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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...RNA production from distal promoters. The discovery of the SV40 viral enhancer was a landmark event more than 40 years ago. The 72 bp DNA sequence encoding the SV40 enhancer increased the expression of a reporter gene by more than two orders of magnitude in a manner that was largely independent of its position...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...elements that underlie genetic effects on gene expression and metabolic traits. However, caQTL discovery has been limited by small sample sizes. Here, we map caQTLs in liver tissue from 138 human donors and identify caQTLs for 35,361 regulatory elements, including population-specific caQTLs driven...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...regeneration and development, including PRRX1, MSX, LIM, MEF2C, ZIC, and HOX family TFs (Fig. 5A,B; Akimenko et al. 1995; Carlson et al. 2001; Karlstrom et al. 2003; Poss et al. 2003; Arnold et al. 2007; Tzchori et al. 2009; Sedykh et al. 2017; Hamada et al. 2019; Lin et al. 2021; Yoshioka et al. 2021; Qin et...
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Research: The spring-loaded genome: Nucleosome redistributions are widespread, transient, and DNA-directed
- Brittany S. Sexton,
- Denis Avey,
- Brooke R. Druliner,
- Justin A. Fincher,
- Daniel L. Vera,
- Daniel J. Grau,
- Mark L. Borowsky,
- Shobhit Gupta,
- Senthil B. Girimurugan,
- Eric Chicken,
- Jinfeng Zhang,
- William S. Noble,
- Fanxiu Zhu,
- Robert E. Kingston,
- and Jonathan H. Dennis
Genome Res. February 2014 24: 251-259; Published in Advance December 5, 2013, doi:10.1101/gr.160150.113
..., and HOX (Richard-Foy and Hager 1987; Agalioti et al. 2000; Boeger et al. 2003; Reinke and Horz 2003; Woo et al. 2010). This expectation has been unfulfilled as whole- studies reveal that nucleosome distributions are remarkably similar between different cell types (Supplemental Fig. 18; Gaffney et al. 2012...
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Research: Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation
- Michael S. Werner,
- Bogdan Sieriebriennikov,
- Neel Prabh,
- Tobias Loschko,
- Christa Lanz,
- and Ralf J. Sommer
Genome Res. November 2018 28: 1675-1687; Published in Advance September 19, 2018, doi:10.1101/gr.234872.118
...of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 1213–1218. ↵Burki F, Kaessmann H. 2004. Birth and adaptive evolution of a hominoid gene that supports high neurotransmitter flux. Nat Genet 36: 1061–1063. ↵The C...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
...below. See Figure 1A for additional annotation. A. thal iana chromatin loops Genome Research 1059 www..org space to form a “repressive chromatin hub,” similar to Polycombtargeted HOX clusters in animals (Fig. 3A; Bantignies and Cavalli 2011; Schoenfelder et al. 2015). From our ChIP-seq data, we...
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Research: Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells
- Daniel W. Hagey,
- Cécile Zaouter,
- Gaëlle Combeau,
- Monika Andersson Lendahl,
- Olov Andersson,
- Mikael Huss,
- and Jonas Muhr
Genome Res. July 2016 26: 908-917; Published in Advance May 2, 2016, doi:10.1101/gr.203513.115
...injection, and the number of live and GFP positive embryos were recorded. Motif mutations were achieved through 2-nt exchange of SOX, HOX, LHX, PBX, or MEIS core motifs. Enhancer DNA was randomized using this website: http://www.faculty.ucr.edu/~mmaduro/random.htm. Morpholinos were obtained from Gene Tools...
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Letter: Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
- Michael Y. Tolstorukov,
- Peter V. Kharchenko,
- Joseph A. Goldman,
- Robert E. Kingston,
- and Peter J. Park
Genome Res. June 2009 19: 967-977; Published in Advance February 26, 2009, doi:10.1101/gr.084830.108
...in yeast is not a general characteristic for the human chromatin. The above assertion is further supported by the absence of 10-bp signal in the nucleosomal sequences detected in a microarray study of human HOX clusters ( Kharchenko et al. 2008 ). Although we cannot exclude that the strong 10-bp...
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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
...and enhancer architectures. Genome Res 23: 1339–1347. Chourrout D, Delsuc F, Chourrout P, Edvardsen RB, Rentzsch F, Renfer E, Jensen MF, Zhu B, de Jong P, Steele RE, et al. 2006. Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements. Nature 442: 684–687. Creyghton MP, Cheng AW...
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Perspective: Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- Lesley T. MacNeil and
- Albertha J.M. Walhout
Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109
...and to only occur in certain cells irrespective of changes in environmental conditions. For instance, Hox genes are expressed in precise patterns that provide anterio– posterior positional information and segment identity to the developing Drosophila embryo (Lewis 1978; Harding et al. 1985). The specific...

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