Searching journal content for articles similar to Ribeiro-dos-Santos et al. 32 (3): 425.

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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
..., even for essential developmental regulators. The effects of genetic variants on TF binding likely depends on the genomic context and complexity of the regulatory region, with promoter regions (TSS-proximal) and cobound regions being less affected (Supplemental Fig. S3D,E).Allele-specific binding...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
..., can function as promoters, enhancers, and/or insulators, thereby regulating both proximal and distal target genes in an allele-specific manner.Genomic imprintingIn the mid-1980s, it was observed that fertilized mouse oocytes containing either two maternal or two paternal s failed to develop to term...
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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
...for barrier dynamics. We thus considered whether orthogonal genomic data sets could help constrain estimates for barrier dynamics in vivo.Barrier dynamics modify insulation of neighboring TADsTo determine the impact of dynamic barriers on 3D organization, we quantified patterns in simulated contact maps...
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Research: H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity
- Kei Fukuda,
- Chikako Shimura,
- and Yoichi Shinkai
Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125
..., Yamanashi 400-8510, Japan Corresponding authors: yshinkai@riken.jp, k.fukuda@yamanashi.ac.jpAbstractThe three-dimensional (3D) structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing topologically associated domains (TADs) and promoter-enhancer loops...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...their relevant context would improve our ability for direct assessment of disease-associated variation. Profiling of allelic transcription factor (TF) activity across multiple cell and tissue types has shown that both genomic and tissue contexts modulate the penetrance of noncoding variants (Halow et al. 2021...
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Research: In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
- Corinne Grey,
- Julie A.J. Clément,
- Jérôme Buard,
- Benjamin Leblanc,
- Ivo Gut,
- Marta Gut,
- Laurent Duret,
- and Bernard de Massy
Genome Res. April 2017 27: 580-590; Published in Advance March 23, 2017, doi:10.1101/gr.217240.116
...PRDM9 is recruited in a DSB-dependent manner. Another subset reveals DSB-independent interactions between PRDM9 and genomic sites, such as the binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...from two controls, four FSHD1 patients, four FSHD2 patients, and two patients with Bosma arhinia microphthalmia syndrome (BAMS) caused by SMCHD1 variants, as well as publicly available data from 30 B-lymphoblastoid cell lines from the 1000 Genomes Project and Human Pan Reference Consortium. We attain...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
....2). Each 575 species’annotation file provided a hierarchical genomic context, enabling precise 576 categorization of TE positions relative to functional regions. Specifically, we extracted: (1) 577 exonic regions (further stratified by synonymous/non-synonymous effects), (2) splicing sites 578 (±2 bp...
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Research: The shared genomic architecture of human nucleolar organizer regions
- Ioanna Floutsakou,
- Saumya Agrawal,
- Thong T. Nguyen,
- Cathal Seoighe,
- Austen R.D. Ganley,
- and Brian McStay
Genome Res. December 2013 23: 2003-2012; Published in Advance August 29, 2013, doi:10.1101/gr.157941.113
...et al. 1999; Boisvert et al. 2007; Zhang et al. 2007; Ganley et al. 2009). The central role of the nucleolus in growth regulation, coupled with the potential for the regions adjacent to the rDNA to contribute to NOR function, prompted us to investigate the genomic context in which the rDNA resides...
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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...domains (TADs), and loops (Szabo et al. 2019). TADs are stable genomic regions separated by insulating proteins, e.g., CCCTC-binding factor (CTCF), and provide an encapsulating domain for constraining the chromatin contacts between regulatory elements and genes (Phillips and Corces 2009; Merkenschlager...

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