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Research: Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
- PingHsun Hsieh,
- Krishna R. Veeramah,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Jeffrey D. Wall,
- Michael F. Hammer,
- and Ryan N. Gutenkunst
Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115
...Corresponding authors: mfh@email.arizona.edu , rgutenk@email.arizona.edu Abstract African Pygmies practicing a mobile hunter-gatherer lifestyle are phenotypically and genetically diverged from other anatomically modern humans, and they likely experienced strong selective pressures due...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
..., Toronto, Ontario, Canada M5S 3E1. ↵ 8 These authors contributed equally to this work. Abstract Developmental genes are regulated by complex, distantly located cis -regulatory modules (CRMs), often forming genomic regulatory blocks (GRBs) that are conserved among vertebrates...
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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
...transcriptional activity. The most well-described types of cis-regulatory regions include proximal cis-acting promoters, as well as distal enhancers, silencers, and insulators.This review focuses on a small family of cis-regulatory regions comprising just more than 20 members: the imprinting control regions (ICRs...
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Research: CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning
- Marlies E. Oomen,
- Anders S. Hansen,
- Yu Liu,
- Xavier Darzacq,
- and Job Dekker
Genome Res. February 2019 29: 236-249; Published in Advance January 17, 2019, doi:10.1101/gr.241547.118
...the two 2-Mb regions (Supplemental Fig. S2). In interphase cells, TADs are readily detected as domains of increased interaction frequencies between loci flanked by CTCF-bound sites (Fig. 1A, representative TAD marked with dashed line). By evaluating the insulation profile along the locus, we can identify...
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Research: Genome accessibility is widely preserved and locally modulated during mitosis
- Chris C.-S. Hsiung,
- Christapher S. Morrissey,
- Maheshi Udugama,
- Christopher L. Frank,
- Cheryl A. Keller,
- Songjoon Baek,
- Belinda Giardine,
- Gregory E. Crawford,
- Myong-Hee Sung,
- Ross C. Hardison,
- and Gerd A. Blobel
Genome Res. February 2015 25: 213-225; Published in Advance November 4, 2014, doi:10.1101/gr.180646.114
.... At the levelmost directly relevant for gene regulation—individual genes and cis-regulatory modules (CRMs)—the structural configuration of the mitotic is of tremendous interest to the study of epigenetics. Mitosis, concomitant with altering chromosome structure, disassembles the metazoan nucleus (G€uttinger et al...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
...be extended to dissect cis regulatory modules in which several transcription factor binding sites are putatively involved in regulatory specificity (Hardison and Taylor 2012; Hnisz et al. 2015). Dynamic regulation of genomic activity and conformation In addition to nuclease-mediated disruption or deletion...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...regulation ( Levine and Tjian 2003 ). However, the evolution of cis -regulatory mechanisms remains poorly understood. This is largely due to the fact that, compared with coding sequences, very little is known about the way in which regulatory information is encoded in the . Developmental programs are thought...
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