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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
...Olga M. Sigalova1,5,6, Mattia Forneris1,5, Frosina Stojanovska2,3, Bingqing Zhao1,7, Rebecca R. Viales1, Adam Rabinowitz1, Fayrouz Hammal4, Benoît Ballester4, Judith B. Zaugg2 and Eileen E.M. Furlong1 1European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany; 2...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...a direct impact on the folding architecture. We find that SVs can cause domain-wide switches, from, for example, A-to-B compartment and early-to-late replication timing, and repression of gene expression. This resembles the recently discovered cis-elements termed “early replication control elements” (ERCEs...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
..., United Kingdom; 7Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany ↵8 These authors contributed equally to the work. Corresponding author: pkorber@lmu.deAbstractMapping of nucleosomes, the basic...
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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...Methods 10: 1213–1218. doi:10.1038/nmeth.2688 ↵Cheng J-H, Pan DZ-C, Tsai ZT-Y, Tsai H-K. 2015. Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues. Sci Rep 5: 12648. doi:10.1038/srep12648 ↵Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS...
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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
...simultaneously. The chromatin composition at the insertion site influences the expression of the reporters, but outside pericentric heterochromatin it consists of multiple redundant effects. This suggests that, for housekeeping genes, the chromatin context acts as a fine-tuningmechanismat a domain-wide scale...
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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
...and regulatory landscape of 446 limb-associated gene loci in mouse using Capture-C, ChIP-seq, and RNA-seq in forelimb, hindlimb at three developmental stages, and midbrain. The fine mapping of chromatin interactions revealed a strong preference for functional genomic regions such as repressed or active domains...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...of the correlations between strains see Supp. Fig. S1. Also, note that96 all genes used in this analysis were expressed at a minimal level across the strains (overall mean of97 5 TPM), so results do not include data from non-expressed genes.98 Figure 1: The first two principal components of each genomic feature...
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Method: Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins
- Dimiter Kunnev,
- Amy Freeland,
- Maochun Qin,
- Robert W. Leach,
- Jianmin Wang,
- Rajani M. Shenoy,
- and Steven C. Pruitt
Genome Res. April 2015 25: 558-569; Published in Advance March 11, 2015, doi:10.1101/gr.176099.114
...deficiency reduces DNA replication initiation in gene-rich regions of the genome. DNA structural properties are shown to correlate with sequence motifs associated with replication origins and with locations that are preferentially affected by MCM2 deficiency. Reduced nascent strand density correlates...
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Research: Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
- Maxim Pimkin,
- Andrew V. Kossenkov,
- Tejaswini Mishra,
- Christapher S. Morrissey,
- Weisheng Wu,
- Cheryl A. Keller,
- Gerd A. Blobel,
- Dongwon Lee,
- Michael A. Beer,
- Ross C. Hardison,
- and Mitchell J. Weiss
Genome Res. December 2014 24: 1932-1944; Published in Advance October 15, 2014, doi:10.1101/gr.164178.113
...modification marks with the gene expression changes that occur during development of primary cultured megakaryocytes (MEG) and primary erythroblasts (ERY) from murine fetal liver hematopoietic stem/progenitor cells. We identified a robust, genome-wide mechanism of MEG-specific lineage priming by a previously...
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Research: Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
- Adam R. Prickett,
- Nikolaos Barkas,
- Ruth B. McCole,
- Siobhan Hughes,
- Samuele M. Amante,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. October 2013 23: 1624-1635; Published in Advance June 26, 2013, doi:10.1101/gr.150136.112
...contributed equally to this work. Abstract DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome...

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