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A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification

https://doi.org/10.1101/2022.03.22.485307

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What this work says

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

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Notch signaling and the emergence of hematopoietic stem cells

inferredcites →https://doi.org/10.1016/0092-8674(81)90413-xopenalex-snapshot

Expression of a β-globin gene is enhanced by remote SV40 DNA sequences

inferredcites →https://doi.org/10.1016/j.cell.2008.01.025openalex-snapshot

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

inferredcites →https://doi.org/10.1016/j.cell.2011.07.006openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2018.11.029openalex-snapshot

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

inferredcites →https://doi.org/10.1016/j.cell.2021.04.048openalex-snapshot

Integrated analysis of multimodal single-cell data

inferredcites →https://doi.org/10.1016/j.celrep.2018.02.040openalex-snapshot

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

inferredcites →https://doi.org/10.1016/j.devcel.2013.02.011openalex-snapshot

Endothelio-Mesenchymal Interaction Controls runx1 Expression and Modulates the notch Pathway to Initiate Aortic Hematopoiesis

inferredcites →https://doi.org/10.1016/j.devcel.2016.01.024openalex-snapshot

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation

inferredcites →https://doi.org/10.1016/j.devcel.2017.08.002openalex-snapshot

YAP/TAZ Orchestrate VEGF Signaling during Developmental Angiogenesis

inferredcites →https://doi.org/10.1016/j.devcel.2020.01.006openalex-snapshot

YAP Regulates Hematopoietic Stem Cell Formation in Response to the Biomechanical Forces of Blood Flow

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.mvr.2016.02.004openalex-snapshot

AP-1 transcription factor mediates VEGF-induced endothelial cell migration and proliferation

inferredcites →https://doi.org/10.1016/j.stem.2010.07.016openalex-snapshot

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

inferredcites →https://doi.org/10.1016/j.stem.2018.06.014openalex-snapshot

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

inferredcites →https://doi.org/10.1016/j.tibs.2014.02.007openalex-snapshot

Enhancer RNAs and regulated transcriptional programs

inferredcites →https://doi.org/10.1016/j.tibs.2020.08.007openalex-snapshot

Spirits in the Material World: Enhancer RNAs in Transcriptional Regulation

inferredcites →https://doi.org/10.1016/s0168-9525(00)02029-1openalex-snapshot

Developmental regulation of eukaryotic gene loci

inferredcites →https://doi.org/10.1038/364064a0openalex-snapshot

An early pre-liver intraembryonic source of CFU-S in the developing mouse

inferredcites →https://doi.org/10.1038/376062a0openalex-snapshot

Failure of blood-island formation and vasculogenesis in Flk-1-deficient mice

inferredcites →https://doi.org/10.1038/emboj.2012.275openalex-snapshot

RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis

inferredcites →https://doi.org/10.1038/nature03122openalex-snapshot

Haemangioblast commitment is initiated in the primitive streak of the mouse embryo

inferredcites →https://doi.org/10.1038/nature07679openalex-snapshot

The haemangioblast generates haematopoietic cells through a haemogenic endothelium stage

inferredcites →https://doi.org/10.1038/nature09033openalex-snapshot

Widespread transcription at neuronal activity-regulated enhancers

inferredcites →https://doi.org/10.1038/nature09692openalex-snapshot

A unique chromatin signature uncovers early developmental enhancers in humans

inferredcites →https://doi.org/10.1038/nature14590openalex-snapshot

Single-cell chromatin accessibility reveals principles of regulatory variation

inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

inferredcites →https://doi.org/10.1038/ncb1403openalex-snapshot

Chromatin signatures of pluripotent cell lines

inferredcites →https://doi.org/10.1038/ncb2724openalex-snapshot

The expression of Sox17 identifies and regulates haemogenic endothelium

inferredcites →https://doi.org/10.1038/ncb3276openalex-snapshot

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1

inferredcites →https://doi.org/10.1038/ncomms8739openalex-snapshot

Repression of arterial genes in hemogenic endothelium is sufficient for haematopoietic fate acquisition

inferredcites →https://doi.org/10.1038/ng.3646openalex-snapshot

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

inferredcites →https://doi.org/10.1038/ng1966openalex-snapshot

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nprot.2009.97openalex-snapshot

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

inferredcites →https://doi.org/10.1038/nprot.2017.124openalex-snapshot

Chromatin-state discovery and genome annotation with ChromHMM

inferredcites →https://doi.org/10.1038/nrm.2016.127openalex-snapshot

A view of human haematopoietic development from the Petri dish

inferredcites →https://doi.org/10.1038/s41467-018-04134-7openalex-snapshot

NOTCH signaling specifies arterial-type definitive hemogenic endothelium from human pluripotent stem cells

inferredcites →https://doi.org/10.1038/s41598-018-28506-7openalex-snapshot

The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification

inferredcites →https://doi.org/10.1038/s41598-019-45839-zopenalex-snapshot

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

inferredcites →https://doi.org/10.1038/sj.embor.7401076openalex-snapshot

Artery and vein formation: a tug of war between different forces

inferredcites →https://doi.org/10.1073/pnas.1016071107openalex-snapshot

Histone H3K27ac separates active from poised enhancers and predicts developmental state

inferredcites →https://doi.org/10.1093/bioinformatics/bth349openalex-snapshot

Java Treeview—extensible visualization of microarray data

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/emboj/19.11.2465openalex-snapshot

Definitive hematopoietic stem cells first develop within the major arterial regions of the mouse embryo

inferredcites →https://doi.org/10.1093/nar/gkl822openalex-snapshot

VISTA Enhancer Browser--a database of tissue-specific human enhancers

inferredcites →https://doi.org/10.1101/163113openalex-snapshot

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

inferredcites →https://doi.org/10.1101/gad.253302.114openalex-snapshot

Inflammatory signaling regulates embryonic hematopoietic stem and progenitor cell production

inferredcites →https://doi.org/10.1101/gad.348738.121openalex-snapshot

Efficient hemogenic endothelial cell specification by RUNX1 is dependent on baseline chromatin accessibility of RUNX1-regulated TGFβ target genes

inferredcites →https://doi.org/10.1111/febs.15735openalex-snapshot

The transcriptional regulation of normal and malignant blood cell development

inferredcites →https://doi.org/10.1111/j.1742-4658.2011.08128.xopenalex-snapshot

Structure and function of active chromatin and DNase I hypersensitive sites

inferredcites →https://doi.org/10.1128/mcb.19.3.2032openalex-snapshot

Vascular Endothelial Growth Factor Activates Nuclear Factor of Activated T Cells in Human Endothelial Cells: a Role for Tissue Factor Gene Expression

inferredcites →https://doi.org/10.1146/annurev-biochem-011420-095916openalex-snapshot

Evaluating Enhancer Function and Transcription

inferredcites →https://doi.org/10.1182/blood-2007-07-100883openalex-snapshot

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer

inferredcites →https://doi.org/10.1182/blood-2010-08-302976openalex-snapshot

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

inferredcites →https://doi.org/10.1182/blood-2011-10-386094openalex-snapshot

GFI1 and GFI1B control the loss of endothelial identity of hemogenic endothelium during hematopoietic commitment

inferredcites →https://doi.org/10.1182/blood-2015-10-677393openalex-snapshot

Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model

inferredcites →https://doi.org/10.1182/blood.2020004801openalex-snapshot

Developmental trajectory of prehematopoietic stem cell formation from endothelium

inferredcites →https://doi.org/10.1182/blood.2020005780openalex-snapshot

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

inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1186/s13072-015-0009-5openalex-snapshot

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility

inferredcites →https://doi.org/10.1242/bio.20136296openalex-snapshot

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

inferredcites →https://doi.org/10.1242/dev.011767openalex-snapshot

The stepwise specification of embryonic stem cells to hematopoietic fate is driven by sequential exposure to Bmp4, activin A, bFGF and VEGF

inferredcites →https://doi.org/10.1242/dev.139857openalex-snapshot

Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate

inferredcites →https://doi.org/10.12688/f1000research.7334.1openalex-snapshot

HiCUP: pipeline for mapping and processing Hi-C data

inferredcites →https://doi.org/10.1371/journal.pcbi.1007337openalex-snapshot

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets

inferredcites →https://doi.org/10.15252/embj.2020105220openalex-snapshot

IL‐2/IL‐7‐inducible factors pioneer the path to T cell differentiation in advance of lineage‐defining factors

inferredcites →https://doi.org/10.26508/lsa.202000864openalex-snapshot

Different mutant RUNX1 oncoproteins program alternate haematopoietic differentiation trajectories

inferredcites →https://doi.org/10.3324/haematol.2012.070789openalex-snapshot

Dlk1 is a negative regulator of emerging hematopoietic stem and progenitor cells

inferredcites →https://doi.org/10.3929/ethz-b-000667478openalex-snapshot

Two new Later Stone Age sites from the Final Pleistocene in the Falémé Valley, eastern Senegal

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

inferred← citeshttps://doi.org/10.21037/sci-2023-011openalex-snapshot

Identification and characterization of enhancer elements controlling cell type-specific and signalling dependent chromatin programming during hematopoietic development

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