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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...a fosmid construct, or did not pass ChIP-seq metrics after recombineering (Paix et al. 2017; Dokshin et al. 2018; Ghanta and Mello 2020). The CRISPR approach has the advantage of being a single copy and retaining the native regulatory context of the TF gene. To test whether this approach impacted TF...
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Method: Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq
- Peng Liu,
- Rajendran Sanalkumar,
- Emery H. Bresnick,
- Sündüz Keleş,
- and Colin N. Dewey
Genome Res. August 2016 26: 1124-1133; Published in Advance July 12, 2016, doi:10.1101/gr.199174.115
...to partition the training set into groups that have distinct RNA-seq read count distributions, and (2) the data set is informative for a large fraction of target genes. We find that Pol II ChIP-seq data meets both requirements. To examine the first requirement, we built a training set for human cell line K562...
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Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Stephen G. Landt,
- Georgi K. Marinov,
- Anshul Kundaje,
- Pouya Kheradpour,
- Florencia Pauli,
- Serafim Batzoglou,
- Bradley E. Bernstein,
- Peter Bickel,
- James B. Brown,
- Philip Cayting,
- Yiwen Chen,
- Gilberto DeSalvo,
- Charles Epstein,
- Katherine I. Fisher-Aylor,
- Ghia Euskirchen,
- Mark Gerstein,
- Jason Gertz,
- Alexander J. Hartemink,
- Michael M. Hoffman,
- Vishwanath R. Iyer,
- Youngsook L. Jung,
- Subhradip Karmakar,
- Manolis Kellis,
- Peter V. Kharchenko,
- Qunhua Li,
- Tao Liu,
- X. Shirley Liu,
- Lijia Ma,
- Aleksandar Milosavljevic,
- Richard M. Myers,
- Peter J. Park,
- Michael J. Pazin,
- Marc D. Perry,
- Debasish Raha,
- Timothy E. Reddy,
- Joel Rozowsky,
- Noam Shoresh,
- Arend Sidow,
- Matthew Slattery,
- John A. Stamatoyannopoulos,
- Michael Y. Tolstorukov,
- Kevin P. White,
- Simon Xi,
- Peggy J. Farnham,
- Jason D. Lieb,
- Barbara J. Wold,
- and Michael Snyder
Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
..., affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE ( http://encodeproject.org/ENCODE/ ) and modENCODE ( http://www.modencode.org/ ) portals. Footnotes ↵ 28 Corresponding authors E-mail mpsnyder...
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Method: Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
- Antonio L.C. Gomes,
- Thomas Abeel,
- Matthew Peterson,
- Elham Azizi,
- Anna Lyubetskaya,
- Luís Carvalho,
- and James Galagan
Genome Res. October 2014 24: 1686-1697; Published in Advance July 14, 2014, doi:10.1101/gr.161711.113
...is essential to understand gene regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a global map of the regulatory binding network. Most ChIPseq analysis tools focus on identifying binding regions from coverage enrichment. However, less work has been performed to infer...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...of the modENCODE Project, we generated deep RNA-seq data sets for C. elegans using a consistent methodology across the life cycle, including a detailed embryonic time course. These data sets provide the community with information about the patterns of protein coding gene and ncRNA expression as well...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...regulatory regions. To verify that our ATAC-seq data correctly identify regulatory regions throughout the epi, we used multiple histone modification ChIP-seq data sets from modENCODE (Li et al. 2009; Ho et al. 2014) and ChromHMM (Ernst and Kellis 2012) to build predictive models of the epi. Chrom...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...leaders. By combining this data set with the modERN ChIP-seq resource, we are able to support and predict gene regulatory relationships. The detailed information on differences and similarities between gene expression in cell lineages and tissues should be of great value to the community and provides...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
..., we performed RNA-seq to determine expression levels of all genes and ChIP-seq using an antibody recognizing the unphosphorylated C-terminal repeat of RNA polymerase II (RNA Pol II), which recognized RNA Pol II bound at the TSSs of active genes in gastrulae (Supplemental Fig. S5) and planulae (Figs. 2...
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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
...the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level. Footnotes...
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Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
- Tess E. Jeffers and
- Jason D. Lieb
Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
...in green and orange, respectively) were considered “fragile” or “resistant.” Jeffers and Lieb 76 Genome Research www..org TFBSs. We collected a set of 35,062 TFBSs bound at any stage of C. elegans development, as identified by TF ChIP-seq from the modENCODE Consortium (Araya et al. 2014). The DNA...

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