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Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis

https://doi.org/10.1182/blood.2020005780

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide

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Five Years of GWAS Discovery

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Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome

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Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

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Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

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Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

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The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

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The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

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The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

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In Situ Capture of Chromatin Interactions by Biotinylated dCas9

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Cohesin Loss Eliminates All Loop Domains

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YY1 Is a Structural Regulator of Enhancer-Promoter Loops

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A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code

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Neuronal CTCF Is Necessary for Basal and Experience-Dependent Gene Regulation, Memory Formation, and Genomic Structure of BDNF and Arc

inferredcites →https://doi.org/10.1016/j.celrep.2017.05.072openalex-snapshot

The LDB1 Complex Co-opts CTCF for Erythroid Lineage-Specific Long-Range Enhancer Interactions

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Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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Discovery of Genes Essential for Heme Biosynthesis through Large-Scale Gene Expression Analysis

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CCCTC-Binding Factor and the Transcription Factor T-bet Orchestrate T Helper 1 Cell-Specific Structure and Function at the Interferon-γ Locus

inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

inferredcites →https://doi.org/10.1016/j.stem.2010.08.004openalex-snapshot

Polycomb Group Proteins Set the Stage for Early Lineage Commitment

inferredcites →https://doi.org/10.1016/j.stem.2015.09.015openalex-snapshot

Targeted Application of Human Genetic Variation Can Improve Red Blood Cell Production from Stem Cells

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Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

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Dynamic long‐range chromatin interactions control Myb proto‐oncogene transcription during erythroid development

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Mitoferrin is essential for erythroid iron assimilation

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The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

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Spatial partitioning of the regulatory landscape of the X-inactivation centre

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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Principles of regulatory information conservation between mouse and human

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Chromatin architecture reorganization during stem cell differentiation

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Two independent modes of chromatin organization revealed by cohesin removal

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GREAT improves functional interpretation of cis-regulatory regions

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Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

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Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

inferredcites →https://doi.org/10.1038/nmeth.3664openalex-snapshot

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

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HiChIP: efficient and sensitive analysis of protein-directed genome architecture

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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

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hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

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Exploiting genetic variation to uncover rules of transcription factor binding and chromatin accessibility

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Long-range enhancer–promoter contacts in gene expression control

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Interrogation of human hematopoiesis at single-cell and single-variant resolution

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C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2

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inferredcites →https://doi.org/10.1074/jbc.m110.164574openalex-snapshot

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De-SUMOylation of CCCTC Binding Factor (CTCF) in Hypoxic Stress-induced Human Corneal Epithelial Cells

inferredcites →https://doi.org/10.1084/jem.20100204openalex-snapshot

DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas

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A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation

inferredcites →https://doi.org/10.1101/gad.303461.117openalex-snapshot

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inferredcites →https://doi.org/10.1101/gad.399506openalex-snapshot

CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus

inferredcites →https://doi.org/10.1101/gr.136101.111openalex-snapshot

Widespread plasticity in CTCF occupancy linked to DNA methylation

inferredcites →https://doi.org/10.1101/gr.136184.111openalex-snapshot

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

inferredcites →https://doi.org/10.1101/gr.212175.116openalex-snapshot

Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response

inferredcites →https://doi.org/10.1101/pdb.prot090803openalex-snapshot

Single Guide RNA Library Design and Construction

inferredcites →https://doi.org/10.1182/blood-2012-04-422253openalex-snapshot

Mutations in the mechanotransduction protein PIEZO1 are associated with hereditary xerocytosis

inferredcites →https://doi.org/10.1182/blood-2013-02-483875openalex-snapshot

Chromatin looping defines expression of TAL1, its flanking genes, and regulation in T-ALL

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Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

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inferredcites →https://doi.org/10.1371/journal.pone.0034915openalex-snapshot

Loss of Maternal CTCF Is Associated with Peri-Implantation Lethality of Ctcf Null Embryos

inferredcites →https://doi.org/10.1371/journal.pone.0041374openalex-snapshot

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome

inferredcites →https://doi.org/10.1371/journal.pone.0059890openalex-snapshot

Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells

inferredcites →https://doi.org/10.1371/journal.pone.0078031openalex-snapshot

The RNA Binding Protein RBM38 (RNPC1) Regulates Splicing during Late Erythroid Differentiation

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Evolutionary Conservation and Functional Diversification of the Rbm24/38 Family in Metazoans

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HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia

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Transposable elements as genome regulators in normal and malignant haematopoiesis

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MYC reshapes CTCF-mediated chromatin architecture in prostate cancer

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Regulation of CTCF loop formation during pancreatic cell differentiation

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The H3K4 methyltransferase KMT2D is an essential cofactor for GATA1 at erythroid gene enhancers

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Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression

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Tcf1–CTCF cooperativity shapes genomic architecture to promote CD8+ T cell homeostasis

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A genetic disorder reveals a hematopoietic stem cell regulatory network co-opted in leukemia

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Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data

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Genotype-integrated single-cell transcriptome analysis reveals the role of DDX41 pR525H in a patient with myelodysplastic neoplasms

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CTCF delimits a DNA methylation transition at the intergenic region between the embryonic and adult α-globin genes

inferred← citeshttps://doi.org/10.1093/nar/gkad468openalex-snapshot

Multidimensional profiling reveals GATA1-modulated stage-specific chromatin states and functional associations during human erythropoiesis

inferred← citeshttps://doi.org/10.1093/nar/gkaf093openalex-snapshot

The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells

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Genomic profiling of HIV-1 integration in microglia links viral insertions to TAD organization

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MBNL1 hijacks a structured single-stranded distal DNA element to sustain FLT3 expression in KMT2A-rearranged leukemias

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Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes

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Rbm38 binds Fech pre-mRNA to prevent anemia and porphyria

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CTCF is selectively required for maintaining chromatin accessibility and gene expression in human erythropoiesis

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Chromatin accessibility and cell cycle progression are controlled by the HDAC-associated Sin3B protein in murine hematopoietic stem cells

inferred← citeshttps://doi.org/10.1371/journal.pone.0340247openalex-snapshot

An upstream secondary DNA motif within the IL3 insulator CTCF binding site is required for enhancer-blocking insulator activity

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Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

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Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

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Co-Regulated Genes and Gene Clusters

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