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Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

https://doi.org/10.1101/620260

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What this work says

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

inferredcites →https://doi.org/10.1002/j.1460-2075.1996.tb00949.xopenalex-snapshot

Targeted disruption of the PU.1 gene results in multiple hematopoietic abnormalities.

inferredcites →https://doi.org/10.1007/978-3-642-29627-7_30openalex-snapshot

Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer

inferredcites →https://doi.org/10.1016/j.cell.2013.02.029openalex-snapshot

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

inferredcites →https://doi.org/10.1016/j.cell.2015.07.048openalex-snapshot

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

inferredcites →https://doi.org/10.1016/j.cell.2015.08.001openalex-snapshot

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

inferredcites →https://doi.org/10.1016/j.cell.2015.12.031openalex-snapshot

LRRC8 Proteins Form Volume-Regulated Anion Channels that Sense Ionic Strength

inferredcites →https://doi.org/10.1016/j.cell.2016.03.041openalex-snapshot

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk

inferredcites →https://doi.org/10.1016/j.cell.2016.09.037openalex-snapshot

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

inferredcites →https://doi.org/10.1016/j.cell.2016.10.026openalex-snapshot

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

inferredcites →https://doi.org/10.1016/j.cell.2016.10.042openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.cell.2018.04.018openalex-snapshot

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

inferredcites →https://doi.org/10.1016/j.chom.2014.04.011openalex-snapshot

The Balancing Act of Neutrophils

inferredcites →https://doi.org/10.1016/j.clineuro.2018.04.008openalex-snapshot

CPEB4 regulates glioblastoma cell proliferation and predicts poor outcome of patients

inferredcites →https://doi.org/10.1016/j.devcel.2014.07.008openalex-snapshot

Cpeb4-Mediated Translational Regulatory Circuitry Controls Terminal Erythroid Differentiation

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.tibs.2007.04.004openalex-snapshot

CPEB: a life in translation

inferredcites →https://doi.org/10.1016/j.tig.2015.10.004openalex-snapshot

The Hierarchy of Transcriptional Activation: From Enhancer to Promoter

inferredcites →https://doi.org/10.1038/nature10730openalex-snapshot

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

inferredcites →https://doi.org/10.1038/nature12615openalex-snapshot

Effect of natural genetic variation on enhancer selection and function

inferredcites →https://doi.org/10.1038/nature13835openalex-snapshot

Genetic and epigenetic fine mapping of causal autoimmune disease variants

inferredcites →https://doi.org/10.1038/ng.2383openalex-snapshot

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

inferredcites →https://doi.org/10.1038/ng.2770openalex-snapshot

Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis

inferredcites →https://doi.org/10.1038/ng.3245openalex-snapshot

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

inferredcites →https://doi.org/10.1038/ng.3286openalex-snapshot

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

inferredcites →https://doi.org/10.1038/ng.3359openalex-snapshot

Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations

inferredcites →https://doi.org/10.1038/ng.3432openalex-snapshot

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

inferredcites →https://doi.org/10.1038/ng.3467openalex-snapshot

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

inferredcites →https://doi.org/10.1038/ng.3570openalex-snapshot

Detection and interpretation of shared genetic influences on 42 human traits

inferredcites →https://doi.org/10.1038/ng.3963openalex-snapshot

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements

inferredcites →https://doi.org/10.1038/ng.543openalex-snapshot

Multiple common variants for celiac disease influencing immune gene expression

inferredcites →https://doi.org/10.1038/nmeth.3582openalex-snapshot

WASP: allele-specific software for robust molecular quantitative trait locus discovery

inferredcites →https://doi.org/10.1038/nprot.2015.127openalex-snapshot

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell

inferredcites →https://doi.org/10.1038/nrg3891openalex-snapshot

The role of regulatory variation in complex traits and disease

inferredcites →https://doi.org/10.1038/s41467-017-01037-xopenalex-snapshot

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution

inferredcites →https://doi.org/10.1038/s41467-019-08940-5openalex-snapshot

Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression

inferredcites →https://doi.org/10.1038/s41586-018-0321-xopenalex-snapshot

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations

inferredcites →https://doi.org/10.1038/s41588-017-0034-3openalex-snapshot

Genetic determinants and epigenetic effects of pioneer-factor occupancy

inferredcites →https://doi.org/10.1038/s41588-018-0156-2openalex-snapshot

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

inferredcites →https://doi.org/10.1038/s41588-018-0278-6openalex-snapshot

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

inferredcites →https://doi.org/10.1038/s41588-018-0322-6openalex-snapshot

GARFIELD classifies disease-relevant genomic features through integration of functional annotations with association signals

inferredcites →https://doi.org/10.1038/srep22223openalex-snapshot

Significant impact of miRNA–target gene networks on genetics of human complex traits

inferredcites →https://doi.org/10.1073/pnas.1530509100openalex-snapshot

Statistical significance for genomewide studies

inferredcites →https://doi.org/10.1074/jbc.m513471200openalex-snapshot

Phospholipase Cϵ Suppresses Integrin Activation

inferredcites →https://doi.org/10.1084/jem.20041535openalex-snapshot

Dynamic regulation of PU.1 expression in multipotent hematopoietic progenitors

inferredcites →https://doi.org/10.1084/jem.20122220openalex-snapshot

Diverse novel functions of neutrophils in immunity, inflammation, and beyond

inferredcites →https://doi.org/10.1086/519795openalex-snapshot

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btv562openalex-snapshot

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot

deepTools2: a next generation web server for deep-sequencing data analysis

inferredcites →https://doi.org/10.1093/nar/gkx618openalex-snapshot

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

inferredcites →https://doi.org/10.1101/003905openalex-snapshot

LIMIX: genetic analysis of multiple traits

inferredcites →https://doi.org/10.1101/gad.13.11.1398openalex-snapshot

Direct interaction of hematopoietic transcription factors PU.1 and GATA-1: functional antagonism in erythroid cells

inferredcites →https://doi.org/10.1101/gad.176826.111openalex-snapshot

Pioneer transcription factors: establishing competence for gene expression

inferredcites →https://doi.org/10.1101/gad.293910.116openalex-snapshot

Comprehensive characterization of neutrophil genome topology

inferredcites →https://doi.org/10.1101/gr.131201.111openalex-snapshot

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

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.155192.113openalex-snapshot

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

inferredcites →https://doi.org/10.1101/gr.185272.114openalex-snapshot

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

inferredcites →https://doi.org/10.1111/j.1471-4159.2006.04399.xopenalex-snapshot

Phospholipase C‐related inactive protein is implicated in the constitutive internalization of GABAAreceptors mediated by clathrin and AP2 adaptor complex

inferredcites →https://doi.org/10.1111/j.1582-4934.2009.00757.xopenalex-snapshot

PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis

inferredcites →https://doi.org/10.1126/science.1183621openalex-snapshot

Variation in Transcription Factor Binding Among Humans

inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

inferredcites →https://doi.org/10.1126/science.1242429openalex-snapshot

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

inferredcites →https://doi.org/10.1126/science.1242463openalex-snapshot

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

inferredcites →https://doi.org/10.1126/science.1242510openalex-snapshot

Extensive Variation in Chromatin States Across Humans

inferredcites →https://doi.org/10.1182/blood-2002-03-0835openalex-snapshot

The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow

inferredcites →https://doi.org/10.1182/blood-2016-07-730135openalex-snapshot

Reduced PU.1 expression underlies aberrant neutrophil maturation and function in β-thalassemia mice and patients

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/gb-2013-14-11-r124openalex-snapshot

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

inferredcites →https://doi.org/10.1186/s13059-016-0992-2openalex-snapshot

CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

inferredcites →https://doi.org/10.1186/s13059-017-1156-8openalex-snapshot

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

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.pgen.1002599openalex-snapshot

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

inferredcites →https://doi.org/10.1371/journal.pgen.1004383openalex-snapshot

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

inferredcites →https://doi.org/10.1371/journal.pgen.1004798openalex-snapshot

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

inferredcites →https://doi.org/10.7554/elife.21926openalex-snapshot

Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2020.01.15.907436openalex-snapshot

Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for twelve immune-mediated diseases

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