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Chromatin accessibility profiling uncovers genetic- and T2D disease state-associated changes in cis -regulatory element use in human islets

https://doi.org/10.1101/192922

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What this work says

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

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Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

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Latent Enhancers Activated by Stimulation in Differentiated Cells

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Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

inferredcites →https://doi.org/10.1016/j.cmet.2010.09.012openalex-snapshot

Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci

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.molcel.2014.08.024openalex-snapshot

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

inferredcites →https://doi.org/10.1016/j.tig.2017.01.010openalex-snapshot

Genomics of Islet (Dys)function and Type 2 Diabetes

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/nature14248openalex-snapshot

Integrative analysis of 111 reference human epigenomes

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A global reference for human genetic variation

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The genetic architecture of type 2 diabetes

inferredcites →https://doi.org/10.1038/ng.2870openalex-snapshot

Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants

inferredcites →https://doi.org/10.1038/ng.288openalex-snapshot

Common variant in MTNR1B associated with increased risk of type 2 diabetes and impaired early insulin secretion

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.3656openalex-snapshot

Next-generation genotype imputation service and methods

inferredcites →https://doi.org/10.1038/ng.3679openalex-snapshot

Reference-based phasing using the Haplotype Reference Consortium panel

inferredcites →https://doi.org/10.1038/ng.530openalex-snapshot

A map of open chromatin in human pancreatic islets

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

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3326openalex-snapshot

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

inferredcites →https://doi.org/10.1038/nn.4632openalex-snapshot

An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome

inferredcites →https://doi.org/10.1073/pnas.1317023110openalex-snapshot

Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

inferredcites →https://doi.org/10.1073/pnas.1402665111openalex-snapshot

Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism

inferredcites →https://doi.org/10.1073/pnas.1621192114openalex-snapshot

Genetic regulatory signatures underlying islet gene expression and type 2 diabetes

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Bach1 Competes with Nrf2 Leading to Negative Regulation of the Antioxidant Response Element (ARE)-mediated NAD(P)H:Quinone Oxidoreductase 1 Gene Expression and Induction in Response to Antioxidants

inferredcites →https://doi.org/10.1084/jem.20170416openalex-snapshot

The chromatin accessibility signature of human immune aging stems from CD8+ T cells

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/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot

edgeR : a Bioconductor package for differential expression analysis of digital gene expression data

inferredcites →https://doi.org/10.1093/bioinformatics/bts034openalex-snapshot

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btv201openalex-snapshot

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

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/hmg/ddv264openalex-snapshot

Recent advances in understanding the genetic architecture of type 2 diabetes

inferredcites →https://doi.org/10.1093/nar/gkv1340openalex-snapshot

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

inferredcites →https://doi.org/10.1101/102392openalex-snapshot

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

inferredcites →https://doi.org/10.1101/142927openalex-snapshot

Brain xQTL map: Integrating the genetic architecture of the human brain transcriptome and epigenome

inferredcites →https://doi.org/10.1101/gr.073817.107openalex-snapshot

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

inferredcites →https://doi.org/10.1101/gr.112623.110openalex-snapshot

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

inferredcites →https://doi.org/10.1126/science.1184655openalex-snapshot

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

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.aad9417openalex-snapshot

RNA splicing is a primary link between genetic variation and disease

inferredcites →https://doi.org/10.1146/annurev-pharmtox-011112-140320openalex-snapshot

Role of Nrf2 in Oxidative Stress and Toxicity

inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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

Model-based Analysis of ChIP-Seq (MACS)

inferredcites →https://doi.org/10.1371/journal.pgen.1005694openalex-snapshot

Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors

inferredcites →https://doi.org/10.2337/db17-0464openalex-snapshot

A Type 2 Diabetes–Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus

What points at this work

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

inferred← citeshttps://doi.org/10.1038/s41588-021-00823-0openalex-snapshot

Single-cell chromatin accessibility identifies pancreatic islet cell type– and state-specific regulatory programs of diabetes risk

inferred← citeshttps://doi.org/10.1093/nar/gky1117openalex-snapshot

BiFET: sequencing Bi as-free transcription factor F ootprint E nrichment T est

inferred← citeshttps://doi.org/10.1101/399139openalex-snapshot

EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and function

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