Genomics and Chromatin Dynamics

EPIraction creates an enhancer-gene interaction atlas using H3K27ac ChIP-Seq data and GWAS SNPs to annotate candidate target genes.

This study shows that cohesin depletion affects locus- and differentiation-specific transcriptional activation and regulatory interactions in mouse ESCs, with some loops and genes being more sensitive than others.

This study identifies two classes of regulatory elements in Drosophila embryos that govern early gene expression, revealing distinct roles for pioneer factors in initiating and maintaining transcriptional activity.

The paper identifies long-range chromosomal loops spanning over 100 Mb and shows they form via multivalent binding, independent of known nuclear structures, suggesting a distributed mechanism for chromosome organization.

The paper presents a Hi-C dataset from rat frontal cortex to study strain-specific chromatin architecture and its impact on gene expression and neurological traits.

The paper identifies H2BK120ac as critical for BRD4 recruitment to intergenic enhancers and shows its role in BRD4-NUT-driven oncogenesis.

The paper identifies Cramp1 as an evolutionarily conserved factor that suppresses transposon mobilization during somatic development by initiating H1 transcription and promoting H3K36me2-established heterochromatin.

The paper uses cryo-CLEM to visualize and analyze the ultrastructural organization of mitotic chromosomes, identifying non-histone macromolecular densities and surface particle clusters.

The paper introduces Consenrich, a method for robust signal recovery from multi-sample functional genomics data, showing improved biological insights in Alzheimer's cohort analysis.

This study identifies two mechanisms by which RECQ5 modulates RNA polymerase II transcription: attenuating elongation via the brake helix and forming a condensate scaffold matrix.

The paper manipulates transcription to show it can advance replication timing but is not required for the switch to early replication.

The paper compares ChIP-Seq and CUT&Tag for chromatin modification detection, finding CUT&Tag better captures repetitive elements and heterochromatin regions.

This study shows ZKSCAN3 represses enhancers by targeting retrotransposons without forming heterochromatin, linking it to neurodevelopmental processes and schizophrenia.

The paper replaces orthologous transcription factors in yeast to show that stable TFIIIC complexes are essential for proper mitotic chromosome segregation.

This study shows largazole suppresses superenhancer accessibility by inhibiting SP1 and BRD4, leading to mitotic chromosome misalignment and cell cycle arrest.

This study shows that N-terminal epitope tags on histone H3 prevent the loss of H3K27 trimethylation caused by the H3K27M mutation.

CANDI improves epigenome imputation by predicting raw counts, handling covariates, and providing uncertainty measures using a self-supervised Transformer model.

This study shows that GAGA motifs 5' to Jk RSSs are essential for nucleosome positioning and Vk-Jk recombination in mice.

The paper shows that SetDB1 auto-methylation at histone-mimic motifs enables heterochromatin spreading and maintenance through interactions with HP1 proteins.

This study maps transcription start sites and active enhancers in Galleria mellonella larvae during fungal infection and treatment using LQ-ssCAGE.

The paper investigates DNA breathing's role in TF-DNA interactions using in vitro and in vivo data, finding correlations between breathing features near motifs and binding affinity across multiple TFs.

The paper introduces IDLI, a method to map nucleosome structures and distortion patterns in mammalian chromatin, revealing widespread and regulated DNA accessibility across cell types.

The paper characterizes native nucleosome-positioning elements in yeast and shows they can be used to study nucleosome repositioning by transcription factors and chromatin remodelers.

This study shows that a Type ISP bacterial restriction-modification enzyme can displace nucleosome octamers using ATP, while a Type III enzyme cannot, suggesting the former could act as an artificial chromatin remodeler.

The paper identifies tissue-specific cis-regulatory elements (CREs) for the CFTR gene in pancreatic and intestinal cells using 3D genomic analysis and functional assays.

The paper uses enhancer scrambling to study a super-enhancer of the OTX2 gene, finding that a single DNase I hypersensitive site predominantly controls its expression.

The paper develops a method to detect combinatorial phosphorylation patterns on RNA polymerase II CTD and shows they recruit TREX for mRNA processing and export.

The paper shows that deleting intervening DNA can bring enhancers closer to silenced genes, reactivating their expression in adult cells.

This study shows that most cis-regulatory element contacts and gene transcription after mitosis occur without loop extrusion, though some loops depend on NIPBL.

This study examines enhancer dynamics and spatial organization in the human spinal cord to understand cellular state transitions and identity.