Genomics and Chromatin Dynamics

This study shows that loss of H3K9me3 in human neural progenitor cells activates L1 retrotransposons by reducing CpG methylation at their promoters.

This study identifies conserved and diverged gene regulatory networks in mammalian cerebellum development using single-nucleus gene expression and chromatin accessibility data from six species.

The paper develops MoDIFI, a Bayesian framework to prioritize cell lines and regulatory regions for testing noncoding variants associated with neurodevelopmental disorders.

The paper shows that chromatin modifiers KMT2D, BAF, and p300 are required for de novo TF binding on enhancers, revealing cooperative interactions rather than a strict hierarchy.

The paper reveals how Set2 deposits H3K36me3 on reassembled nucleosomes during transcription elongation using Cryo-EM structures of the EC-Set2-nucleosome complex.

AlphaGenome predicts functional genomic measurements from DNA sequences with high resolution and accuracy across multiple modalities, outperforming existing methods in variant effect prediction.

The paper identifies HDAC3's role in regulating histone lactylation during Drosophila oogenesis, showing its importance for chromatin architecture and fertility.

This study analyzes histone modifications, chromatin accessibility, and transcription in Schistosoma mansoni gonads to uncover the histone code governing gene expression and reproductive development.

The paper identifies 3D chromatin changes during human muscle stem cell state transition, showing increased CTCF binding at PAX7 enhancers stabilizes the stem cell state.

This study investigates the regulation of CtISWI activity through AutoN and HSS domain interactions, revealing a two-step mechanism for conformational activation and ATPase regulation.

This study shows that H2B variants, particularly H2B1O, alter chromatin accessibility and induce EMT in breast cancer, suggesting their role as onco-histones and potential therapeutic targets.

This study identifies NuMA's role in stabilizing linker histone H1 on chromatin to promote heterochromatin compaction and maintain epigenetic repression.

The paper shows classical enhancers influence 3D genome structure by linking DNA sequence to transcriptional condensates and chromatin organization through specific transcription factors.

The paper identifies chromatin regulatory factors in C. elegans germline that influence zygotic transcription activation during oocyte-to-embryo transition.

The paper shows PARP1 binding weakens nucleosome core contacts using optical tweezers.

This paper shows that AURKB drives the dissolution of CIZ1-RNA assemblies from the inactive X chromosome during mitosis by phosphorylating CIZ1's C-terminal extensions, disrupting its RNA interactions.

This study investigates regulatory turnover in human segmental duplications using T2T genome assembly and ChIP-seq data, finding that regulatory elements are rarely conserved but gene expression and spatial proximity are preserved.

EpiTADformer uses epigenomic signal embeddings to detect TAD boundaries with higher resolution than Hi-C-based methods.

This study investigates chromosome size determinants in fission yeast and finds that condensin levels, not cell or nuclear volume or mitosis duration, primarily influence chromosome dimensions.

The paper uses Monte Carlo simulations to study how chromatin compaction and DNA breaks influence gene translocation probabilities.

The paper determines the intrinsic substrate selectivity of the Drosophila Tip60 acetyltransferase complex using synthetic nucleosome arrays and identifies variable acetylation site effectiveness of an inhibitor.

This study uses single-molecule optical tweezers to show that high-concentration, high-molecular-weight PEG promotes chromatin compaction by enhancing internucleosomal interactions.

The paper introduces STARK, a toolkit for processing sc3DG-seq data, benchmarks 11 technologies, and establishes scNucleome as a resource for 3D genome research.

The paper models X-chromosome inactivation at multiple scales, showing how chromatin reorganization drives Xist expression and silences Tsix through structural changes.

The paper develops eTRex, a variational Bayesian model, to analyze 4,819 ATAC-seq datasets and create a pan-cancer atlas of transcriptional regulator profiles, revealing common and context-specific regulators.

This study shows ATAD2 regulates chromatin-bound histone chaperone turnover, affecting H3.3 localization and gene transcription during spermatogenesis.

This study shows that phosphorylation of DEK at S287/S288 by CK2 regulates its chromatin binding and transcriptional activity in a cell-type-specific manner, affecting chromatin compaction and oncogenic pathways in melanoma.

This paper introduces WaveTAD, a wavelet-based method for analyzing 3D genome structures, showing improved accuracy and revealing new biological insights across species and conditions.

The paper shows that functional synergy between transcription factors explains why most TF binding does not affect gene expression, and highlights the need for more expressive regulatory network models.