7 papers
Weifang Wu, Jacob E. Greene, Kami Ahmad, Steven Henikoff
N3-kethoxal labeling of single-stranded DNA within CUT&Tag maps Pol II transcription bubbles; bubble density tracks nascent transcription, shifts with transcription inhibitors and TFIIS loss, and peaks at histone genes.
bioRxiv · Oct 9, 2026 · PreprintGenomics✦ In-depth digest
John Patrick Flores, Andrea A. Perreault, Zachary Drum, Chenxi Xu, Doris Cruz Alonso, Tooba Rashid, Jeremy D. Burgess, Geoffrey Fox, Gelila Petros, Yijia Wu, Ivana Yoseli Quiroga, HyunAh Kim, Isha R Sahasrabudhe, Ye Jin Lee, Ethan Black, , Douglas H. Phanstiel
One hour of 200 mM sorbitol collapses most chromatin loops in human cells while several hundred transient, cohesin-dependent, CTCF-independent loops form at active promoters, preceding anchor-gene activation.
bioRxiv · Oct 9, 2026 · PreprintGenomics✦ In-depth digest
Yaqiang Cao, Guangzhe Ge, Keji Zhao
Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.
bioRxiv · Sep 15, 2026 · PreprintBioinformatics✦ In-depth digest
Zhu Meng, Shiwen Zhang, Ziyang Zhuang, Jiayi He, Fei Liu, Lingyun Wu, Xiangrong Sun, Jingsheng Lu, Xinyi Li, Hao Yang, Mian Gong, Xiaolong Du, Qiao Mei, Hao Li, Guoqing Zhang, , Zhangyuan Pan
SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.
bioRxiv · Aug 26, 2026 · PreprintGenetics✦ In-depth digest
Dean Y Zhang, Hufeng Zhou, Maya U. Sheth, Andreas R. Gschwind, J Engreitz, Xihong Lin, Hongbo Liu
A web atlas counts evidence from 24 types for 188,634,118 variant-gene pairs across 50 human tissues; 1,530,420 pairs pass a high-confidence cutoff, 87% of them tissue-specific.
bioRxiv · Aug 20, 2026 · PreprintGenomics✦ In-depth digest
Fanny Boulet, Manthan Patel, Zeinab Shadman Zanjani, Nuria Andrés-Sánchez, Anam Ijaz, Debosree Pal, Pankaj Dubey, Aoife Murray, Dean Nižetić, Michael D. LeClaire, Karina L. Bursch, Brian C. Smith, Pradeepa M. Madapura
Acute BRD4 degradation and BD2 mutations de-repress bivalent developmental and neuronal genes in human stem cells and organoids, consistent with BRD4 recruitment by H3K14ac/H3K23ac and interaction with PRC1.6.
bioRxiv · Aug 5, 2026 · PreprintMolecular Biology✦ In-depth digest
Yanqing Sun, Shijie Wan, Lei Nie, Dan Yu, Feifei Zhou, Yi Yang, Xiangyu Yang, An Liu, Quanyu Chen, Kezhi Fu, Qingyang Ni, Yaoxi He, Bing Su, Yafei Mao, Kai Ye, , Wu Dongya
Over 8,000 gapless human centromeres reveal population-stratified satellite-array, inversion and haplotype variation, multiple candidate kinetochore sites in 16.8% of centromeres, and single-base substitution rates comparable to flanking pericentromeres.
bioRxiv · Jul 24, 2026 · PreprintGenomics✦ In-depth digest