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Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response

https://doi.org/10.1101/102392
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What this work says

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

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ggplot2: Elegant Graphics for Data Analysis
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Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples
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An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants
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A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling
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Pattern Recognition Receptors and Inflammation
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Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling
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Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration
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Latent Enhancers Activated by Stimulation in Differentiated Cells
inferredcites →https://doi.org/10.1016/j.cell.2014.08.009openalex-snapshot
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
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.2016.09.025openalex-snapshot
Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens
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.celrep.2014.11.011openalex-snapshot
A Distal Locus Element Mediates IFN-γ Priming of Lipopolysaccharide-Stimulated TNF Gene Expression
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Cross-regulation of Signaling Pathways by Interferon-γ: Implications for Immune Responses and Autoimmune Diseases
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Synergistic Activation of Inflammatory Cytokine Genes by Interferon-γ-Induced Chromatin Remodeling and Toll-like Receptor Signaling
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.2015.02.013openalex-snapshot
Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates
inferredcites →https://doi.org/10.1016/j.tig.2011.07.002openalex-snapshot
Pioneer factors: directing transcriptional regulators within the chromatin environment
inferredcites →https://doi.org/10.1038/cr.2016.1openalex-snapshot
The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin
inferredcites →https://doi.org/10.1038/nature10808openalex-snapshot
DNase I sensitivity QTLs are a major determinant of human expression variation
inferredcites →https://doi.org/10.1038/nature12615openalex-snapshot
Effect of natural genetic variation on enhancer selection and function
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A high-resolution map of the three-dimensional chromatin interactome in human cells
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Genetics of rheumatoid arthritis contributes to biology and drug discovery
inferredcites →https://doi.org/10.1038/nature13417openalex-snapshot
Enhancer loops appear stable during development and are associated with paused polymerase
inferredcites →https://doi.org/10.1038/nature13595openalex-snapshot
Biological insights from 108 schizophrenia-associated genetic loci
inferredcites →https://doi.org/10.1038/nature13835openalex-snapshot
Genetic and epigenetic fine mapping of causal autoimmune disease variants
inferredcites →https://doi.org/10.1038/nature22403openalex-snapshot
Common genetic variation drives molecular heterogeneity in human iPSCs
inferredcites →https://doi.org/10.1038/nbt.2798openalex-snapshot
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape
inferredcites →https://doi.org/10.1038/ncomms6236openalex-snapshot
Characterizing the genetic basis of innate immune response in TLR4-activated human monocytes
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.2802openalex-snapshot
Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease
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.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.3434openalex-snapshot
Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus
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.3538openalex-snapshot
Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets
inferredcites →https://doi.org/10.1038/ng.3606openalex-snapshot
Hierarchy within the mammary STAT5-driven Wap super-enhancer
inferredcites →https://doi.org/10.1038/ng.3760openalex-snapshot
Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease
inferredcites →https://doi.org/10.1038/ng.3795openalex-snapshot
Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types
inferredcites →https://doi.org/10.1038/ng.998openalex-snapshot
Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease
inferredcites →https://doi.org/10.1038/nm.4139openalex-snapshot
Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi
inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
inferredcites →https://doi.org/10.1038/nprot.2011.457openalex-snapshot
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
inferredcites →https://doi.org/10.1038/s41467-017-00366-1openalex-snapshot
Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations
inferredcites →https://doi.org/10.1038/srep12524openalex-snapshot
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription
inferredcites →https://doi.org/10.1073/pnas.1017214108openalex-snapshot
PU.1 and C/EBPα synergistically program distinct response to NF-κB activation through establishing monocyte specific enhancers
inferredcites →https://doi.org/10.1073/pnas.1115761109openalex-snapshot
Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
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/bioinformatics/btr064openalex-snapshot
FIMO: scanning for occurrences of a given motif
inferredcites →https://doi.org/10.1093/bioinformatics/bts606openalex-snapshot
A high-performance computing toolset for relatedness and principal component analysis of SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt343openalex-snapshot
GAT: a simulation framework for testing the association of genomic intervals
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btt730openalex-snapshot
CrossMap: a versatile tool for coordinate conversion between genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btv722openalex-snapshot
Fast and efficient QTL mapper for thousands of molecular phenotypes
inferredcites →https://doi.org/10.1093/bioinformatics/btw024openalex-snapshot
TFBSTools: an R/bioconductor package for transcription factor binding site analysis
inferredcites →https://doi.org/10.1093/biostatistics/kxr054openalex-snapshot
Removing technical variability in RNA-seq data using conditional quantile normalization
inferredcites →https://doi.org/10.1093/hmg/ddv077openalex-snapshot
Integration of disease association and eQTL data using a Bayesian colocalisation approach highlights six candidate causal genes in immune-mediated diseases
inferredcites →https://doi.org/10.1093/hmg/ddx043openalex-snapshot
Conditional eQTL analysis reveals allelic heterogeneity of gene expression
inferredcites →https://doi.org/10.1093/nar/gkw1283openalex-snapshot
Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements
inferredcites →https://doi.org/10.1093/nar/gkw199openalex-snapshot
g:Profiler—a web server for functional interpretation of gene lists (2016 update)
inferredcites →https://doi.org/10.1101/085738openalex-snapshot
GARFIELD - GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
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.1246949openalex-snapshot
Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression
inferredcites →https://doi.org/10.1126/science.1246980openalex-snapshot
Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells
inferredcites →https://doi.org/10.1186/1471-2105-15-182openalex-snapshot
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
inferredcites →https://doi.org/10.1186/1471-2164-14-892openalex-snapshot
RNA-Seq optimization with eQTL gold standards
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-2014-15-2-r29openalex-snapshot
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-015-0762-6openalex-snapshot
Tools and best practices for data processing in allelic expression analysis
inferredcites →https://doi.org/10.1189/jlb.0603252openalex-snapshot
Interferon-γ: an overview of signals, mechanisms and functions
inferredcites →https://doi.org/10.1371/journal.pgen.1003270openalex-snapshot
ImmunoChip Study Implicates Antigen Presentation to T Cells in Narcolepsy
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.1005061openalex-snapshot
Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates PPAP2B Expression through Altered C/EBP-Beta Binding
inferredcites →https://doi.org/10.1371/journal.pgen.1005111openalex-snapshot
Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection
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Efficient, Long Term Production of Monocyte-Derived Macrophages from Human Pluripotent Stem Cells under Partly-Defined and Fully-Defined Conditions
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Mfuzz: A software package for soft clustering of microarray data

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.3322367openalex-extracted
Dissecting Regulatory Mechanisms Underlying Noncoding GWAS SNPs on 20 Autoimmune Disease
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An Expanded View of Complex Traits: From Polygenic to Omnigenic
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Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations
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Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma
inferred← citeshttps://doi.org/10.1073/pnas.1714765115openalex-snapshot
Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges
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Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques
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Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions
inferred← citeshttps://doi.org/10.1101/192922openalex-snapshot
Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis -regulatory element use in human islets
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Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation
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Impact of regulatory variation across human iPSCs and differentiated cells
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Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
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Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions
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