Genomics and Chromatin Dynamics

U-Chrom provides a unified framework for analyzing single-cell and spatial 3D genome data, showing consistent cell-type differences across assays.

This study uncouples Mediator's role in RNAPII transcription initiation from its effects on promoter-proximal pausing, showing Mediator regulates paused RNAPII stability rather than P-TEFb recruitment.

The paper characterizes nucleosome organization across 23 cancer types using ATAC-seq and shows its utility for cancer classification and detection using cell-free DNA.

The paper investigates chromatin state reorganization during leg regeneration in pancrustaceans, finding a conserved sequence of chromatin resetting and pioneer factor activation across species.

The paper shows alcohol exposure disrupts chromatin by altering CTCF and cohesin occupancy at guanine-rich sites, leading to lasting gene expression changes.

This study shows how INO80 distinguishes DNA sequence asymmetry in the +1 nucleosome of the SWH1 gene through inhibited and active binding modes, influencing nucleosome positioning.

Footprint-seq quantitatively maps protein-DNA interactions in vitro with high resolution and sensitivity, demonstrating its effectiveness for bacterial systems.

The paper investigates Polycomb-mediated 3D chromatin interactions and finds that cPRC1 is not essential for their formation.

This paper develops a biophysical model of loop extrusion that links motor dynamics to chromatin accessibility and compaction, revealing how nucleosome spacing affects extrusion speed.

The paper shows that mammalian cells produce extended HP1β isoforms that alter effector binding preferences, affecting heterochromatin organization.

This paper introduces Borzoi-SE, a deep learning framework that identifies super-enhancers and detects pathogenic variants directly from DNA sequence across multiple human cell lineages.

This study shows that Ctcf deficiency in myofibers leads to genome reprogramming and myopathy by disrupting 3D genome structure and gene regulation.

This study investigates the role of SETD2 and H3K36me3 in transcriptional dynamics by analyzing gene expression and splicing in murine C2C12 myoblast cells following their depletion.

The paper evaluates how response representation affects enhancer-gene prediction in human astrocytes using CRISPR-interference data and finds that whole-enhancer deletion responses improve prediction performance.

The paper quantifies how transcription is silenced during mitosis in Drosophila embryos by analyzing initiation, elongation, and termination kinetics.

The paper investigates the role of core promoters in gene expression specificity by testing their interaction with enhancers in Drosophila.

The paper identifies extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors using ChIP-seq, interactome data, and chromatin interaction maps.

The paper uses CRISPR activation to engineer regulatory states in RPE-1 cells, revealing hidden genetic effects in AMD by analyzing chromatin accessibility and transcriptional interactions.

The paper shows that structural variants from donor-specific assemblies influence chromatin contact divergence in humans, with many SVs linked to regulatory contexts and expression variation.

This study shows that SA1/2 are not essential for V(D)J recombination in G0/G1-arrested cells, but their absence disrupts chromatin loops and long-range Igh recombination, while Ig{kappa} recombination remains functional.

PostChicago provides a workflow for analyzing and comparing chromatin interactions from Capture-(Hi)C data, including quality control and visualization of metaprofiles.

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

This study shows how transcription factor interactions enable binding to non-cognate DNA sites by bridging across nucleosomal DNA gyres.

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.

The paper uses long-read sequencing to study how nucleosome positioning affects isoform expression by analyzing chromatin and RNA in yeast.

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.

The paper uses live-imaging and computational modeling to show that Dorsal hub formation in Drosophila embryos depends on TF-DNA binding kinetics, not enhancer sequence or higher-order regulatory structures.

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

The paper shows that centromeric islands like Giglio constrain CENP-A domain size and position but are not required for centromere identity.

The paper identifies the NFYA-NURF axis as essential for maintaining accessible chromatin at poised meiotic promoters, which is required for meiotic entry in mice.