Genomics and Chromatin Dynamics

Comprehensive landscape of potential CTCF-binding sites across the complete telomere-to-telomere human genome

The paper identifies a comprehensive catalog of potential CTCF-binding sites across the complete telomere-to-telomere human genome and characterizes their functional roles in repetitive regions.

Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding.

The paper investigates how nucleosome positioning, DNA structure, and transcription factor binding contribute to the function of ultra-conserved developmental enhancers.

Architectural chromatin interactions provide a framework for context-dependent gene regulation

The paper develops an integrative framework to classify and interpret promoter-centric chromatin interactions by combining Hi-C, ChIA-PET, and functional genomic data, identifying a distinct class of architectural promoter-enhancer interactions with context-dependent regulatory roles.

Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq.

The paper introduces UNIChro-seq, a method for quantifying chromatin accessibility at target loci, and demonstrates its application in analyzing disease risk alleles and genome-edited variants.

Histone Acetylation Differentially Modulates CTCF-CTCF Loops and Intra-TAD Interactions

This study shows histone hyperacetylation disrupts TAD intra-interactions but preserves CTCF-CTCF loops, revealing distinct cohesin populations with different sensitivity to acetylation.

ORC binding to Heterochromatin Protein 1 through intrinsically disordered regions is required for heterochromatin structure and function

This study shows that ORC interacts with HP1a via specific motifs to regulate heterochromatin structure and function in Drosophila.

A Promoter Competition Hub Orchestrates Runx1 Alternative Promoter Usage during Skeletal Muscle Stem Cell Activation

Reconstructing sequence-grammar trajectories enables interpretable and tunable cis-regulatory element design

This paper introduces GO-CRE, a method for designing cell-type-specific cis-regulatory elements by reconstructing sequence-grammar trajectories and using reinforcement learning with predictor guidance.

Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

The paper investigates enhancer-promoter interactions in a native chromatin context, revealing transcription factor synergy and the role of facilitators and repressive promoters in regulating gene activation.

Massively parallel characterization and predictive modelling of neuronal regulatory variation

The paper characterizes regulatory variants in human neurons using lentiMPRA and shows that variant effects are influenced by regulatory element activity and sequence context, not population frequency.

CASCADE recovers promoter-associated regulatory motifs from cell-type-resolved DNA language-model attributions

The paper introduces CASCADE, a method to identify promoter-associated regulatory motifs from cell-type-resolved DNA language model attributions in soybean.

Foundation model reveals the shared organization of transcription and topologically associating domains

The paper develops a foundation model to analyze TADs and their impact on transcription, finding that TADs enhance co-regulation and this effect declines with aging and changes in cancer cells.

A hierarchy of spatial confinements governs chromatin dynamics and genomic encounters

The paper investigates how transcription and loop extrusion create spatial confinements that regulate genomic encounters in the immunoglobulin heavy chain locus.

TFIIIC regulates SMC complex binding and 3D DNA contacts between tRNA genes

This study shows TFIIIC regulates SMC complex binding and 3D DNA contacts between tRNA genes independently of RNA Pol III.

Wiz regulates clustered protocadherin genes by restricting CTCF/cohesin loop extrusion in a genomic-distance biased manner

The paper introduces COP, a deep learning framework to predict ZFP genomic enrichments, identifies Wiz as a key regulator of cPcdh genes by affecting CTCF/cohesin loop extrusion.

Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions

The paper identifies functional insulators (FINs) through Hi-C meta-analysis, showing they block enhancer-promoter interactions and are distinct from TAD boundaries.

The novel HP1a interactor Clump/CG30403 safeguards transposon silencing and reproductive resilience in the Drosophila ovary

A Translocation within the Ogataea Species Complex Alters Local Subtelomeric Chromatin while Maintaining Overall Genome Organization

The paper compares chromatin composition, gene expression, and genome organization between two closely related yeast species, finding conserved global patterns but distinct local changes due to a chromosomal translocation.

Hierarchical Gene Cluster Regulation Across Vertebrate Skins: Developmental Control of Keratin Gene Expression

The paper investigates how keratin gene clusters are organized in vertebrate skin to enable developmental competence and gene-level selectivity during epidermal differentiation.

Shared binding sites for the chromosomal architectural protein Su(Hw) mediate physical interactions between Drosophila TAD boundaries

The paper investigates how shared Su(Hw) binding sites between TAD boundaries affect long-distance regulation and physical interactions in Drosophila.

Axolotl regeneration reveals a dormant cis-regulatory grammar conserved across vertebrate genomes

The paper identifies a conserved cis-regulatory grammar in axolotl limb regeneration and shows it is dormant in mammalian genomes, suggesting a potential for reactivating regenerative programs.

Promoter-associated RNA polymerase III shapes RNA polymerase II-dependent inflammatory gene expression during viral infection

Pol III occupies TATA-enriched, TBP-dependent inflammatory gene promoters, primes basal expression, then restrains Pol II induction during MHV68, HSV-1 and influenza A infection.

Decoding Promoter Activity from DNA Sequence using Pre-trained Language Models

The paper trains a transformer-based model on synthetic Drosophila promoters to predict promoter activity and shows it achieves high accuracy with sequence alone and improves with biological context.

Enhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts

This study shows that enhancer position within a cis-regulatory landscape modulates transcriptional burst frequency and uniformity in single cells.

The Metaphase Chromatin Unit: A Novel Unit of Higher-Order Chromosome Organization in Human Mitotic Cells

The paper identifies a quantitative unit of mitotic chromosome organization, the Metaphase Chromatin Unit (MCU), by analyzing metaphase lengths and DNA content across human chromosomes.

Drought reshapes enhancer-like nascent transcription and gene regulation in Oryza sativa

This study identifies drought-responsive enhancer-like nascent transcription in rice using PRO-seq and dREG, revealing 2,428 prioritized cis-regulatory elements.

Context-aware sequence-to-function model of human gene regulation

The paper introduces Corgi, a context-aware sequence-to-function model that predicts gene expression and epigenetic signals across unseen cell types using DNA sequence and trans-regulator expression.

Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction

This paper introduces Free Energy Spectroscopy (FES) to characterize chromatin compaction by analyzing end-to-end distance and nucleosome stacking interactions, revealing three mechanisms by which linker histones reshape compaction energetics.

Harnessing machine learning models for epigenome to transcriptome association studies

The paper benchmarks machine learning models for predicting gene expression from epigenomic data using the IHEC EpiATLAS dataset and identifies genes linked to B-cell leukemia.

Charge Imbalance Drives Salt-Optimized Nucleosome Phase Separation under Physiological Conditions

The paper uses simulations to show that charge imbalance in nucleosomes drives phase separation under physiological salt conditions, influenced by DNA mechanics and histone modifications.