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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...cells to re-enter the cell cycle partially restores a youthful H3K27me3 landscape, suggesting that DNA replication may rejuvenate chromatin structure (Yang et al. 2023). However, even mitotically active somatic stem cells display age-related increases in Polycomb repression: Aged Drosophila intestinal...
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Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
...rDNA (Zellner et al. 2007), and a recent biochemical analysis showed that purifiedORC could bind toG4 RNA or DNA (Hoshina et al. 2013). In the Drosophila , ORC binding sites contain a central GC-rich region surrounded by AT-rich sequences (Vorobyeva et al. 2013). G-rich motifs/G4 may help...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...Center, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Corresponding authors: cgutierrez@cbm.csic.es, ubastolla@cbm.csic.esAbstractEukaryotic replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology...
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Research: Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
- Gaetano Ivan Dellino,
- Davide Cittaro,
- Rossana Piccioni,
- Lucilla Luzi,
- Stefania Banfi,
- Simona Segalla,
- Matteo Cesaroni,
- Ramiro Mendoza-Maldonado,
- Mauro Giacca,
- and Pier Giuseppe Pelicci
Genome Res. January 2013 23: 1-11; Published in Advance November 27, 2012, doi:10.1101/gr.142331.112
...of chromatin fragments based on their protein/DNA ratio and has been used to purify bulk chromatin (density: 1.42–1.39 g/cm3) from freeDNA (»1.69 g/cm3) or cross-linked proteins (»1.25 g/cm3) (Solomon et al. 1988). Specific chromatin regions, such as enhancers, transcribed exons, or active promoters, show low...
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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
...animals were flash-frozen before isolation of nuclei, our results represent DNA supercoiling states arrested at the time of freezing.BP was used previously to visualize transcription-dependent supercoils in Drosophila polytene chromosomes (Matsumoto and Hirose 2004) via microscopy. BP was also used...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...) regulate the expression of my gene of interest (GOI) directly on its promoter. However, answering this is not straightforward. Genes exist within multilayered microenvironments of proximal and distal promoter–enhancer interactions, DNA accessibility, histone post-translational modifications (PTMs), and DNA...
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Research: Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- Andre J. Faure,
- Dominic Schmidt,
- Stephen Watt,
- Petra C. Schwalie,
- Michael D. Wilson,
- Huiling Xu,
- Robert G. Ramsay,
- Duncan T. Odom,
- and Paul Flicek
Genome Res. November 2012 22: 2163-2175; Published in Advance July 10, 2012, doi:10.1101/gr.136507.111
...#2;15; Fig. 1B). CNC sites that occur within promoter regions (#2.5 kb from the annotated TSS), are highly enriched for RNAP2 binding compared with cohesin-bound promoters in general (Fisher’s exact test P < 10#2;15). These results are similar to those in Drosophila, where cohesin lacks a functional...
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Research: Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development
- Vladimir B. Teif,
- Daria A. Beshnova,
- Yevhen Vainshtein,
- Caroline Marth,
- Jan-Philipp Mallm,
- Thomas Höfer,
- and Karsten Rippe
Genome Res. August 2014 24: 1285-1295; Published in Advance May 8, 2014, doi:10.1101/gr.164418.113
...of cell differentiation (Reddington et al. 2013; Smith and Meissner 2013). The site-specific locations of these DNA modifications have been linked to disease development through nucleosome positioning (Portela et al. 2013), transcription factor (TF) binding (Stadler et al. 2011), and differential gene...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...al. 2005; Potthoff and Olson 2007; Zdobnov et al. 2020), with highly conserved DNA-binding domains (Carlsson and Mahlapuu 2002; Chang et al. 2015).View larger version: In this window In a new window Figure 1. Profiling transcription factor (TF) binding in F1 embryos of Drosophila melanogaster. (A...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
...conformation capture data. By reporting on all tools’ performance in classifying CTCF-cohesin anchored stripes, enhancer–promoter interacting stripes, and indeterminate stripes, we also demonstrate a thorough, integrated analysis to determine the output stripes’ quality. Our work provides a flexible...
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