Searching journal content for articles similar to Luo et al. 32 (6): 1183.

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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...).To characterize the dynamic barrier model, we quantified FRiP across a range of barrier bound time and occupancies (Fig. 3B; Supplemental Fig. S2A). We found that FRiP generally displayed the opposite trend as loop size as a function of bound time (τb): more potent barriers lead to higher FRiP (Supplemental Fig...
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Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
- Iris Dror,
- Tamar Golan,
- Carmit Levy,
- Remo Rohs,
- and Yael Mandel-Gutfreund
Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
...binding sites. [Supplemental material is available for this article.] Transcriptional regulation is highly dependent on the binding of transcription factors (TFs) to short DNA binding motifs (Matys et al. 2003; Bryne et al. 2008).Whereas such short sequencemotifs can appear a myriad of times in the , only...
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Resource: Impact of regulatory variation across human iPSCs and differentiated cells
- Nicholas E. Banovich,
- Yang I. Li,
- Anil Raj,
- Michelle C. Ward,
- Peyton Greenside,
- Diego Calderon,
- Po Yuan Tung,
- Jonathan E. Burnett,
- Marsha Myrthil,
- Samantha M. Thomas,
- Courtney K. Burrows,
- Irene Gallego Romero,
- Bryan J. Pavlovic,
- Anshul Kundaje,
- Jonathan K. Pritchard,
- and Yoav Gilad
Genome Res. January 2018 28: 122-131; Published in Advance December 5, 2017, doi:10.1101/gr.224436.117
...accessibility, and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell-type–specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell...
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Resource: Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps
- Ali Mortazavi,
- Shirley Pepke,
- Camden Jansen,
- Georgi K. Marinov,
- Jason Ernst,
- Manolis Kellis,
- Ross C. Hardison,
- Richard M. Myers,
- and Barbara J. Wold
Genome Res. December 2013 23: 2136-2148; Published in Advance October 29, 2013, doi:10.1101/gr.158261.113
...the resulting SOM to identify chromatin signatures related to sequence-specific transcription factor occupancy, sequence motif enrichment, and biological functions. To highlight clusters enriched for specific functions such as transcriptional promoters or enhancers, we overlaid onto the map additional data sets...
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Method: High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression
- Philippe Batut,
- Alexander Dobin,
- Charles Plessy,
- Piero Carninci,
- and Thomas R. Gingeras
Genome Res. January 2013 23: 169-180; Published in Advance August 30, 2012, doi:10.1101/gr.139618.112
...). The regulatory blueprints that orchestrate the spatiotemporal dynamics of eukaryotic transcriptomes mirror this complexity. Large-scale surveys of chromatin modifications and transcription factor occupancy in diverse organisms have started to shed light on the abundance of cis-regulatory modules (Ernst et al...
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Research: E4F1 and ZNF148 are transcriptional activators of the −57A > C and wild-type TERT promoter
- Boon Haow Chua,
- Nurkaiyisah Zaal Anuar,
- Laure Ferry,
- Cecilia Domrane,
- Anna Wittek,
- Vineeth T. Mukundan,
- Sudhakar Jha,
- Falk Butter,
- Daniel G. Tenen,
- Pierre-Antoine Defossez,
- and Dennis Kappei
Genome Res. November 2023 33: 1893-1905; Published in Advance November 2, 2023, doi:10.1101/gr.277724.123
...2F1, whereas the nonmethylated region grants access to activating transcription factors (Renaud et al. 2007; Zhang et al. 2014). In comparison, noncancerous primary cell lines are generally hypomethylated across the CpG islands (Renaud et al. 2007; Esopi et al. 2020). TERT is also often expressed...
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Research: Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity
- Zdenek Andrysik,
- Matthew D. Galbraith,
- Anna L. Guarnieri,
- Sara Zaccara,
- Kelly D. Sullivan,
- Ahwan Pandey,
- Morgan MacBeth,
- Alberto Inga,
- and Joaquín M. Espinosa
Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
.... We found that although TP53 elicits vastly divergent signaling cascades across cell lines, it directly activates a core transcriptional program of ∼100 genes with diverse biological functions, regardless of cell type or cellular response to TP53 activation. This core program is associated with high-occupancy...
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Research: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh,
- Yuna Asriyan,
- Adam Richards,
- Ryan G. Christensen,
- Victoria L. Hall,
- Majid Kazemian,
- Cong Zhu,
- Hannah Pham,
- Qiong Cheng,
- Charles Blatti,
- Jessie A. Brasefield,
- Matthew D. Basciotta,
- Jianhong Ou,
- Joseph C. McNulty,
- Lihua J. Zhu,
- Susan E. Celniker,
- Saurabh Sinha,
- Gary D. Stormo,
- Michael H. Brodsky,
- and Scot A. Wolfe
Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
...with high-throughput sequencing technology has fueled the -wide analysis of nucleosome occupancy, chromatin modification states, insulator elements, transcription factor (TF) and RNA polymerase II binding sites, and tissue and temporal gene expression patterns (MacArthur et al. 2009; Schuettengruber et al...

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