CUT&Tag

FiberBrowser: a unified framework for single-molecule genomics

FiberBrowser converts diverse single-molecule footprinting datasets into a unified representation for analyzing chromatin structure and function across assays.

Deciphering Spatial Cellular Organization through RNA-Anchored Multi-Omics Deconvolution

SMODER deconvolves spatial multi-omics data by prioritizing RNA for cell-type identification and integrating other modalities, improving accuracy and spatial coherence.

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.

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

RISC-Bound Small RNA Sequencing Provides Insights into Guide Strand Selection and siRNA Trimming and Tailing Following Insecticidal dsRNA Delivery

The paper profiles RISC-bound siRNAs from insect larvae to understand guide strand selection and siRNA modifications, identifying sequence features that influence strand bias and terminal modifications.

Juvenile social isolation induces gene expression alterations and histone modification dysregulations in nucleus accumbens (NAc) neurons of female mice

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.

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

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.

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.

mV2G: a multiomic atlas for tissue-specific variant-to-gene prioritization

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.

Multidimensional variation and population stratification across 8000 complete human centromeres

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.

Differential multi-omics analysis of pulmonary arterial hypertension microvascular endothelial cells for differential drug response

The paper uses a multi-omics framework to analyze PAH endothelial cells and identifies kinase-related alterations and potential drug targets.

Multi-omic Profiling of Recurrence Risk Across Breast Cancer Subtypes

This study identifies subtype-specific molecular and immune features associated with recurrence risk in breast cancer using multi-omic analysis of 340 tumors and validates predictive models in an external cohort.

Arginine methyltransferase PRMT1 equipoises trophoblast development to prevent early pregnancy loss

This study identifies PRMT1 as a critical regulator of trophoblast development, showing its role in preventing early pregnancy loss through epigenetic control of stemness and differentiation.

Regulation of Human Erythroferrone Expression

This study identifies the transcriptional regulatory mechanisms governing ERFE expression in human erythroblasts using genomic approaches.

Leukemia Risk Factor ARID5B Coordinates HDAC-Mediated Transcriptional Repression

This study identifies ARID5B as a chromatin repressor that interacts with HDAC1/2 to repress B cell-specific genes, linking its germline variants to B-ALL risk.

A multiscale chromatin collapse underlies vascular pathology in Hutchinson -Gilford progeria syndrome

This study identifies chromatin reorganization and histone mark changes in HGPS VSMCs, linking them to vascular pathology through disrupted enhancer-promoter interactions.

PATTY corrects open chromatin bias for improved bulk and single-cell CUT&Tag profiling

PATTY corrects open chromatin bias in CUT&Tag data using ATAC-seq and machine learning, improving detection of histone modifications and cell clustering in single-cell analyses.

Chromatin State Distinguishes Injury-Responsive from State-Stabilizing Transcriptional Programs in Hybrid Hepatocytes

The paper identifies chromatin features distinguishing injury-responsive from state-stabilizing transcriptional programs in hybrid hepatocytes using multi-omics data.

Cross-assay RNA modeling reveals cancer biomarkers

This paper integrates multiple transcriptomics assays to identify cancer biomarkers, finding GBP4 as a predictor of recurrence and immune remodeling.

GNOMES: an integrated framework for genome-wide normalization and differential binding analysis of CUT&RUN and ChIP-seq data

GNOMES normalizes and analyzes ChIP-seq and CUT&RUN data, providing differential binding results and quality control metrics through an integrated workflow.

FOXA1 preserves cell polarity and restrains lysosome biogenesis in non-small cell lung adenocarcinoma

This study shows FOXA1 maintains cell polarity and limits lysosome biogenesis in lung adenocarcinoma by regulating transcriptional circuits and interacting with TFE3.

snoFlake: A network model for snoRNA-RBP complexes reveals SNORD22 as a U5 snRNP-associated splicing regulator

snoFlake identifies snoRNA-RBP complexes and reveals SNORD22 as a splicing regulator by interacting with U5 snRNP components.

3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis

The paper defines a 3D chromatin compartment blueprint that programs histone-to-protamine exchange during spermiogenesis using ATAC-seq, CUT&Tag, and Hi-C.

Genome compartments guide protamine replacement and genome stability during spermiogenesis

This study maps chromatin accessibility and protamine incorporation during spermiogenesis, revealing compartment-specific dynamics and their role in genome stability.

Out with the Old: Contrasting Histone Marks are Associated with Dosage Compensation on the Ancient and New Z of a Moth with Complex Sex Chromosomes

This study investigates dosage compensation mechanisms on sex chromosomes in a moth, revealing distinct patterns on ancestral and neo-sex chromosomes and suggesting new mechanisms evolved in neo-sex chromosomes.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Multiomics reveals epigenetic control of fibroblast activity after myocardial infarction and a key role for RUNX transcription factors

This study uses multi-omics approaches to show that Runx1 regulates cardiac fibroblast activity and differentiation after myocardial infarction, with its deletion improving cardiac repair.

Impact of Sperm Fractionation on Chromosome Positioning, Chromatin Integrity, DNA Methylation and Hydroxymethylation Level

This study examines how sperm fractionation methods affect chromosome positioning, chromatin integrity, and DNA methylation/hydroxymethylation levels in human sperm.

Human stem cell models for group 3 medulloblastoma uncover JARID1B as a regulator of the chromatin landscape.