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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. April 2026 36: 695-712; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and compared with all HCNEs (Fig. 4H; Supplemental Figs. S14–S18).Consistent with expectations, our analyses reveal a highly significant association between endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including HMG domain-containing and chromatin binding factors. Notably...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...of the complex relationship between chromatin organization and transcription.Every eukaryotic encodes the information necessary for cellular viability and growth. Although the underlying instructions embedded in the DNA are identical among the cells of an organism, complex regulatory mechanisms transform...
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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...regulatory genomic phenomena, including gene expression (RNA-seq), protein–DNA interactions (ChIP-seq), and chromatin accessibility (ATAC-seq). Although longer read sequencing techniques like Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) have been established, many regulatory genomics...
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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
...of an individual genomic locus by DNA sequencing. Here we used a dedicated comprehensive chromatin library (Chrom-3×BC) to determine the changes in local chromatin proteomes upon inhibition of Pol II by chemical means or by physiological signals during quiescence.PH is a potent inhibitor of Pol II and has...
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Method: Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins
- Haoyi Wang,
- David Mayhew,
- Xuhua Chen,
- Mark Johnston,
- and Robi David Mitra
Genome Res. May 2011 21: 748-755; Published in Advance April 6, 2011, doi:10.1101/gr.114850.110
.... Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions...
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Resource: Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
- Bony De Kumar,
- Mark E. Parrish,
- Brian D. Slaughter,
- Jay R. Unruh,
- Madelaine Gogol,
- Christopher Seidel,
- Ariel Paulson,
- Hua Li,
- Karin Gaudenz,
- Allison Peak,
- William McDowell,
- Brian Fleharty,
- Youngwook Ahn,
- Chengqi Lin,
- Edwin Smith,
- Ali Shilatifard,
- and Robb Krumlauf
Genome Res. August 2015 25: 1229-1243; Published in Advance May 29, 2015, doi:10.1101/gr.184978.114
...for the 39 murine Hox genes and five endogenous controls, were used to quantitate changes. To monitor transcription from coding and noncoding regions, we designed custom tiling arrays (Agilent) with probes covering both strands of DNA. These spanned the four Hox clusters and large areas of their flanking DNA...
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Research: Combinatorial binding of transcription factors in the pluripotency control regions of the genome
- Luciana Ferraris,
- Allan P. Stewart,
- Jinsuk Kang,
- Alec M. DeSimone,
- Matthew Gemberling,
- Dean Tantin,
- and William G. Fairbrother
Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110
...complexes on;400 kb of transcriptional control regions that regulate pluripotency in ES cells (i.e., regions bound simultaneously by POU5F1, SOX2, andNANOG in vivo).We mapped protein occupancy on these DNA targets at a resolution of 10 nucleotides (nt). We discovered that while POU2F1 and POU5F1 share...
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Method: Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
- Arttu Jolma,
- Teemu Kivioja,
- Jarkko Toivonen,
- Lu Cheng,
- Gonghong Wei,
- Martin Enge,
- Mikko Taipale,
- Juan M. Vaquerizas,
- Jian Yan,
- Mikko J. Sillanpää,
- Martin Bonke,
- Kimmo Palin,
- Shaheynoor Talukder,
- Timothy R. Hughes,
- Nicholas M. Luscombe,
- Esko Ukkonen,
- and Jussi Taipale
Genome Res. June 2010 20: 861-873; Published in Advance April 8, 2010, doi:10.1101/gr.100552.109
...structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the ∼1400 human...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...or duplication of segments of DNA. Amplification of segments of DNA sequence, a type of copy number variation (CNV), is an important source of rapid adaptive evolution. In the short term, gene amplification can result in increased gene expression, which provides a selective advantage facilitating adaptation...
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RESOURCE: An effective model for natural selection in promoters
- Michael M. Hoffman and
- Ewan Birney
Genome Res. May 2010 20: 685-692; Published in Advance March 1, 2010, doi:10.1101/gr.096719.109
...a binding profile of transcription factors to DNA sequences, in which different factors compete for the same potential binding sites. The parametrized model simultaneously estimates a continuous measurement of binding occupancy across the genomic sequence for each factor. We can then introduce a localized...
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