Topic 89

chromatin hi topologically tad tads domains 3d organization associating ctcf chromosome genome boundaries cohesin conformation architecture loops interactions contacts enhancer genomics regulation gene capture boundary transcription genomic promoter spatial structure wide dimensional domain regulatory loop genes chromosomal transcriptional loci structures expression promoters nuclear chromosomes elements maps regions resolution interaction contact architectural compartment nucleus enhancers looping enriched polymer compartments structural sites cell topological cells binding proximity active insulation at depletion formation extrusion nucleosome inactive detect super mammalian physical territories long associated into insulator principles gam within heterochromatin chip units interior cluster histone seq positioning map order find types 3c function sprite

99 items. Top items listed below.

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

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

3D genome evolution and reorganization in the Drosophila melanogaster species group 89 31 21 9 5

Genes on Different Strands Mark Boundaries Associated with Co-regulation Domains 89 31 9

A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells 89 31 18 8 4

Topologically associating domain (TAD) boundaries stable across diverse cell types are evolutionarily constrained and enriched for heritability 89 19 9 5

Simultaneous smoothing and detection of topological units of genome organization from sparse chromatin contact count matrices with matrix factorization 89 31 4

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

Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification 89 31 26 4

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

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

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

Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers 89 31

Sister-chromatid-sensitive Hi-C reveals the conformation of replicated human chromosomes 89 46 31 8

Hierarchical Markov Random Field model captures spatial dependency in gene expression, demonstrating regulation via the 3D genome 89 31 4

Identifying regulatory and spatial genomic architectural elements using cell type independent machine and deep learning models 89 26 4

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

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

Systematic Chromatin Architecture Analysis in Xenopus tropicalis Reveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes 89 31 20 8 3

preciseTAD: A machine learning framework for precise 3D domain boundary prediction at base-level resolution 89 31 26 4

Nucleosome-constrained loop extrusion model for the origin of topologically associating domains 89 31 8

A functional overlap between actively transcribed genes and chromatin boundary elements 89 31 8 3

Topologically associating domains and their role in the evolution of genome structure and function in Drosophila 89 40 21 9 5

High-Resolution Single-Cell 3D-Models of Chromatin Ensembles during Drosophila Embryogenesis 89 31 8

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C 89 31 9 4

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

Topologically associating domain boundaries are enriched in early firing origins and restrict replication fork progression 89 31 3

DiffGR: Detecting differentially interacting genomic regions from Hi-C contact maps 89 13 4

Detecting local changes in chromatin architecture with false discovery control 89 4

How subtle changes in 3D structure can create large changes in transcription 89 31 8

Toward an understanding of the relation between gene regulation and 3D genome organization 89 31 9

Anopheles mosquitoes revealed new principles of 3D genome organization in insects 89 31 9 5

BART3D: Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data 89 31 9 4

Making sense of the linear genome, gene function and TADs 89 31 9

A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C 89 4

MCM complexes are barriers that restrict cohesin-mediated loop extrusion 89 46 8 3

Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency 89 31 8 3

Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III 89 31 9 3

CTCF-binding element regulates ESC differentiation via orchestrating long-range chromatin interaction between enhancers and HoxA 89 20 3

Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during development 89 7 3

Chromatin folding variability across single-cells results from state degeneracy in phase-separation 89 31 8

A CRISPR Screen Identifies Myc-associated Zinc Finger Protein (MAZ) as an Insulator Functioning at CTCF boundaries in Hox Clusters 89 31 20 3

Si-C: method to infer biologically valid super-resolution intact genome structure from single-cell Hi-C data 89 4

HMGB1 coordinates SASP-related chromatin folding and RNA homeostasis on the path to senescence 89 31 9 3

Regulatory architecture of the RCA gene cluster captures an intragenic TAD boundary and enhancer elements in B cells 89 31 9 3

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

STAG2 loss-of-function affects short-range genomic contacts and modulates urothelial differentiation in bladder cancer cells 89 31 9 3

3D reconstruction of genomic regions from sparse interaction data 89 31 4

SPIN reveals genome-wide landscape of nuclear compartmentalization 89 31 9

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

MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments 89 4

Simultaneous Epigenetic Perturbation and Genome Imaging Reveal Distinct Roles of H3K9me3 in Chromatin Architecture and Transcription 89 31 20 3

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation 89 31 9 3

Connecting high-resolution 3D chromatin organization with epigenomics 89 31 26 4

Probing multi-way chromatin interaction with hypergraph representation learning 89 4

Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin 89 31 8 3

Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics 89 31 8

Chromatin Topology And The Timing Of Enhancer Function At The HoxD Locus 89 31 20 3

Chemically Induced Chromosomal Interaction (CICI): A New Tool to Study Chromosome Dynamics and Its Biological Roles 89 46 8

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding at cis-regulatory elements and TAD boundaries 89 31 20 3

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

Cohesin depleted cells rebuild functional nuclear compartments after endomitosis 89 8 3

Lessons from the analysis of TAD boundary deletions in normal population 89 9

Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells 89 31 18

Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation 46 31 3

Protein hyperacylation links mitochondrial dysfunction with nuclear organization 89 31 3

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

Nanoscale Chromatin Imaging and Analysis (nano-ChIA) platform bridges 4-D chromatin organization with molecular function 89 18 8

HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps 89 13 4

Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin 89 4

Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming 89 20 8

Towards A 3D Chromosome Shape Alphabet 89 4

CRISPR-based Live Imaging of Epigenetic Modification-Mediated Genome Reorganization 89 31 8 3

Loop extrusion model predicts CTCF interaction specificity 7

Lamin C regulates genome organization after mitosis 89 68 34 20 3

Purifying selection on noncoding deletions of human regulatory elements detected using their cellular pleiotropy 89 31 9

Functional signatures of evolutionarily young CTCF binding sites 89 31 9 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

Data-driven polymer model for mechanistic exploration of diploid genome organization 89 38 4

Single-Cell Analysis of the 3D Topologies of Genomic Loci Using Genome Architecture Mapping 89 4

3D Genome Analysis Identifies Enhancer Hijacking Mechanism for High-Risk Factors in Human T-Lineage Acute Lymphoblastic Leukemia 89 9 3

Antigenic variation by switching inter-chromosomal interactions with an RNA splicing locus in trypanosomes 89 31 9 3

Domain segregated 3D chromatin structure and segmented DNA methylation in carcinogenesis 89 31 9

Coupling chromatin structure and dynamics by live super-resolution imaging 89 70 18 8

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies 89 31 11 9 3

Chromatin 3D interaction analysis of the STARD10 locus unveils FCHSD2 as a new regulator of insulin secretion 109 89 31 9 3

Polymer modelling unveils the roles of heterochromatin andnucleolar organizing regions in shaping 3D genome organization inArabidopsis thaliana 89 31 8

Integrative identification by Hi-C revealed distinct advanced structural variations in Lung Adenocarcinoma tissue 89 9

Cohesin residency determines chromatin loop patterns 89 46 31 3

Multi-contact 3C data reveal that the human genome is largely unentangled 89 31 8

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

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

TSA-Seq reveals a largely hardwired genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes 89 31 9 3

Boundary sequences flanking the mouse tyrosinase locus ensure faithful pattern of gene expression 31 9 3

SACSANN: identifying sequence-based determinants of chromosomal compartments 13 4

Principal Curve Approaches For Inferring 3D Chromatin Architecture 89 4

Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation 13 4

Live imaging of chromatin distribution in muscle nuclei reveals novel principles of nuclear architecture and chromatin compartmentalization 89 3

TCF7L2 Silencing Reprograms the 4D Nucleome of Colorectal Cancer Cells 89 31 9 3

MyoD is a structure organizer of 3D genome architecture in muscle cells 89 31 20 3