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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...type–dependent differences in CTCF retention and that mitotic chromosome conformation is adaptable through modulation of loop sizes to generate chromosomes of appropriate dimensions.ResultsA subset of CTCF sites remains bound in mitotic mESCsIn recent years, several genomics studies have reported...
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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
...al. Genome-wide capture of promoter interactions The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements Stefan Schoenfelder,1,9 Mayra Furlan-Magaril,1,9 Borbala Mifsud,2,3,9 Filipe Tavares-Cadete,2,3,9 Robert Sugar,3,4 Biola-Maria Javierre,1 Takashi Nagano...
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Method: Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
- Nicola H. Dryden,
- Laura R. Broome,
- Frank Dudbridge,
- Nichola Johnson,
- Nick Orr,
- Stefan Schoenfelder,
- Takashi Nagano,
- Simon Andrews,
- Steven Wingett,
- Iwanka Kozarewa,
- Ioannis Assiotis,
- Kerry Fenwick,
- Sarah L. Maguire,
- James Campbell,
- Rachael Natrajan,
- Maryou Lambros,
- Eleni Perrakis,
- Alan Ashworth,
- Peter Fraser,
- and Olivia Fletcher
Genome Res. November 2014 24: 1854-1868; Published in Advance August 13, 2014, doi:10.1101/gr.175034.114
...genotypes in relation to expression of nearby genes (eQTL), and the use of chromatin association methods (chromosome conformation capture [3C] and chromatin interaction analysis by paired-end tag sequencing [ChIA-PET]) of regulatory regions to determine the identity of target genes.While 3C...
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Research: Genome-wide map of regulatory interactions in the human genome
- Nastaran Heidari,
- Douglas H. Phanstiel,
- Chao He,
- Fabian Grubert,
- Fereshteh Jahanbani,
- Maya Kasowski,
- Michael Q. Zhang,
- and Michael P. Snyder
Genome Res. December 2014 24: 1905-1917; Published in Advance September 16, 2014, doi:10.1101/gr.176586.114
..., Richardson, Texas 75080-3021, USA Corresponding author: mpsnyder@stanford.edu ↵ 5 These authors contributed equally to this work. Abstract Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene...
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Methods: Ab initio identification of functionally interacting pairs of cis-regulatory elements
- Brad A. Friedman,
- Michael B. Stadler,
- Noam Shomron,
- Ye Ding,
- and Christopher B. Burge
Genome Res. October 2008 18: 1643-1651; Published in Advance September 17, 2008, doi:10.1101/gr.080085.108
....1101/gr.080085.108 1088-9051 genome;gr.080085.108 Ab initio identification of functionally interacting pairs of cis-regulatory elements Ab initio identification of functionally interacting pairs of cis -regulatory elements Brad A. Friedman 1 , 2 , 4 , 6 , Michael B. Stadler 1 , 5 , Noam Shomron 1 , Ye...
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LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- David C. King,
- James Taylor,
- Ying Zhang,
- Yong Cheng,
- Heather A. Lawson,
- Joel Martin,
- ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
...this promoter is distal to the HBB complex along the linear chromosome, it is close to the locus control region of the HBB complex in the nucleus of K562 cells, as revealed by chromosome conformation capture (3C; Dekker et al. 2002 ). The interaction frequency measured by 3C ( Fig. 6 ) is determined by cross...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...characterize the genomic functional elements in the interaction regions, the genomic features were assessed. As a result, >30% of the interaction regions were predominantly overlapped with promoter elements, which only accounted for 2.75% of the whole (Fig. 1E), indicating that DNA interaction was nonrandom...
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Method: Long-read single-molecule maps of the functional methylome
- Hila Sharim,
- Assaf Grunwald,
- Tslil Gabrieli,
- Yael Michaeli,
- Sapir Margalit,
- Dmitry Torchinsky,
- Rani Arielly,
- Gil Nifker,
- Matyas Juhasz,
- Felix Gularek,
- Miguel Almalvez,
- Brandon Dufault,
- Sreetama Sen Chandra,
- Alexander Liu,
- Surajit Bhattacharya,
- Yi-Wen Chen,
- Eric Vilain,
- Kathryn R. Wagner,
- Jonathan Pevsner,
- Jeff Reifenberger,
- Ernest T. Lam,
- Alex R. Hastie,
- Han Cao,
- Hayk Barseghyan,
- Elmar Weinhold,
- and Yuval Ebenstein
Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
...on Chromosome 4q.DNA methylation of the five-carbon of cytosine is the most studied and among the most significant epigenetic modifications (Bird 2002). In mammalian DNA, methylation mostly occurs on cytosine residues within CpG dinucleotides (DNA motifs in which the cytosine is followed by a guanine residue...
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Research: A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
- Lei Zhang,
- Anshun He,
- Bohan Chen,
- Jinfang Bi,
- Jun Chen,
- Dianhao Guo,
- Yuyang Qian,
- Wenbin Wang,
- Tengfei Shi,
- Zhongfang Zhao,
- Jiandang Shi,
- Woojin An,
- Frank Attenello,
- and Wange Lu
Genome Res. February 2020 30: 155-163; Published in Advance January 17, 2020, doi:10.1101/gr.251058.119
..., Nusbaum C, et al. 2006. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16: 1299–1309. doi:10.1101/gr.5571506 ↵Guardiola-Serrano F, Haendeler J, Lukosz M, Sturm K, Melchner H, Altschmied J. 2008. Gene trapping...
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Research: Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
- Nathan H. Lazar,
- Kimberly A. Nevonen,
- Brendan O'Connell,
- Christine McCann,
- Rachel J. O'Neill,
- Richard E. Green,
- Thomas J. Meyer,
- Mariam Okhovat,
- and Lucia Carbone
Genome Res. July 2018 28: 983-997; Published in Advance June 18, 2018, doi:10.1101/gr.233874.117
...performed -wide chromatin conformation capture sequencing (Hi-C) using a lymphoblastoid cell line (LCL) that we established from a male northern white-cheeked gibbon (Nomascus leucogenys, Vok, #NLL600) belonging to the same species used to generate the gibbon reference (Supplemental Table S1; Carbone et al...

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