Ma F, Ollikainen N, Du H, Braikia F, Cui N, Bianchi A
Nat Commun. 2025; 16(1):2148.
PMID: 40032827
PMC: 11876664.
DOI: 10.1038/s41467-025-57373-w.
Fu Y, Yang X, Li S, Ma C, An Y, Cheng T
Nat Commun. 2025; 16(1):1640.
PMID: 39952932
PMC: 11828908.
DOI: 10.1038/s41467-025-56735-8.
Yang L, Qi C, Lu S, Ye X, Merikhian P, Zhang D
Nat Commun. 2025; 16(1):524.
PMID: 39789010
PMC: 11718104.
DOI: 10.1038/s41467-024-55738-1.
Lee H, Friedman M, Kim S, Oh S
BMB Rep. 2024; 57(12):509-520.
PMID: 39523506
PMC: 11693600.
Anfossi S, Darbaniyan F, Quinlan J, Calin S, Shimizu M, Chen M
Mol Cancer. 2024; 23(1):235.
PMID: 39434078
PMC: 11492698.
DOI: 10.1186/s12943-024-02094-9.
Drought-responsive dynamics of H3K9ac-marked 3D chromatin interactions are integrated by OsbZIP23-associated super-enhancer-like promoter regions in rice.
Chang Y, Liu J, Guo M, Ouyang W, Yan J, Xiong L
Genome Biol. 2024; 25(1):262.
PMID: 39390531
PMC: 11465533.
DOI: 10.1186/s13059-024-03408-2.
Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma.
Xiong S, Zhou J, Tan T, Chung T, Tan T, Toh S
Nat Commun. 2024; 15(1):6810.
PMID: 39122682
PMC: 11316114.
DOI: 10.1038/s41467-024-50910-z.
Statistical modeling and significance estimation of multi-way chromatin contacts with HyperloopFinder.
Wang W, Ye Y, Gao L
Brief Bioinform. 2024; 25(4).
PMID: 39003726
PMC: 11246602.
DOI: 10.1093/bib/bbae341.
cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.
Nocente M, Mesihovic Karamitsos A, Drouineau E, Soleil M, Albawardi W, Dulary C
Nat Struct Mol Biol. 2024; 31(11):1756-1768.
PMID: 38956169
DOI: 10.1038/s41594-024-01344-0.
Benchmarking tools for transcription factor prioritization.
Schubert Santana L, Reyes A, Hoersch S, Ferrero E, Kolter C, Gaulis S
Comput Struct Biotechnol J. 2024; 23():2190-2199.
PMID: 38817966
PMC: 11137382.
DOI: 10.1016/j.csbj.2024.05.016.
Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.
Mowery C, Freimer J, Chen Z, Casani-Galdon S, Umhoefer J, Arce M
Nat Genet. 2024; 56(6):1156-1167.
PMID: 38811842
PMC: 11176074.
DOI: 10.1038/s41588-024-01743-5.
Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs.
Li Y, Tan M, Akkari-Henic A, Zhang L, Kip M, Sun S
Nat Biomed Eng. 2024; 8(7):890-908.
PMID: 38778183
PMC: 11310080.
DOI: 10.1038/s41551-024-01204-8.
Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations.
Hsiung C, Wilson C, Sambold N, Dai R, Chen Q, Teyssier N
Nat Biotechnol. 2024; .
PMID: 38760567
DOI: 10.1038/s41587-024-02224-0.
Genomic context sensitizes regulatory elements to genetic disruption.
Ordonez R, Zhang W, Ellis G, Zhu Y, Ashe H, Ribeiro-Dos-Santos A
Mol Cell. 2024; 84(10):1842-1854.e7.
PMID: 38759624
PMC: 11104518.
DOI: 10.1016/j.molcel.2024.04.013.
Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns.
Wu C, Huang J
BMC Genomics. 2024; 25(1):483.
PMID: 38750461
PMC: 11097474.
DOI: 10.1186/s12864-024-10408-w.
Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells.
Li J, Zhu J, Gray O, Sobreira D, Wu D, Huang R
J Cell Biol. 2024; 223(3).
PMID: 38231044
PMC: 10794123.
DOI: 10.1083/jcb.202211125.
A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development.
Wilderman A, Dhaene E, Baetens M, Yankee T, Winchester E, Glidden N
Nat Commun. 2024; 15(1):136.
PMID: 38167838
PMC: 10762089.
DOI: 10.1038/s41467-023-44506-2.
Super-enhancers include classical enhancers and facilitators to fully activate gene expression.
Blayney J, Francis H, Rampasekova A, Camellato B, Mitchell L, Stolper R
Cell. 2023; 186(26):5826-5839.e18.
PMID: 38101409
PMC: 10858684.
DOI: 10.1016/j.cell.2023.11.030.
Genomic context sensitizes regulatory elements to genetic disruption.
Ordonez R, Zhang W, Ellis G, Zhu Y, Ashe H, Ribeiro-Dos-Santos A
bioRxiv. 2023; .
PMID: 37781588
PMC: 10541140.
DOI: 10.1101/2023.07.02.547201.
Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation.
Herbert A
J Biol Chem. 2023; 299(9):105140.
PMID: 37544644
PMC: 10474125.
DOI: 10.1016/j.jbc.2023.105140.
