Genomics and Chromatin Dynamics

Kinetic decoupling of early transcription reveals Mediator regulates paused RNA polymerase II stability

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.

Pan-cancer nucleosome landscapes reveal tumor heterogeneity and inform cell-free DNA-based detection

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.

Genome-wide chromatin reset at the onset of leg regeneration in pancrustaceans

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

Guanine content in the CTCF motif encodes a vulnerability to persistent, alcohol-induced redistribution

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

Sequence-dependent binding modes of INO80 control +1 nucleosome positioning

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: a simple method to quantitatively map in vitro protein-DNA interactions on a genome-wide scale at high spatial resolution

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

Dissection of Polycomb complexes reveals canonical PRC1-independent 3D chromatin interactions

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

Understanding the role of chromatin accessibility and compaction on loop extrusion dynamics

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.

Translational isoforms of mammalian heterochromatin protein 1 (HP1) tune its interactions with chromatin effectors

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

Decoding super-enhancer regulatory grammar and pathogenic gain-of-function variants directly from DNA sequence

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.

Ctcf deficiency in myofibers induces pathological genome reprogramming toward the spontaneous development of myopathy

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

Linking H3K36me3 to transcriptional dynamics

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.

Response representation shapes AlphaGenome enhancer-gene prediction in human astrocytes

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.

Distinct regulation across the transcription cycle drives mitotic transcriptional silencing

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

The Core Promoter has an active role in interpreting patterning information

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

Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors

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

Engineered regulatory states resolve context-dependent genetics in macular degeneration

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.

Structural variants from donor-specific assemblies affect recurrent chromatin contact divergence in humans

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.

Robust V(D)J Recombination in the Absence of SA1/2-mediated Chromatin Loops

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.

Capture-(Hi)C analysis with PostChicago: Integrative metaprofiling and quantitative comparison of chromatin interactions

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

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

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.

Transcription factor interactions promote binding to non-cognate DNA sites

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

KAS-CUT&Tag for direct mapping of transcription bubbles

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.

Multi-omic long-read sequencing reveals nucleosome control of transcriptional fidelity at the isoform level

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

Hyperosmotic stress induces rewiring of 3D chromatin interactions

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.

Enhancer binding kinetics explain transcription factor hub formation

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.

High-throughput identification of chromatin-opening transcription factors

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

Centromeric islands constrain CENP-A domain size and position

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

Active maintenance of accessible chromatin at poised meiotic promoters by the NFYA-NURF axis is required for meiotic entry in mice

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.

Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens

This paper introduces Swap-seq, a method to systematically delete and quantify the effects of enhancers, silencers, and topological elements on gene expression in human cells.