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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...release. These common genes are enriched in protein synthesis functions (Supplemental Fig. S6H), including Ribi and RP genes. However, 24% of the promoter-bound RNAPII showing pervasive transcription upon release in lactate ethanol are not pervasively expressed in glucose. These are enriched for functions...
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Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
- Dongwon Lee,
- Ashish Kapoor,
- Alexias Safi,
- Lingyun Song,
- Marc K. Halushka,
- Gregory E. Crawford,
- and Aravinda Chakravarti
Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
..., New York, NY 10016, USA; 5University of Texas Health Science Center at Houston, Houston, TX 77030, USA Corresponding authors: aravinda.chakravarti@nyumc.org, dongwon.lee@nyumc.orgAbstractCis-regulatory elements (CRE), short DNA sequences through which transcription factors (TFs) exert regulatory...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
...↵11 These authors contributed equally to this work. Corresponding authors: pavlopoulos@fleming.gr, izg5139@psu.eduAbstractG-quadruplex DNA structures exhibit a profound influence on essential biological processes, including transcription, replication, telomere maintenance, and genomic stability...
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Research: Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations
- Daniel M. Ibrahim,
- Peter Hansen,
- Christian Rödelsperger,
- Asita C. Stiege,
- Sandra C. Doelken,
- Denise Horn,
- Marten Jäger,
- Catrin Janetzki,
- Peter Krawitz,
- Gundula Leschik,
- Florian Wagner,
- Till Scheuer,
- Mareen Schmidt-von Kegler,
- Petra Seemann,
- Bernd Timmermann,
- Peter N. Robinson,
- Stefan Mundlos,
- and Jochen Hecht
Genome Res. December 2013 23: 2091-2102; Published in Advance August 30, 2013, doi:10.1101/gr.157610.113
...for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml ). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/ . Jochen Hecht...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
...significantly enriched in genes with sequence-specific DNA-binding transcription factor activity (GO:3700; P < 10#2;12), particularly those with a homeobox domain (Pfam, P < 10#2;6). They were also enriched in genes with promoter regions, which comprise motives for binding of POU2F1 (P = 1.1 3 10#2;4), growth...
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Research: DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure
- Sahar Gelfman,
- Noa Cohen,
- Ahuvi Yearim,
- and Gil Ast
Genome Res. May 2013 23: 789-799; Published in Advance March 15, 2013, doi:10.1101/gr.143503.112
..., including embryogenesis and development, genomic imprinting, and regulation of gene transcription (Li et al. 1992; Okano et al. 1999; Bestor 2000; Reik 2007). Due to dramatic advances in high-throughput DNA sequencing methods, several groups have recently mapped DNA methylation across the whole at single...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...et al. 2018; Marsico et al. 2019). In mammals, the genomic distribution of G4s is not random but rather peculiar to specific genomic regions, such as telomeres, gene promoters, transcription factor binding sites, and sites with DNA double-strand breaks (Biffi et al. 2013; Varshney et al. 2020; Zheng...
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Method: Delineating yeast cleavage and polyadenylation signals using deep learning
- Emily Kunce Stroup and
- Zhe Ji
Genome Res. July 2024 34: 1066-1080; Published in Advance June 24, 2024, doi:10.1101/gr.278606.123
...address this issue by developing deep learning models to deconvolute degenerate cis-regulatory elements and quantify their positional importance in mediating yeast poly(A) site formation, cleavage heterogeneity, and strength. In S. cerevisiae, cleavage heterogeneity is promoted by the depletion of U...
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Research: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
- Guillaume Andrey,
- Robert Schöpflin,
- Ivana Jerković,
- Verena Heinrich,
- Daniel M. Ibrahim,
- Christina Paliou,
- Myriam Hochradel,
- Bernd Timmermann,
- Stefan Haas,
- Martin Vingron,
- and Stefan Mundlos
Genome Res. February 2017 27: 223-233; Published in Advance December 6, 2016, doi:10.1101/gr.213066.116
...This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml ). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International...
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Method: Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints
- Ron Schwessinger,
- Maria C. Suciu,
- Simon J. McGowan,
- Jelena Telenius,
- Stephen Taylor,
- Doug R. Higgs,
- and Jim R. Hughes
Genome Res. October 2017 27: 1730-1742; Published in Advance September 13, 2017, doi:10.1101/gr.220202.117
...al. 1736 Genome Research www..org most variants found in GWAS studies lie in noncoding DNA, and therefore, being able to discriminate between true regulatory SNPs and variants in LD with them is a major roadblock in interpreting GWAS. Most regulatory elements can be identified by DNase-seq and...

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