DNA methylation

A three-factor model can explain symmetry breaking and the n-1 rule during X-chromosome inactivation

This paper introduces a three-factor mathematical model to explain symmetry breaking and the n-1 rule in X-chromosome inactivation by integrating Xist, an X-linked activator, and SPEN.

The long noncoding RNA FOSIL shapes the dynamics of FOS induction

This study shows that the lncRNA FOSIL regulates the timing and resolution of FOS induction by modulating chromatin structure and nuclear speckle dynamics.

Predicting single-molecule chromatin distribution from DNA sequence

This paper introduces a sequence-to-distribution framework to predict single-molecule chromatin states from DNA sequence, revealing new regulatory mechanisms and variant effects.

Exclusion from DNA double-strand breaks is a pervasive feature of the hnRNP family

The paper shows that most hnRNP proteins are excluded from DNA double-strand breaks, with hnRNPH1's exclusion dependent on its GYR domain and independent of recruitment pathways.

FoxO1 and HNF1α cooperatively remodel nucleosome architecture and mechanical stability to activate transcription

This study shows FoxO1 and HNF1α work together to change nucleosome structure and stability to activate transcription.

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.

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

The paper identifies two rodent-specific transposable element subfamilies that function as cell-type-specific enhancers in the mouse immune system, contributing to cell identity and gene regulation.

KMT2C and KMT2D regulate skeletal development through stage-specific epigenetic control of chondrogenesis

This study shows that KMT2C and KMT2D regulate skeletal development through epigenetic control of chondrogenesis, with redundancy in their function during bone formation.

DNA damage at Lamina-Associated Domains triggers nuclear envelope reorganization and chromatin detachment to prevent nuclear envelope blebbing and genome instability.

Mimic: A Unified Neural Network Architecture for Modelling Genomic Sequences and Module-level Comparison

This paper introduces Mimic, a unified neural network architecture for genomic sequence modeling, showing it outperforms existing models in protein-DNA interactions and enhancer activity.

CTCF gradually acquires novel function modalities during bilaterian evolution

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

FBRSL1 couples ncPRC1.3 to CoREST to repress cell-cycle genes during human neuronal differentiation

This study shows FBRSL1 couples ncPRC1.3 to CoREST for transcriptional repression during neuronal differentiation, contrasting AUTS2's activating role.

Predicting cell-state-specific gene regulation from DNA across species

Bolero predicts cell-state-specific gene regulation from DNA across species by integrating cell-state embeddings and biological variables.

PeakLocus: A transcript-aware toolkit for RNA-Centric Genomic Annotation

PeakLocus assigns RNA features to transcript intervals with high accuracy, outperforming existing tools in benchmark tests across multiple species.

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

This study introduces cgNA+, a model predicting sequence-dependent mechanical properties of dsNAs with high accuracy, revealing hidden regulatory layers in nucleic acid mechanics.

Separable downmodulation of meiotic axis protein deposition and DNA break induction at chromosome ends

The paper shows that multiple mechanisms suppress meiotic recombination near chromosome ends in yeast, involving both axis protein downregulation and DNA break suppression.

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.

A single epigenetic repressor controls opposing developmental tempos in human neural and cranial neural crest lineages

This study identifies ZNF462 as an epigenetic repressor that controls opposing developmental tempos in human neural and cranial neural crest lineages by regulating lineage-specific enhancers.

CRISCross: Integration of Epigenetic Information for Deep-Learning-Based Prediction of CRISPR-Cas9 Off-Targets Across Cell Types

CRISCross improves CRISPR-Cas9 off-target prediction by integrating epigenetic features with sequence data across cell types, showing better performance than sequence-only models.

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.

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a multigraph framework for analyzing genomic organization and multi-omics data across scales, revealing gene expression clumping and circadian regulation in a photosynthetic alga.

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.

MacroH2A1 and H3K27me3 target cGAS to facultative heterochromatin to restrain innate immune activation

This study shows that macroH2A1 and H3K27me3 bind cGAS to sequester it in heterochromatin, preventing innate immune activation.

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.

Artificial Intelligence Applied to Epigenomic Data in Leukemia: A Systematic Review of Diagnostic, Prognostic and Monitoring Models

This paper reviews AI models using epigenomic data for leukemia diagnosis, prognosis, and monitoring, finding high accuracy in classification but limited external validation and prospective testing.

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.

CBFA2T3-GLIS2 establishes transcriptionally permissive enhancer hypermethylation associated with venetoclax response in pediatric AML

The paper identifies enhancer hypermethylation as a feature of C/G AML linked to venetoclax response and shows DNMT3B inhibition enhances treatment efficacy.

ATRX Deficiency Drives Aberrant Type I Interferon Signalling Through cGAS-Dependent Transcriptional Dysregulation

This study identifies ATRX deficiency as a driver of aberrant type I interferon signaling via cGAS-dependent transcriptional dysregulation in patients with cerebral white matter disease.

tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models

tangermeme provides tools to interpret deep learning models for cis-regulatory analysis, extracting human-readable insights from genomic predictions.

DNA replication stress redistributes the histone methyltransferase G9a and activates lineage-specific gene expression

The paper shows DNA replication stress redistributes G9a to stalled forks, activates gamma-globin genes, and explains how hydroxyurea increases fetal hemoglobin in sickle cell anemia.