Genomics and Chromatin Dynamics

Chromatin accessibility classification of TAD boundaries discloses new architectural proteins

The paper classifies TAD boundaries by chromatin accessibility in K562 cells and identifies ZNF316 as a novel architectural protein that contributes to boundary strength.

Developmental expression of the skeletal muscle determination gene, MyoD, is regulated by novel enhancer elements that interact with the core enhancer and distal regulatory region

The paper identifies novel enhancer elements that regulate MyoD expression during skeletal muscle development and show they are part of a cis-regulatory network.

map3C: a computational tool for processing multiomic single-cell Hi-C data

map3C improves the quality of multiomic single-cell Hi-C data and aids in identifying structural variant locations.

The linker histone H1.4 condenses chromatin in maturing postmitotic neurons

Epitope-tagged knockin mice show histone H1.4 protein accumulates in postmitotic neurons, shifts toward B-compartment heterochromatin with maturation, and H1f2/H1f4 loss impairs cerebellar granule neuron chromatin compaction.

Histone methyltransferase MET-2 differentially regulates autosome and X-chromosome structure and transcription during meiosis in C. elegans

This study shows MET-2 differentially regulates autosome and X-chromosome structure and transcription in C. elegans meiosis, with noncatalytic roles in chromosome compaction and gene expression.

Physiological re-replication during human stem cell differentiation

The paper shows re-replication is a physiological mechanism in human stem cell differentiation, increasing gene copy numbers to meet protein demands during differentiation.

Drosophila co-insulator proteins Pzg and Chro but not CP190 interact with promoter-proximal insulator-binding protein BEAF from a distance

The paper investigates interactions between BEAF and co-insulator proteins in Drosophila, finding that Pzg and Chro, but not CP190, can interact with BEAF from a distance to activate reporter genes.

Locus-Scale Massively Parallel Reporter Assays

The paper introduces LAMPRAs to measure how cis-regulatory element composition affects gene expression using synthetic loci.

Functional interplay between H2B ubiquitylation and H2A.Z deposition

This study shows that H2B ubiquitylation inhibits H2A.Z deposition by SWR1C and is required for H2A.Z re-localization during replication stress.

Rotational settings quantize nucleosome movement by chromatin regulators

The paper shows DNA sequence guides nucleosome rotation and positioning across species, with chromatin regulators navigating rather than overriding these settings.

TRIM28 preserves ovarian identity by stabilising lineage-specific transcription factor hubs

This study identifies TRIM28's role in preserving ovarian identity by stabilizing lineage-specific transcription factor hubs rather than through H3K9me3-dependent heterochromatin.

Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

The paper develops a pipeline to analyze chromatin structure in Plasmodium falciparum and shows that its chromatin has a regular structure with stage-specific changes.

Mu-seq reveals previously undetected long-range contact patterns in the Escherichia coli nucleoid

Mu-seq maps long-range DNA-DNA contacts in E. coli without crosslinking, revealing new interaction patterns not detectable by Hi-C.

Effect of nuclear electrostatic potential on the nucleoplasmic distribution of histones and nucleosome stability

This study shows that differences in electrostatic potential between heterochromatin and euchromatin affect nucleosome stability and transcription factor access, explaining transcriptional differences.

Gene clustering coordinates transcriptional output of disparate biological processes in eukaryotes

The paper identifies conserved and species-specific gene clusters coordinating disparate biological processes across eukaryotes, revealing regulatory proximity as a mechanism for transcriptional coherence.

A sequence-encoded promoter proximal super pause stabilizes an offline RNA polymerase II state

A reconstituted, direct-RNA-sequencing transcription assay on 1,000 human promoter-proximal sequences identified a TFIIS-insensitive consensus super pause, whose cryo-EM structure shows a one-nucleotide sidetracked polymerase state.

Lineage-specific regulation and RNA-associated functions of SATB1 in mature B-cells

The paper investigates SATB1 regulation and RNA-associated functions in mature B-cells, identifying alternative promoters, splicing, and RNA-binding interactions.

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina

The paper performs single-cell multiomics analysis of the human retina to identify regulatory elements and develop predictors for non-coding risk variants.

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Integrating epigenomic features reveals principles of chromatin-state organization

The paper integrates epigenomic features to identify chromatin-state classes and shows Polycomb-associated chromatin drives cell-type-specific differences.

HiC2Self: self-supervised denoising for bulk and single-cell Hi-C contact maps

HiC2Self denoises Hi-C contact maps using self-supervised learning, reconstructing 3D chromatin structures from low-coverage data across bulk and single-cell samples.

Evolution of regulatory chromatin contacts: insights from duplicated genes

The paper studies the evolution of regulatory chromatin contacts in duplicated genes using Hi-C data, finding faster divergence in chromatin contacts compared to expression patterns.

Sequence-based modeling of plant epigenomes reveals cell-type-specific cis-regulatory grammar

The paper introduces PEAgent, a deep-learning framework predicting single-cell chromatin accessibility from DNA sequence in plants, revealing cell-type-specific cis-regulatory patterns and their conservation.

Comparative analyses reveal rapid turnover and emergence of transitory 3D genome architectures in the fungal kingdom

This study compares 3D genome architectures across 55 fungal species, identifying novel configurations and challenging existing classifications.

Using Deep Learning to predict replication timing reveals baseline control of genomic DNA sequence

This study uses deep learning to predict replication timing and finds DNA sequence provides sufficient information for prediction, with epigenetic features adding complementary value.

A conserved mechanism for targeted cohesin loading organises specialised chromosomal domains

This study identifies a conserved mechanism for targeted cohesin loading that organises specialised chromosomal domains in S. pombe.

DNA Sequence and Histone Variant H2A.Z Jointly Govern Nucleosome Unwrapping Pathways

The paper shows DNA sequence and H2A.Z histone variant jointly determine nucleosome unwrapping directionality through simulations and NMR data.

Active histone modifications fine-tune DNA N-6 methyladenine deposition and maintain transcriptional stability

The paper characterizes the genome-wide interaction between active histone modifications and DNA 6mA in Rhizopus microsporus, showing they define chromatin domains and regulate transcriptional stability.

3D genome remodelling underlies PU.1-dependent granulocyte maturation

This study shows that PU.1 regulates granulocyte maturation by controlling transcriptional programs and 3D chromatin architecture through its binding sites.

An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.