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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...The role of transposon activity in shaping cis-regulatory element evolution after whole- duplication Øystein Monsen1,6, Lars Grønvold1,6, Alex Datsomor1, Thomas Harvey1, James Kijas2, Alexander Suh3,4,7, Torgeir R. Hvidsten5 and Simen Rød Sandve1 1Department of Animal and Aquacultural Sciences...
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Method: Probabilistic association of differentially expressed genes with cis-regulatory elements
- Brian S. Roberts,
- Ashlyn G. Anderson,
- E. Christopher Partridge,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. April 2024 34: 620-632; Published in Advance April 17, 2024, doi:10.1101/gr.278598.123
...Corresponding authors: gcooper@hudsonalpha.org, rmyers@hudsonalpha.orgAbstractDifferential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements...
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Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...-rod homeobox (CRX) are linked with human blinding diseases that vary in their severity and age of onset. How different variants in this single TF alter its function in ways that lead to a range of phenotypes is unclear. We characterized the effects of human disease-causing variants on CRX cis-regulatory...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...AUG TIS recognition. ML can systematically identify RNA cis-regulatory codes of plant alternative TISs and provide more accurate TIS annotations. ML frameworks, which build mathematical models and identify patterns in large data sets, have successfully elucidated complex gene regulatory networks...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...of core-promoters of a KRAB family of zinc fingers. This similarity is captured as a distinct long motif, resulting in a module distinct from module 6. Modules depleted of promoters are characterized with motifs of H1 ESC-specific TFs (SOX2 and POU5F1::SOX2), along with motifs of other pioneer factors (AP...
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Research: Genomic environments scale the activities of diverse core promoters
- Clarice K.Y. Hong and
- Barak A. Cohen
Genome Res. January 2022 32: 85-96; Published in Advance December 27, 2021, doi:10.1101/gr.276025.121
....View larger version: In this window In a new window Figure 1. Measurements of a core promoter library at four genomic locations by patchMPRA. (A) Schematic of gene regulation by the core promoter, adjacent cis-regulatory sequences, and the genomic environment. (B) Schematic of patchMPRA method (see Methods...
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Research: Local sequence features that influence AP-1 cis-regulatory activity
- Hemangi G. Chaudhari and
- Barak A. Cohen
Genome Res. February 2018 28: 171-181; Published in Advance January 5, 2018, doi:10.1101/gr.226530.117
...the sequence determinants of local cis-regulatory activity. The AP-1 binding site is the most predictive sequence feature of cis-regulatory activity in K562 cells (Kwasnieski et al. 2014). Although the “core” AP-1 motif consists of seven high information nucleotides (5′-TGAG/CTCA-3′), the Position Weight...
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Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...determinants of core promoters and proximal promoter regions, from broad aspects of mapping their location and orientation in the to in-depth characterization of the cis-regulatory elements driving their expression, including core promoter elements and TF binding sites.ResultsAccurate measurements of about 15...
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Method: Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants
- Dongwon Lee,
- Ashish Kapoor,
- Alexias Safi,
- Lingyun Song,
- Marc K. Halushka,
- Gregory E. Crawford,
- and Aravinda Chakravarti
Genome Res. October 2018 28: 1577-1588; Published in Advance August 23, 2018, doi:10.1101/gr.234633.118
..., New York, NY 10016, USA; 5University of Texas Health Science Center at Houston, Houston, TX 77030, USA Corresponding authors: aravinda.chakravarti@nyumc.org, dongwon.lee@nyumc.orgAbstractCis-regulatory elements (CRE), short DNA sequences through which transcription factors (TFs) exert regulatory...
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Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
- Julie Dubois-Chevalier,
- Vanessa Dubois,
- Hélène Dehondt,
- Parisa Mazrooei,
- Claire Mazuy,
- Aurélien A. Sérandour,
- Céline Gheeraert,
- Penderia Guillaume,
- Eric Baugé,
- Bruno Derudas,
- Nathalie Hennuyer,
- Réjane Paumelle,
- Guillemette Marot,
- Jason S. Carroll,
- Mathieu Lupien,
- Bart Staels,
- Philippe Lefebvre,
- and Jérôme Eeckhoute
Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
...-box motifs (BMAL1_MOUSE.H10MO.C; Bonferroni-corrected P-value = 3.36 × 10−72), which mediate core circadian transcription factor (ARNTL, CLOCK, and NPAS2) recruitment (Supplemental Fig. S20). Promoters and enhancers were separately considered in these analyses since module combinations differ at these CRMs...

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