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Research: 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
- Alice Cortesi,
- Matthieu Pesant,
- Shruti Sinha,
- Federica Marasca,
- Eleonora Sala,
- Francesco Gregoretti,
- Laura Antonelli,
- Gennaro Oliva,
- Chiara Chiereghin,
- Giulia Soldà,
- and Beatrice Bodega
Genome Res. June 2019 29: 883-895; Published in Advance May 16, 2019, doi:10.1101/gr.233288.117
...and hypomethylated 4q-D4Z4 array causes an impairment of D4Z4 interactome, leading to a chromatin switch toward an active state (mainly enhancer and promoter regions), which in turn results in the transcriptional up-regulation of the atrophic genes.We propose that the genetic deletion of 4q-D4Z4 array in FSHD1...
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Research: Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
- Sergey V. Ulianov,
- Ekaterina E. Khrameeva,
- Alexey A. Gavrilov,
- Ilya M. Flyamer,
- Pavel Kos,
- Elena A. Mikhaleva,
- Aleksey A. Penin,
- Maria D. Logacheva,
- Maxim V. Imakaev,
- Alexander Chertovich,
- Mikhail S. Gelfand,
- Yuri Y. Shevelyov,
- and Sergey V. Razin
Genome Res. January 2016 26: 70-84; Published in Advance October 30, 2015, doi:10.1101/gr.196006.115
...reported that 42% of TADs are shared between Kc167 cells and 16-h embryos. Active chromatin and transcription but not architectural proteins dCTCF and Su(Hw) are typical for TAD boundaries and inter-TAD regions Previous studies revealed that TAD boundaries in 16-h Drosophila embryos (Sexton et al. 2012...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...regulatory regions. Other studies have shown that demethylation at enhancers is associated with gene reactivation during differentiation (Mahé et al. 2017). However we do not know whether DNA methylation changes at enhacers is simply the readout of transcription factor availability or the mechanisms...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...tissues, for collared flycatcher, pied flycatcher, and their F1 hybrids.A characteristic signature of spermatogenesis is spurious transcription as a result of a permissive chromatin environment during this process (Soumillon et al. 2013). Thus, if spermatogenesis is interrupted at an early stage in the F1...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...Corresponding authors: saurabhagarwal23@gmail.com, biren@ucsd.edu, siwase@umich.eduAbstractTranscriptional enhancers enable exquisite spatiotemporal control of gene expression in metazoans. Enrichment of monomethylation of histone H3 lysine 4 (H3K4me1) is a major chromatin signature of transcriptional enhancers...
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Research: A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA
- Shiyan Wang,
- Jiahuan Chen,
- Sara P. Garcia,
- Xiaodong Liang,
- Fang Zhang,
- Pengyi Yan,
- Huijing Yu,
- Weiting Wei,
- Zixuan Li,
- Jingfang Wang,
- Huangying Le,
- Zeguang Han,
- Xusheng Luo,
- Daniel S. Day,
- Sean M. Stevens,
- Yan Zhang,
- Peter J. Park,
- Zhi-jie Liu,
- Kun Sun,
- Guo-cheng Yuan,
- William T. Pu,
- and Bing Zhang
Genome Res. February 2019 29: 193-207; Published in Advance January 22, 2019, doi:10.1101/gr.239053.118
...of the VEGFA transcriptional program and angiogenesis. Collectively these results revealed that extracellular stimuli rapidly reconfigure the chromatin landscape to coordinately regulate biological responses.Divergent gene programs control distinct cell identities and biological functions. Environmental...
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Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
- Ian C. McDowell,
- Alejandro Barrera,
- Anthony M. D'Ippolito,
- Christopher M. Vockley,
- Linda K. Hong,
- Sarah M. Leichter,
- Luke C. Bartelt,
- William H. Majoros,
- Lingyun Song,
- Alexias Safi,
- D. Dewran Koçak,
- Charles A. Gersbach,
- Alexander J. Hartemink,
- Gregory E. Crawford,
- Barbara E. Engelhardt,
- and Timothy E. Reddy
Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
...). The model that has emerged from these findings posits that cell-specific pioneer factor binding creates a chromatin landscape that predetermines GR binding (John et al. 2011; Biddie and John 2014). It has also been reported that GR can act as a pioneer factor at a minority of binding sites, which have...
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Research: Binding of nuclear factor κB to noncanonical consensus sites reveals its multimodal role during the early inflammatory response
- Petros Kolovos,
- Theodore Georgomanolis,
- Anna Koeferle,
- Joshua D. Larkin,
- Lilija Brant,
- Miloš Nikolicć,
- Eduardo G. Gusmao,
- Anne Zirkel,
- Tobias A. Knoch,
- Wilfred F. van Ijcken,
- Peter R. Cook,
- Ivan G. Costa,
- Frank G. Grosveld,
- and Argyris Papantonis
Genome Res. November 2016 26: 1478-1489; Published in Advance September 15, 2016, doi:10.1101/gr.210005.116
...endothelial cells. NF-κB, the transcription factor complex driving the response, interferes with the regulatory machinery by binding active enhancers already in interaction with gene promoters. Notably, &gt;50% of these enhancers do not encode canonical NF-κB binding motifs. Using a combination of genomics...
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Perspective: Insights into neural crest development and evolution from genomic analysis
- Marcos Simões-Costa and
- Marianne E. Bronner
Genome Res. July 2013 23: 1069-1080; doi:10.1101/gr.157586.113
...and signaling molecules that act in concert to provide this cell population with its defining features (Sauka-Spengler and Bronner-Fraser 2008b). In order to interrogate such a complex regulatory program, we and others have assembled a multistep neural crest GRN that integrates transcriptional inputs...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...where the same local region also harbored enhancer chromatin signatures. These enhancer-marked DMRs comprised 30% of the tissue-specific DMRs, >70% of the cell type-specific DMRs, and >40% of the individual-specific DMR landscape. Results Summary of the M&M algorithm Differentially methylated regions...
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