Transcription Factor Binding Sites
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Related Articles from SNS
Mapping Genome-wide Transcription Factor Binding Sites in two Rhodanobacter strains Isolated from Extreme Environments
Identification of target genes for bacterial transcription factors (TFs) provide a deeper understanding of bacterial response to environmental conditions. We focused on two Rhodanobacter sp. isolates from the subsurface of the U.S. Department of Energy Oak Ridge Reservation (ORR), an environment characterized by high-concentration mixed-waste contamination plumes. Bacterial strains in this subsurface ecosystem experience changing and complex environmental conditions, including variable...
D&D-seq maps DNA-protein interactions in single cells with multi-omics compatibility
D&D-seq maps DNA-protein interactions in single cells with multi-omics compatibility Sadie Harley Scientific Editor Robert Egan Associate Editor A new technology allows scientists to map, in single cells, the DNA binding sites of transcription factors and other regulatory proteins that control gene activity, according to a study led by investigators at Weill Cornell Medicine and the New York Genome Center. With key advantages over methods currently in use, the technology is expected to be a...
Cooperative FOXA1-HNF4A binding emerges from motif spacing and nucleosome architecture
The pioneer factor hypothesis posits that specialized transcription factors access nucleosomal DNA to enable binding of secondary factors, implying a hierarchical mechanism of chromatin opening. However, recent evidence indicates that cooperative binding between pioneer and non-pioneer factors can occur in a context-dependent manner. Here we define the sequence and chromatin features that specify cooperative binding between FOXA1 and HNF4A. Using dual-induction of FOXA1 and HNF4A in naive...
KDM: embedding DNA/RNA motifs and sequences in a shared k-mer space for unified discovery, analysis and binding prediction
Motif discovery and binding-site prediction in DNA and RNA sequences are central tasks in regulatory genomics, yet the methodological landscape is split between interpretable but rigid position weight matrices (PWMs) and high-performing but opaque machine-learning models. We present KDM, a unifying framework in which both motifs and sequences are represented as probability distributions over a shared k-mer dictionary, embedded via the Hellinger transformation. This common geometry enables...
Whole-genome duplication shaped cell-type evolution in the vertebrate brain
Abstract The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show...
Molecular glue degraders of HuR suppress BRAF-mutant colorectal cancer
Abstract BRAF gain-of-function mutations, particularly BRAF(V600E), affect roughly 10% of all patients with colorectal cancer (CRC), and portend poor prognosis with limited therapeutic interventions. BRAF inhibitors such as encorafenib are ineffective due to MAPK pathway reactivation driven by BRAF dimerization. Combined inhibition of BRAF and EGFR, although approved therapies, results in short survival benefits and frequent treatment resistance and relapse1,2,3.
Epigenetic Profiling of Human Insulinomas Reveals AP-1 Family as Critical Regulators of Beta Cell Maturation
Insulinomas are rare and benign human pancreatic adenomas that overproduce insulin and display increased beta cell mass. We and others have shown that transcriptomic and genomic profiling on insulinomas provides a data mine for identifying targets that can be manipulated to induce human beta cell regeneration. Majority of causative genetic variants in insulinomas involve epigenetic regulatory genes.
Extracellular NAD(P) activates systemic acquired resistance through LecRK-VI.2-mediated phosphorylation of NPR1
Systemic acquired resistance (SAR) is a long-lasting, broad-spectrum immune response induced in distal tissues by signals generated at primary infection sites. Although numerous mobile immune signals have been implicated in SAR, how these signals are perceived and mechanistically coupled to transcriptional reprogramming in systemic tissues remains poorly understood. functions as a key integrative SAR signal that activates immunity through the plasma membrane-localized lectin receptor kinase...
Trichome and inflorescence evolution in the paleopolyploid tree genus Greyia Hook. & Harv.
The southern African endemic tree genus Greyia Hook. & Harv. (Francoaceae, Geraniales) comprises three species distinguished by striking variation in trichome morphology and floral architecture, yet the genomic and regulatory basis of these traits has remained largely unexplored. Here, we present chromosome-scale genome assemblies for all recognized Greyia species, namely Greyia radlkoferi, Greyia sutherlandii, and Greyia flanaganii, providing the first high-quality genomic resources for...
SIRT7 regulates dosage compensation and safeguards the female X chromosome
Abstract Sirtuins are deacetylases implicated in stress responses and longevity in mammals1,2. Although their differential impact on disease for the two sexes has been noted3,4,5,6,7, the underlying reasons are unclear. Here, using Sirt7 as a model in mice, we examine the mechanisms leading to sex differences and find that Sirt7−/− female mice have decreased fitness throughout their lifespan.