ATAC-seq

Local chromatin, 3D genome folding and transposon cargo shape Sleeping Beauty transposition

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

Transient Partial Inhibition of DNA Polymerase α Promotes Chromatin Plasticity and Enhances Human Cell Reprogramming

Transient low-dose inhibition of DNA polymerase α enhances human cell reprogramming by promoting chromatin plasticity while maintaining genomic stability.

Hepatocyte nuclear factor-1β recruits the nucleosome remodeling and deacetylase complex to activate gene transcription

This study identifies HNF-1β's role in recruiting the NuRD complex to activate gene transcription through chromatin remodeling and acetylation.

HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids

HyARQ is a Snakemake workflow for allele-specific read counting and quality control across multiple assays in F1 hybrids, showing accurate recovery of parental proportions.

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.

MYC drives endothelial transformation and dedifferentiation in angiosarcoma

This study shows MYC drives endothelial transformation and dedifferentiation in angiosarcoma by promoting lineage plasticity and cell growth.

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

PWK genetic background reprograms heterochromatin and malignant epithelial states in Neu-driven mammary tumors

The paper shows that the PWK genetic background alters transcriptional programs, heterochromatin organization, and malignant epithelial state trajectories in NeuT mammary tumors.

Jasmonate-induced expansion of the MYC2 cistrome occurs within a preconfigured chromatin landscape

This study defines the native MYC2 cistrome in Arabidopsis under basal and JA-induced conditions, showing that JA treatment expands MYC2 binding sites while chromatin accessibility remains largely unchanged.

EWS::WT1 Isoform-Dependent Regulation of Neogenes in Desmoplastic Small Round Cell Tumors

This study identifies DSRCT-specific neogenes regulated by the EWS::WT1 fusion protein and shows their potential as biomarkers and therapeutic targets in desmoplastic small round cell tumors.

HDAC inhibitor treatment restores transcriptome, chromatin accessibility and memory deficits in a mouse model for Down syndrome

Induction of hysteretic chromatin states by CRISPRa reveals locus-specific encoding of transcriptional memory

The paper uses CRISPRa to show that transcriptional memory can be induced in MSCs through locus-specific activation, linked to H3K27me3 loss and increased transcription factor reacquisition.

Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility

Glucocorticoid receptor activation reorganizes Wnt/LEF1 regulatory circuitry associated with therapeutic response in B-cell acute lymphoblastic leukemia

This study shows that GR activation reorganizes Wnt/LEF1 regulatory circuitry in B-ALL, influencing therapeutic response and resistance through chromatin state changes and gene regulation.

Variation in enhancer activity across brain regions defines neurological disease risk and shapes cellular pathology

The paper identifies brain region-specific enhancers linked to neurological disease risk and shows their role in cellular pathology using enhancer activity data and GWAS integration.

Distinct RNA-RNA spatial interaction sub-networks of transcription factors in hepatic cells

The paper uses RIC-seq and integrates multi-omics data to classify transcription factors into two clusters based on RNA-RNA spatial interactions and their genomic and clinical features.

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

Ryder: Epigenome normalization using a two-tier model and internal reference regions

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.

ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility

This study compares ATAC-seq and MNase-seq in budding yeast, showing they detect distinct chromatin states and functional roles in gene regulation.

Paclitaxel induces NM2-dependent cellular contraction through GEF-H1 dissociation from microtubules and RhoA/ROCK activation in cancer cells

This study shows paclitaxel induces cancer cell contraction via GEF-H1 dissociation from microtubules and RhoA/ROCK activation, with tubulin acetylation regulating this process.

CHD8 orchestrates chromatin landscapes during early female neuronal differentiation

This study investigates CHD8's role in female neuronal differentiation using multi-omics analysis, revealing its impact on chromatin structure and gene regulation in mouse models.

SOX2 can associate with chromatin directly by binding to DNA or indirectly via association with other chromatin-bound proteins

This study shows SOX2 can regulate gene expression both directly via DNA binding and indirectly through interactions with other chromatin proteins.

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

This study identifies DPF3a as a chromatin remodeler that regulates myogenesis through three-dimensional genome organization rather than local chromatin accessibility.

RapidMACS: MACS3-identical peak calling, 50x faster

RapidMACS provides a faster narrow peak caller for ATAC-seq and related data, achieving 3.5 to 51x speed improvements over MACS3 while producing identical output.

WAVE2 and REST/NRSF Regulate Clustered Gene Expression by Maintaining Heterochromatin Organization

This study shows WAVE2 and REST/NRSF regulate clustered gene expression by maintaining heterochromatin organization through chromatin dynamics and spatial reorganization.

Zone Equalisation Normalisation For Improved Alignment of Epigenetic Signal

This paper introduces ZEN, a normalization method for genomic data that reduces technical noise while preserving biological signals, improving alignment across different experimental platforms.

Dual profiling of DNA modifications with enhancer features during the exit of naive pluripotency

The paper uses Methyl-ATAC and Methyl-CUT&Tag to study 5mC and 5hmC dynamics during mESC differentiation, revealing their role in enhancer regulation.

Autism-associated NRXN1α deletion rewires the H3K27me3 landscape and epigenetically disrupts human neural induction.

This study shows that NRXN1 deletion alters the H3K27me3 landscape and disrupts neural induction through epigenetic changes and spliceosome dysregulation.

The epigenomic landscape of deep lineage divergence: The case of the European sea bass

The paper identifies regulatory variation driving lineage divergence in European sea bass by analyzing epigenomic and genomic data from Atlantic and Mediterranean populations.