelin
Genome Res. January 2008 18: 1-12; Published in Advance November 21, 2007, doi:10.1101/gr.6831208
...on the method used to indicate accessibility. While the MM may be practically used to pinpoint the exact start sites from other technologies with lower resolution, such as ChIP-chip with antibodies targeting parts of the preinitiation complex, we consider the main utility of our method to be on the conceptual...
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Research: H2A.B facilitates transcription elongation at methylated CpG loci
- Yibin Chen,
- Qiang Chen,
- Richard C. McEachin,
- James D. Cavalcoli,
- and Xiaochun Yu
Genome Res. April 2014 24: 570-579; Published in Advance January 8, 2014, doi:10.1101/gr.156877.113
...enriched region groups is associated with 5mC (Fig. 1E). Further analyses across the H2A.B enrichment regions show that the 5mC profile is also associated with the H2A.B profile in gene bodies (Fig. 1F). Moreover, we randomly picked three H2A.B-enriched regions and performed ChIP assays to confirm the high...
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LETTER: Evolution of the mammalian transcription factor binding repertoire via transposable elements
- Guillaume Bourque,
- Bernard Leong,
- Vinsensius B. Vega,
- Xi Chen,
- Yen Ling Lee,
- Kandhadayar G. Srinivasan,
- Joon-Lin Chew,
- Yijun Ruan,
- Chia-Lin Wei,
- Huck Hui Ng,
- and Edison T. Liu
Genome Res. November 2008 18: 1752-1762; Published in Advance August 5, 2008, doi:10.1101/gr.080663.108
...transcriptional regulation and to further quantify the significance of species-specific regulation, we analyzed, from an evolutionary perspective, seven whole- occupancy data sets obtained in vivo by chromatin immunoprecipitation (ChIP) (see Table 1 ). The studied transcription factors (TFs) are: ESR1 (also known...
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LETTER: Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
- David S. Johnson,
- Wei Li,
- D. Benjamin Gordon,
- Arindam Bhattacharjee,
- Bo Curry,
- Jayati Ghosh,
- Leonardo Brizuela,
- Jason S. Carroll,
- Myles Brown,
- Paul Flicek,
- Christoph M. Koch,
- Ian Dunham,
- Mark Bieda,
- Xiaoqin Xu,
- Peggy J. Farnham,
- Philipp Kapranov,
- David A. Nix,
- Thomas R. Gingeras,
- Xinmin Zhang,
- Heather Holster,
- Nan Jiang,
- Roland D. Green,
- Jun S. Song,
- Scott A. McCuine,
- Elizabeth Anton,
- Loan Nguyen,
- Nathan D. Trinklein,
- Zhen Ye,
- Keith Ching,
- David Hawkins,
- Bing Ren,
- Peter C. Scacheri,
- Joel Rozowsky,
- Alexander Karpikov,
- Ghia Euskirchen,
- Sherman Weissman,
- Mark Gerstein,
- Michael Snyder,
- Annie Yang,
- Zarmik Moqtaderi,
- Heather Hirsch,
- Hennady P. Shulha,
- Yutao Fu,
- Zhiping Weng,
- Kevin Struhl,
- Richard M. Myers,
- Jason D. Lieb,
- and X. Shirley Liu
Genome Res. March 2008 18: 393-403; Published in Advance February 7, 2008, doi:10.1101/gr.7080508
.... Thus the results from the expression array spike-in experiments are not necessarily directly relevant to tiling-array experiments. One recent study compared the performance of array-based (ChIP-chip) and sequence-based (ChIP-PET) technologies on a real ChIP experiment ( Euskirchen et al. 2007...
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Method: Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
- David U. Gorkin,
- Dongwon Lee,
- Xylena Reed,
- Christopher Fletez-Brant,
- Seneca L. Bessling,
- Stacie K. Loftus,
- Michael A. Beer,
- William J. Pavan,
- and Andrew S. McCallion
Genome Res. November 2012 22: 2290-2301; Published in Advance September 27, 2012, doi:10.1101/gr.139360.112
..., the transcriptional coactivator EP300 and the histone modification H3K4me1 have proven particularly effective (Heintzman et al. 2007, 2009; Visel et al. 2009a; Blow et al. 2010; Bulger and Groudine 2011). Though ChIP-seq and ChIP-chip have dramatically increased the throughput with which putative enhancers can...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...precipitation by a transcription factor-specific antibody, the DNA is fragmented into small pieces averaging 100–500 bp. After precipitation, reversal of the cross-linking reaction releases the DNA for subsequent detection by PCR amplification. Caveats to the ChIP assay include an inability to detect precise...
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Research: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
- Sharmistha Pal,
- Ravi Gupta,
- Hyunsoo Kim,
- Priyankara Wickramasinghe,
- Valérie Baubet,
- Louise C. Showe,
- Nadia Dahmane,
- and Ramana V. Davuluri
Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
...parallel sequencing-based methods (mRNA-seq and ChIP-seq) and integrative bioinformatics analysis to (1) identify the active and repressed promoters, their expressed transcript variants, and their epigenetic profiles; (2) generate a digital inventory of transcripts including the transcript variants...
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Method: Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Andrew J. Sharp,
- Eugenia Migliavacca,
- Yann Dupre,
- Elisavet Stathaki,
- Mohammad Reza Sailani,
- Alessandra Baumer,
- Albert Schinzel,
- Deborah J. Mackay,
- David O. Robinson,
- Gilda Cobellis,
- Luigi Cobellis,
- Han G. Brunner,
- Bernhard Steiner,
- and Stylianos E. Antonarakis
Genome Res. September 2010 20: 1271-1278; Published in Advance July 14, 2010, doi:10.1101/gr.108597.110
...(Supplementary Table 1). As (1) underlying copy-number variations (CNVs) can sometimes cause false signals in ChIP data thatmimic enrichment peaks (Vega et al. 2009; A Sharp, unpubl.), (2) nonunique sequences are highly enriched for CNVs and yield lower quality microarrays data due to cross...

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