Genomics and Chromatin Dynamics

This paper describes a protocol using Saccharomyces cerevisiae chromatin as a spike-in control to normalize ChIP signals for S. pombe heterochromatin-associated proteins.

This study investigates the distinct roles of SMRT and NCOR in the HDAC3 corepressor complex, showing they differentially regulate inflammatory and metabolic pathways in macrophages through chromatin and transcriptional mechanisms.

The paper identifies a noncanonical role for KZFPs in restricting TE-derived regulatory elements to maintain cell-type identity, independent of TRIM28.

This study shows that RNA polymerase II transcribes the H3-H4 octasome more efficiently than the nucleosome, with distinct pausing patterns and stepwise tetramer disassembly.

The paper introduces HiddenFoot, a probabilistic model to infer TF, nucleosome, and Pol II occupancy from single-molecule data, revealing binding dynamics and heterogeneity in mouse, Drosophila, and human cells.

The paper examines nucleosome positioning and sensitivity in the purple sea urchin genome, revealing unique patterns distinct from other eukaryotes.

This study uses UV ChIP-seq to identify novel CTCF-DNA interactions, revealing previously undetected binding sites and noncanonical motifs.

This study investigates how histone chaperone Nap1 and acetylation of histone H3/H4 tails regulate phase-separation of chromatin arrays through dynamic DNA-histone interactions.

This study analyzes the diversification of PDS5 proteins across eukaryotes, revealing distinct evolutionary trajectories and specialized cohesin regulatory mechanisms in different lineages.

The paper investigates how genetic variation in two mouse strains affects chromatin accessibility and TF binding in adipose tissue, linking these changes to gene regulation and disease susceptibility.

This study shows RNA Pol I is essential for chromatin organization and H3K4me3 gradients in oogenesis, independent of ribosome synthesis in C. elegans.

The paper uses live-cell imaging and kinetic analysis to show that transcription initiation efficiency is influenced by Pol II dynamics and the order of pre-initiation complex assembly.

The paper shows that DNA breaks caused by TOP2B in neuronal genes enhance transcriptional responses and memory through chromatin changes.

This paper introduces Dam-IT, a method that simultaneously captures TF-DNA binding, direct gene regulation, and chromatin accessibility, revealing the 'Hit-and-Run' mechanism of transcription by bZIP1.

The paper introduces Cleopatra, a deep learning model that predicts high-resolution 3D genome maps across human cell types, revealing cell-type-specific loops and gene regulation patterns.

This study investigates how promoter strength and position influence promoter competition by inserting diverse promoters into the Sox2 locus and measuring their effect on endogenous Sox2 expression.

The paper proposes a three-layer loop-extrusion model to explain mitotic chromosome folding, showing it can reproduce structural features observed in Hi-C maps and microscopy.

The paper shows that genome-lamina interactions are reconfigured during limb development to prime regulatory domains for gene activation and support cell-fate decisions.

The paper uses scATAC-seq to study chromatin accessibility changes during neural plate border cell fate specification, identifying new regulatory mechanisms involving Foxk2.

This study uses numerical experiments and theoretical modeling to investigate the physical processes in DNA-DNA proximity ligation assays and their impact on experimental outcomes.

The paper presents a single-cell multi-omics atlas of human development and uses deep learning to analyze regulatory DNA motifs and their impact on chromatin accessibility and gene expression.

This study identifies NMNAT1's role in transcriptional regulation by showing its binding to gene promoters and enhancers and its impact on RNA Polymerase II occupancy.

The paper investigates how pulling forces and intra-chromatin interactions influence chromosome pairing and unfolding during meiosis in fission yeast.

The paper identifies TRE motifs as indirect MYC binding sites that synergize with AP-1 at enhancers, leading to transcriptional rewiring in cancer.

TransAgent automates transcriptional regulation analysis by integrating multi-omics data and tools, improving efficiency and uncovering biological insights in cancer and differentiation studies.

The paper investigates the effect of Trichostatin A on nuclear compartments in cells lacking H3K9me, H3K27me3, and uH2A, finding minimal impact on compartment structure despite increased H3K27ac levels.

The paper identifies trans-homologous chromatin interactions in Drosophila Hi-C data and links them to regulatory regions and developmental processes.

This study identifies a splicing-independent role for Sxl in regulating RNA Polymerase III activity and tRNA synthesis in Drosophila neurons, impacting neuronal metabolism and ageing.

This study shows that embryonic stem cells (ESCs) have a chromatin structure similar to differentiated cells, challenging the idea that their pluripotency is driven by a globally open chromatin conformation.