Topic 31

chromatin transcription regulatory transcriptional histone gene promoters dna regulation binding accessibility genome expression genes factors enhancer enhancers promoter factor elements sites epigenetic seq genomics rna cis chip wide tfs tf atac specific marks methylation regions motifs enriched polymerase genomic modifications active ctcf regulated repression biology repressive molecular nucleosome nucleosomes cells domains landscape occupancy regulators cell sequence regulate element heterochromatin at h3 organization epigenomic motif loci h3k27me3 activation accessible silencing lysine regulating h3k27ac start embryonic differentiation conserved dependent topologically ii activity polycomb complex role transcribed upstream initiation interactions architecture bind nuclear proximal distal mechanism regulator pol mechanisms chromosome co modification here

729 items. Top items listed below.

The regulatory genome of the malaria vector Anopheles gambiae: integrating chromatin accessibility and gene expression 31 9 3

Defining a critical enhancer near Nanog using chromatin-focused approaches identifies RNA Pol II recruitment as required for expression 31 9

Multiomics analysis reveals extensive epigenome remodeling during cortical development 31 9 3

Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation 31 9 3

Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated 134 31 9 5

SOX9 is sufficient to drive endothelial cells towards a mesenchymal fate by altering the chromatin landscape. 31 20 3

Loss of the Pioneer Factor FOXA1 Results in Genome-wide Epigenetic Reprogramming and activation of Interferon-Response Genes including CD274/PD-L1 31 9 3

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure 89 19 9 4

Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis 31 9 3

TATA and paused promoters active in differentiated tissues have distinct expression characteristics 31 9

Functional mapping of androgen receptor enhancer activity 31 9 3

Dynamics of the 4D genome during lineage specification, differentiation and maturation in vivo 89 31 20 9 3

Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors 31 9 3

STAT5 regulation of sex-dependent hepatic CpG methylation at distal regulatory elements mapping to sex-biased genes 31 9 3

Accurate transcription start sites enable mining for the cis-regulatory determinants of tissue specific gene expression 134 31 9 4

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning 89 7 3

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data 31 7 4

Co-expression signatures of combinatorial gene regulation 134 31 9 3

Cooperative Binding of Transcription Factors is a Hallmark of Active Enhancers 31 9 3

Nucleoid openness profiling links bacterial genome structure to phenotype 31 9 3

The histone variant macroH2A1.1 regulates gene expression by direct association with their transcription start site. 31 9 3

TINC - a method to dissect transcriptional complexes at single locus resolution - reveals novel Nanog regulators in mouse embryonic stem cells 31 9 3

A transcriptional regulatory atlas of human pancreatic islets reveals non-coding functional signatures at GWAS loci 31 9

Towards understanding the regulation of histone H1 somatic subtypes with OMICs. 31 9 3

The Drosophila HP1 family is associated with active gene expression across chromatin contexts 31 9 3

Regulatory plasticity within a complex cytokine-sensing mammary enhancer during lactation 31 9 3

Subtype-specific epigenomic landscape and 3D genome structure in bladder cancer 31 9 3

Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation. 31 9 3

Integrative Analysis Reveals Histone Demethylase LSD1/KDM1A Associates with RNA Polymerase II Pausing 31 20 3

β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture 31 20 9 3

A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb targets 192 31 9 3

Pan-Cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. 31 9 3

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells 89 31 20 9 3

CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains 89 31 20 3

Mitotic retention of H3K27 acetylation promotes rapid topological and transcriptional resetting of stem cell-related genes and enhancers upon G1 entry 31 20 9 3

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression 89 31 20 3

Chromatin accessibility and histone acetylation in the regulation of competence in early development 192 31 20 3

Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs 31 9 5

Aging leads to stochastic loss of silencing at transposons in mammary luminal epithelial cells 81 31 9 3

Linking the dynamics of chromatin occupancy and transcription with predictive models 7

RNA promotes the formation of spatial compartments in the nucleus 89 31 9 8 3

RoboCOP: Jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data 31 4

A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans-regulatory elements of Oct4 in embryonic stem cells 31 9 3

The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes 31 20 9 5

Regulatory Sharing Between Estrogen Receptor α Bound Enhancers 31 9 3

Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation 31 20 3

Gene regulatory network of human GM-CSF secreting T helper cells 31 9 3

PRC1 drives Polycomb-mediated gene repression by controlling transcription initiation and burst frequency 93 31 20 3

Chromatin accessibility analysis uncovers regulatory element landscape in prostate cancer progression 31 9 3

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay 31 9 3

Cell signaling coordinates global Polycomb Repressive Complex 2 recruitment and gene expression in murine embryonic stem cells 93 31 20 3

Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation 31 9 3

mTOR inhibition in primary neurons and the developing brain represses transcription of cholesterol biosynthesis genes and alters cholesterol levels 133 31 3

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle 89 31 9 3

Unraveling transcription factor functions through integrative inference of transcriptional networks in Arabidopsis thaliana yields novel regulators involved in reactive oxygen species stress signaling 134 31 16 9 4

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukemia 31 9 3

The CCCTC-binding factor CTCF represses hepatitis B virus Enhancer I and regulates viral transcription 31 9 3

Constructing Gene Regulatory Networks using Epigenetic Data 134 31 9 4

The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana 134 31 9 4

Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage 134 9

Evolutionarily Conserved Transcription Factors Drive the Oxidative Stress Response in Drosophila 134 31 9 3

Epigenetic regulation of differentially expressed genes between various glioma types 31 9

Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice 9 3

Pancreatic β-cell specific loss of E2f1 impairs insulin secretion and β-cell identity through the epigenetic repression of non β-cell programs 109 93 31 3

Genome-wide analysis of cis-regulatory changes in the metabolic adaptation of cavefish 31 9 3

Identification of cellular context sensitive regulatory variation in mouse genomes 31 9 4

High throughput screening identifies SOX2 as a Super Pioneer Factor that inhibits DNA methylation maintenance at its binding sites 93 31 3

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence 31 4

Transcriptome and epigenome characterization of mouse spermatogonial cells reveals distinct chromatin regulatory landscapes in postnatal and adult testis 31 9 3

Transcription factor binding dynamics shape noise across biological processes 134 31 9 3

The regulatory landscape of early maize inflorescence development 134 31 9

Selective silencing rather than targeted activation of gene expression underlies fate choice in human hematopoietic stem cells. 31 20 9 3

FAK regulates IL-33 expression via chromatin accessibility and c-Jun 31 9 3

Mapping chromatin accessibility and active regulatory elements reveals new pathological mechanisms in human gliomas 31 9 3

Androgen and glucocorticoid receptor direct distinct transcriptional programs by receptor-specific and shared DNA binding sites 31 9 3

A transcription-centric model of SNP-Age interaction 31 9 3

Functional and structural basis of extreme non-coding conservation in vertebrate mRNAs 134 49 31 9 3

Iterative Epigenomic Analyses in the Same Single Cell 93 31 9 4

Inferring active cis-regulatory modules to predict functional regulatory elements 134 31 4

Predicting transcription factor binding in single cells through deep learning 31 26 4

Impact of 3-dimensional genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver 89 31 9 3

Activation-induced re-organization of chromatin in human T cells 89 31 9 3

Transcriptional networks are dynamically regulated during cell cycle progression in human Pluripotent Stem Cells 31 20 9 3

Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy 31 20 3

scATAC-Seq reveals epigenetic heterogeneity associated with an EMT-like process in male germline stem cells and its regulation by G9a 98 31 9 3

A long-range chromatin interaction regulates SATB homeobox 1 gene expression in trophoblast stem cells 31 20 3

Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation 31 20 9 3

Human library of cardiac promoters and enhancers 134 31 9

The impact of chromatin remodeling on gene expression at the single cell level in Arabidopsis thaliana 43 31 9 3

The pregnant myometrium is epigenetically activated at contractility-driving gene loci prior to the onset of labor in mice 31 9 3

The histone variant H2A.Z is required to establish normal patterns of H3K27 methylation in Neurospora crassa 93 31 9 3

3D Epigenomic Characterization Reveals Insights Into Gene Regulation and Lineage Specification During Corticogenesis 31 9 3

ETV4 is necessary for estrogen signaling and growth in endometrial cancer cells 31 3

Integrated requirement of non-specific and sequence-specific DNA binding in MYC-driven transcription 31 3

Epigenome-based Splicing Prediction using a Recurrent Neural Network 31 9 4

Single nuclei chromatin profiles of ventral midbrain reveal cell identity transcription factors and cell type-specific gene regulatory variation 9 3

Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits 7 3

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

Identification of MAZ as a novel transcription factor regulating erythropoiesis 31 9 3

BRD4 Interacts with GATA4 to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes 31 3