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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...of heterochromatin by rendering it more accessible (Wu et al. 2009).Only 6% of P10 → P90−GO or P49 → P90−GO overlapped with ENCODE candidate cis-regulatory elements (cCREs) that are identified by either histone modifications (H3K4me3 and H3K27ac) or CTCF-binding data. This percentage ranged between 48% and 77...
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Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
- Stefan Schoenfelder,
- Mayra Furlan-Magaril,
- Borbala Mifsud,
- Filipe Tavares-Cadete,
- Robert Sugar,
- Biola-Maria Javierre,
- Takashi Nagano,
- Yulia Katsman,
- Moorthy Sakthidevi,
- Steven W. Wingett,
- Emilia Dimitrova,
- Andrew Dimond,
- Lucas B. Edelman,
- Sarah Elderkin,
- Kristina Tabbada,
- Elodie Darbo,
- Simon Andrews,
- Bram Herman,
- Andy Higgs,
- Emily LeProust,
- Cameron S. Osborne,
- Jennifer A. Mitchell,
- Nicholas M. Luscombe,
- and Peter Fraser
Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
...1735.61 Mb 35.81 Mb CHi-C Hi-C CHi-C Hi-C CHi-C Hi-C -log10(q-value) Hist1h2ae st1 st1 i C0 . c lin fr . c lin fr Chr. 13 . c lin fr Wnt6 Wnt6 0 10 15 20 25 30 0 0.5 1.5 2.5 . c lin fr Alleles 100 200 300 400 77% 23% Hist1h4h to Hist1h2ai Hist1h4h to Vmn1r DNA FISH FLC Hist1h4h to Hist1h2ai Hist1h4h...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...implicated these factors in CM maturation (Zhang et al. 2023). Motifs for TCF/LEF-associated Wnt response factors were enriched in peaks increasing in accessibility (Fig. 1E). These factors are crucial for cardiac development and are expressed in immature CMs (Ye et al. 2019). CTCF binding motifs were...
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Research: Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer
- Yueqiang Song,
- Fuyuan Li,
- Shangzi Wang,
- Yuntong Wang,
- Cong Lai,
- Lian Chen,
- Ning Jiang,
- Jin Li,
- Xingdong Chen,
- Swneke D. Bailey,
- and Xiaoyang Zhang
Genome Res. October 2024 34: 1514-1527; Published in Advance October 18, 2024, doi:10.1101/gr.278418.123
...-gene-duplication hotspots are significantly enriched with ATAC sites distal to gene promoters (Fig. 2B). In contrast, promoter ATAC sites are only enriched in the gene-harboring hotspots (Supplemental Fig. S2A). We also examined the ENCODE SCREEN data set that has defined promoters, enhancers, and CTCF-only regions across...
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Method: Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility
- Qiao Rui Xing,
- Chadi A El Farran,
- Ying Ying Zeng,
- Yao Yi,
- Tushar Warrier,
- Pradeep Gautam,
- James J. Collins,
- Jian Xu,
- Peter Dröge,
- Cheng-Gee Koh,
- Hu Li,
- Li-Feng Zhang,
- and Yuin-Han Loh
Genome Res. July 2020 30: 1027-1039; Published in Advance July 22, 2020, doi:10.1101/gr.257840.119
...highly expressed in cluster 1 cells (Fig. 2I; Supplemental Table 2). An earlier study reported lower genomic looping frequencies in 2i cells compared with mESCs (Krijger et al. 2016), supporting the higher CTCF regulon activity detected in cluster 1. On the contrary, motifs of TFCP2L1, NFE2L2, KLF6, TCF7...
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Research: Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
- Angel Carlos Román,
- Francisco J. González-Rico,
- Eduardo Moltó,
- Henar Hernando,
- Ana Neto,
- Cristina Vicente-Garcia,
- Esteban Ballestar,
- José L. Gómez-Skarmeta,
- Jana Vavrova-Anderson,
- Robert J. White,
- Lluís Montoliu,
- and Pedro M. Fernández-Salguero
Genome Res. March 2011 21: 422-432; Published in Advance February 3, 2011, doi:10.1101/gr.111203.110
...flanking human Alu repeats are implicated in ependymomas (Xie et al. 2010). In addition, we have shown that the insulator activity of B1-X35S involves binding of parylated CTCF, an established insulator-binding protein involved in loop formation and the recruitment of repressive complexes to chromatin (Han...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
...a promoter independently of the position and orientation relative to that promoter. This suggests that chromatin looping of enhancers to their target promoters in Nematostella occurs through CTCF-independent cohesin binding, which plays a role in enhancer looping in bilaterians (Pauli et al. 2008; Schuldiner...
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Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
- Federico Comoglio,
- Hyun Jung Park,
- Stefan Schoenfelder,
- Iros Barozzi,
- Daniel Bode,
- Peter Fraser,
- and Anthony R. Green
Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
...associated with open and closed chromatin domains, respectively; (2) topologically associating domains (TADs) (Dixon et al. 2012; Nora et al. 2012; Sexton et al. 2012), also referred to as contact domains (Rao et al. 2017), chromosomal units that spatially constrain cis-regulatory interactions; and (3) CTCF...
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Research: SORBS2 transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy
- Jérôme D. Robin,
- Andrew T. Ludlow,
- Kimberly Batten,
- Marie-Cécile Gaillard,
- Guido Stadler,
- Frédérique Magdinier,
- Woodring E. Wright,
- and Jerry W. Shay
Genome Res. December 2015 25: 1781-1790; Published in Advance September 10, 2015, doi:10.1101/gr.190660.115
.... 2013. Wnt/β-catenin signaling suppresses DUX4 expression and prevents apoptosis of FSHD muscle cells. Hum Mol Genet 22: 4661–4672. Bodega B, Ramirez GD, Grasser F, Cheli S, Brunelli S, Mora M, Meneveri R, Marozzi A, Mueller S, Battaglioli E, et al. 2009. Remodeling of the chromatin structure...
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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
...by the Cohesin-CTCF interactions, as formulated in the loop extrusion model, and variable ones could be the product of a “roadblock” of the Cohesin translocating complex induced by the presence of tissue-specific transcription factors and associated protein complexes (Sanborn et al. 2015; Fudenberg et al. 2016...

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