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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
...transcriptional unit or when no MIMIC line (Venken et al. 2011) was available to produce a tagged TF.View this table: In this window In a new window Table 1. Summary of strains, ChIP-seq data sets, and stages for worm and fly TFsFor worms, we primarily utilized the recombineered fosmid resource Transgene...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...at sites bound by the C. elegans ortholog of NIPBL and loop extrudes in an effectively two-sided manner. ChIP-seq analyses show that cohesin translocation along the fountain trajectory depends on a fully intact complex and is extended upon WAPL-1 depletion. Hi-C contact patterns at individual fountains...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...and purification of psoralen-bound DNA fragments.View larger version: In this window In a new window Figure 1. Genome-wide mapping strategy for DNA supercoils reveals negative supercoiling at transcription start sites (TSSs) of embryos. (A,B) Strategy for -wide mapping of DNA supercoils (BP-seq). (A) When...
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Resource: Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
- Margaret C.W. Ho,
- Porfirio Quintero-Cadena,
- and Paul W. Sternberg
Genome Res. December 2017 27: 2108-2119; Published in Advance October 26, 2017, doi:10.1101/gr.223735.117
...their target ceh-13 (Kuntz et al. 2008). Overall, systematic identification of C. elegans CRMs has proved difficult.ChIP-seq experiments, which measure binding of a TF of interest to regions of the , generate data that can be mined for putative CRMs (Ren et al. 2000; Robertson et al. 2007; Visel et al. 2009...
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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
...isoforms. Results A novel RNA-seq quantification method using a Pol II ChIP-seq data-derived prior The pRSEM framework was built upon the RSEM statistical model for RNA-seq quantification (Li et al. 2010; Li andDewey 2011)with two novel features. First, pRSEM places a prior distribution over transcript...
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Research: Genome-wide uniformity of human ‘open’ pre-initiation complexes
- William K.M. Lai and
- B. Franklin Pugh
Genome Res. January 2017 27: 15-26; Published in Advance November 10, 2016, doi:10.1101/gr.210955.116
...stable PICs have been detected. However, even these PICs rapidly move into elongating complexes (Jeronimo and Robert 2014; Wong et al. 2014). The presence of TFIIB within the PIC active site suggests that experimentally coupling the single-nucleotide resolution of permanganate reactivity in openDNAwithChIP-seq...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...assays in IGN, such as transcriptome profiling (RNA-seq), histone modification profiling via chromatin immunoprecipitation (ChIP-seq), and chromatin accessibility profiling via assay for transposon-accessible chromatin (ATAC-seq) (Sanchez et al. 2023).In this study, we characterized C. elegans chromatin...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...-throughput sequencing (ChIP-seq), which provides a statistically identified snapshot of regions referred to as peaks (Barski et al. 2007; Johnson et al. 2007; Robertson et al. 2007; Kharchenko et al. 2008; Zhang et al. 2008; Savic et al. 2015; Meadows et al. 2020). For those TFs with DNA sequence specificity...
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Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...al. 2004], 26%ofNANOG targets and 50%of POU5F1 targets in mice [Loh et al. 2006], and ;10% of hlh-1 targets in C. elegans [Kuntz et al. 2012; for review, see Spitz and Furlong 2012]). By analyzing ChIP-seq data in combination with data sets describing genes altered upon single transcription factor...
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Research: Genome-wide map of regulatory interactions in the human genome
- Nastaran Heidari,
- Douglas H. Phanstiel,
- Chao He,
- Fabian Grubert,
- Fereshteh Jahanbani,
- Maya Kasowski,
- Michael Q. Zhang,
- and Michael P. Snyder
Genome Res. December 2014 24: 1905-1917; Published in Advance September 16, 2014, doi:10.1101/gr.176586.114
...hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison...
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