CUT&Tag

Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.

This study shows H5N1 influenza virus can be transmitted vertically through placental and mammary routes in pregnant mice, causing developmental impairments in offspring.

This study identifies PRMT1 as a critical regulator of trophoblast development, showing its role in preventing early pregnancy loss through epigenetic control of stemness and differentiation.

This study shows that reducing DNA methyltransferase 1 in endothelial cells enhances anti-tumor immunity by altering the tumor microenvironment and improving immune cell infiltration.

The paper identifies chromatin features distinguishing injury-responsive from state-stabilizing transcriptional programs in hybrid hepatocytes using multi-omics data.

CLASHub integrates CLASH datasets with expression data to study miRNA-target interactions and identifies a novel TDMD trigger for miR-335-3p degradation.

This study shows FOXA1 maintains cell polarity and limits lysosome biogenesis in lung adenocarcinoma by regulating transcriptional circuits and interacting with TFE3.

The paper defines a 3D chromatin compartment blueprint that programs histone-to-protamine exchange during spermiogenesis using ATAC-seq, CUT&Tag, and Hi-C.

This study maps chromatin accessibility and protamine incorporation during spermiogenesis, revealing compartment-specific dynamics and their role in genome stability.

This study investigates dosage compensation mechanisms on sex chromosomes in a moth, revealing distinct patterns on ancestral and neo-sex chromosomes and suggesting new mechanisms evolved in neo-sex chromosomes.

This study identifies PRDM16 as a critical regulator of chondrogenesis and chondrocyte identity in the knee joint through DNA binding and histone modification.

This study uses multi-omics approaches to show that Runx1 regulates cardiac fibroblast activity and differentiation after myocardial infarction, with its deletion improving cardiac repair.

Super-CUT&Tag improves spatial epigenomic profiling by increasing sensitivity and resolution, revealing active-chromatin heterogeneity in mouse embryonic tissues.

This study shows OTX2 controls chromatin accessibility to promote somatic differentiation over germline fate in embryonic cells.

The paper identifies ADGRL2's role in epidermal differentiation through Gα13 activation and structural interactions, using CRISPR, Perturb-seq, and cryo-EM.

The paper identifies a HOXA10-TWIST2 antagonistic circuit that drives partial epithelial-to-mesenchymal transition in the endometrium, essential for embryo implantation.

The paper identifies pachytene piRNAs as precise gene regulators during meiosis, showing they target specific mRNAs through near-perfect complementarity.

This study generates genomic and epigenomic maps of mouse centromeres and pericentromeres using long-read sequencing and epigenetic analyses, revealing satellite DNA composition and chromatin state differences.

This study investigates METTL3's role in retinal development by integrating multi-omics data, revealing its impact on m6A regulation and chromatin accessibility independent of transcription.

This study shows that Ritlecitinib reduces neointima formation and enhances endothelial recovery after vascular injury by modulating JAK3 signaling and VEGF-A/TSP-1 pathways.

This study shows that a single dose of Salmonella YB1 vaccine induces long-term protective trained immunity in NK cells, enhancing their ability to combat cancer metastasis.

The paper identifies a 101-biomarker signature predicting radiotherapy response in colorectal cancer using multi-omics and supervised learning, achieving 89% accuracy.

This study investigates how Zic transcription factors regulate gene expression during cerebellar granule neuron maturation by analyzing their binding patterns and interactions with other transcription factors.

Spatial tri-omic sequencing (DBiT ARP-seq and DBiT CTRP-seq) and CODEX imaging map chromatin, RNA, and protein dynamics across mammalian brain development and lysolecithin-induced neuroinflammation.

The paper uses G4-DNABERT to map G-quadruplexes to enhancer and promoter regions, supporting their role in chromatin looping and gene regulation.

This study shows BCOR is essential for syncytiotrophoblast differentiation in mice and humans by repressing stem cell genes and alternate lineage factors.

This study shows that Scx is required for satellite cell expansion and muscle regeneration, with distinct target genes from tendon development.

The paper shows that G1 phase length regulates H3K27me3 levels in stem and tumor cells, with longer G1 increasing and shorter G1 decreasing H3K27me3.

This study shows that inhibiting Notch signaling and NFI factors can efficiently reprogram adult mammalian retinal glia into neurons, with enhanced effects under retinal injury.