Searching journal content for articles similar to Komashko et al. 18 (4): 521.

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  1. Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
    • Nina Koenecke,
    • Jeff Johnston,
    • Qiye He,
    • Samuel Meier,
    • and Julia Zeitlinger
    Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
    ...in the tissue where the enhancers are not induced, including at enhancers that are known to be repressed by a transcriptional repressor. These results suggest that, rather than serving exclusively as an intermediate step before future activation, the poised enhancer state may be a mark for spatial regulation...
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  2. Method: Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
    • Yiming Kang,
    • Nikhil R. Patel,
    • Christian Shively,
    • Pamela Samantha Recio,
    • Xuhua Chen,
    • Bernd J. Wranik,
    • Griffin Kim,
    • R. Scott McIsaac,
    • Robi Mitra,
    • and Michael R. Brent
    Genome Res. March 2020 30: 459-471; Published in Advance February 14, 2020, doi:10.1101/gr.259655.119
    .... Such data are available, however, for human cell lines. We analyze large data sets on human K562 cells (The ENCODE Project Consortium 2012; Sloan et al. 2016) and HEK293 cells (Schmitges et al. 2016), producing TF networks for each cell type.ResultsSimple comparison of yeast ChIP-chip to expression profiles...
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  3. Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
    • Ozren Bogdanović,
    • Steven W. Long,
    • Simon J. van Heeringen,
    • Arie B. Brinkman,
    • Jose Luis Gómez-Skarmeta,
    • Hendrik G. Stunnenberg,
    • Peter L. Jones,
    • and Gert Jan C. Veenstra
    Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
    ...Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis Ozren Bogdanović 1 , Steven W. Long 2 , Simon J. van Heeringen 1 , Arie B. Brinkman 1 , Jose Luis Gómez-Skarmeta 3 , Hendrik G. Stunnenberg 1...
  4. Research: Developmental control of gene copy number by repression of replication initiation and fork progression
    • Noa Sher,
    • George W. Bell,
    • Sharon Li,
    • Jared Nordman,
    • Thomas Eng,
    • Matthew L. Eaton,
    • David M. MacAlpine,
    • and Terry L. Orr-Weaver
    Genome Res. January 2012 22: 64-75; Published in Advance November 16, 2011, doi:10.1101/gr.126003.111
    ...associated with transcriptional repression of euchromatic regions (Schwartz and Pirrotta 2007) and has recently been shown to be the only repressive histone modification tested whose binding pattern parallels chromatin accessibility (Bell et al. 2010). Therefore, we checked, by ChIP-chip of third...
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  5. Resource: Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
    • Matthew Slattery,
    • Lijia Ma,
    • Rebecca F. Spokony,
    • Robert K. Arthur,
    • Pouya Kheradpour,
    • Anshul Kundaje,
    • Nicolas Nègre,
    • Alex Crofts,
    • Ryan Ptashkin,
    • Jennifer Zieba,
    • Alexander Ostapenko,
    • Sarah Suchy,
    • Alec Victorsen,
    • Nader Jameel,
    • A. Jason Grundstad,
    • Wenxuan Gao,
    • Jennifer R. Moran,
    • E. Jay Rehm,
    • Robert L. Grossman,
    • Manolis Kellis,
    • and Kevin P. White
    Genome Res. July 2014 24: 1224-1235; Published in Advance July 1, 2014, doi:10.1101/gr.168807.113
    ...on an Illumina HiSeq 2000 according to the manufacturer’s standard protocols. Data processing ChIP-chip peak calls are as previously described (Li et al. 2008; MacArthur et al. 2009; Zinzen et al. 2009; Nègre et al. 2011). For ChIP-seq experiments, biological replicates were scored against an appropriate input...
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  6. Research: Understanding transcriptional regulation by integrative analysis of transcription factor binding data
    • Chao Cheng,
    • Roger Alexander,
    • Renqiang Min,
    • Jing Leng,
    • Kevin Y. Yip,
    • Joel Rozowsky,
    • Koon-Kiu Yan,
    • Xianjun Dong,
    • Sarah Djebali,
    • Yijun Ruan,
    • Carrie A. Davis,
    • Piero Carninci,
    • Timo Lassman,
    • Thomas R. Gingeras,
    • Roderic Guigó,
    • Ewan Birney,
    • Zhiping Weng,
    • Michael Snyder,
    • and Mark Gerstein
    Genome Res. September 2012 22: 1658-1667; doi:10.1101/gr.136838.111
    ...(Schena et al. 1995), only recently has the -wide identification of TF-binding sites become possible, owing to the development of chromatin immunoprecipitation followed by microarray (ChIP-chip) and sequencing (ChIP-seq) technologies (Ren et al. 2000; Johnson et al. 2007). In several previous studies...
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  7. Method: Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
    • Daniel Marbach,
    • Sushmita Roy,
    • Ferhat Ay,
    • Patrick E. Meyer,
    • Rogerio Candeias,
    • Tamer Kahveci,
    • Christopher A. Bristow,
    • and Manolis Kellis
    Genome Res. July 2012 22: 1334-1349; Published in Advance March 28, 2012, doi:10.1101/gr.127191.111
    ...Nègre et al. 2011 Network inference Gene expression Microarray Developmental time-course 11,990 28 Hooper et al. 2007 Network inference Histone marks ChIP-chip Developmental time-course 13,494 12 Nègre et al. 2011 Network inference Histone marks ChIP-chip Cell lines 13,494 2 Kharchenko et al. 2011...
  8. Research: Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
    • Congmao Wang,
    • Chang Liu,
    • Damian Roqueiro,
    • Dominik Grimm,
    • Rebecca Schwab,
    • Claude Becker,
    • Christa Lanz,
    • and Detlef Weigel
    Genome Res. February 2015 25: 246-256; Published in Advance November 3, 2014, doi:10.1101/gr.170332.113
    ..., sequencing, and read alignmentwere performed as described (Becker et al. 2011). Integration of epi data Published ChIP-seq and ChIP-chip data (Zhang et al. 2009; Costas et al. 2011; Roudier et al. 2011; Luo et al. 2012; Park et al. 2012; Stroud et al. 2012) were originally mapped to the TAIR8 version...
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  9. Method: A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
    • René A.M. Dirks,
    • Peter C. Thomas,
    • Haoyu Wu,
    • Robert C. Jones,
    • Hendrik G. Stunnenberg,
    • and Hendrik Marks
    Genome Res. May 2021 31: 919-933; Published in Advance March 11, 2021, doi:10.1101/gr.260745.120
    ...San Francisco, California 94080, USA Corresponding author: hendrik.marks@ru.nlAbstractEpigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for -wide identification of regulatory elements, for defining transcriptional regulatory networks...
  10. Research: Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome
    • Keerthi T. Chathoth and
    • Nicolae Radu Zabet
    Genome Res. April 2019 29: 613-625; Published in Advance February 1, 2019, doi:10.1101/gr.246710.118
    ...plotted considering 1 kb around each border. We performed a nonparametric Mann–Whitney U test considering the highest levels at each TAD border between embryonic and neuronal cells (see P-values). (D–F) Average Pol II ChIP-chip signal (log2 ChIP/input) at the borders of the three different TAD classes...
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