CUT&Tag

Synthetic chromatin engineering for STAT1 reactivation toward restoring cisplatin sensitivity in breast cancer

This study reactivates STAT1 in cisplatin-resistant breast cancer using synthetic chromatin engineering, restoring cisplatin sensitivity through enhanced nuclear translocation and transcriptional activation.

RPI-Zero: Zero-shot RNA-Protein Interaction Prediction

RPI-Zero predicts RNA-protein interactions without prior data by using a sequence-only model trained on a large benchmark of CLIP experiments.

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.

Myogenic and neural transcriptional circuitry determines PAX3::FOXO1 driven initiation of rhabdomyosarcoma

This study uses a PAX3::FOXO1 inducible model to show P3F initiates ARMS transformation but is not required for maintaining proliferation or transcriptional programs.

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.

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.

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.

G4SCOPE identifies sequence features and epigenetic contexts of chromatin G-quadruplexes

G4SCOPE predicts chromatin G-quadruplex occupancy from DNA sequence, revealing epigenetic differences in BRCA1 and BRCA2 deficient cells.

Not all TOP RNAs are created equal: 3'UTR length and TSS selection predict the translational regulation of LARP1-bound mRNAs in CD4+ T cells

The paper investigates how 3'UTR length and TSS selection influence the translational regulation of LARP1-bound TOP RNAs in CD4+ T cells, revealing differential dependencies on LARP1 and MTORC1.

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

miRstring: An RNA language model enables mature miRNA decoding and artificial small RNA design across species

miRstring decodes mature miRNA boundaries from precursor context across species and designs artificial miRNAs effectively.

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.

BRD4 represses developmental and neuronal genes through interaction with PRC1.6

Acute BRD4 degradation and BD2 mutations de-repress bivalent developmental and neuronal genes in human stem cells and organoids, consistent with BRD4 recruitment by H3K14ac/H3K23ac and interaction with PRC1.6.

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.

Regulation of Human Erythroferrone Expression

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

Aberrant chromatin looping by NUP98-HOXA9 is constrained by CTCF and facilitated by cohesin

This study investigates how NUP98-HOXA9 drives aberrant chromatin looping in AML by interacting with CTCF and cohesin, revealing a non-canonical mechanism involving phase separation and loop extrusion.

Enhancer pioneering activity of Wnt/β-catenin signaling

This study shows Wnt/β-catenin signaling can establish new regulatory elements by remodeling chromatin, beyond its traditional role as a molecular switch.

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.

Benchmarking normalisation methods for differential binding analysis in CUT&RUN

This study benchmarks normalization methods for differential binding analysis in CUT&RUN, finding data-driven normalization to be most robust and highlighting variable performance of spike-in normalization.

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.