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Multi-tissue analysis reveals short tandem repeats as ubiquitous regulators of gene expression and complex traits

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What this work says

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

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Tandem repeat sequence variation as causative Cis-eQTLs for protein-coding gene expression variation: The case of CSTB

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RNA-Binding Protein Misregulation in Microsatellite Expansion Disorders

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Functional IFNG polymorphism in intron 1 in association with an increased risk to promote sporadic breast cancer

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De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder

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Human RFT1 Deficiency Leads to a Disorder of N-Linked Glycosylation

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Expansion of Intronic GGCCTG Hexanucleotide Repeat in NOP56 Causes SCA36, a Type of Spinocerebellar Ataxia Accompanied by Motor Neuron Involvement

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Beyond GWASs: Illuminating the Dark Road from Association to Function

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Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

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Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates

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10 Years of GWAS Discovery: Biology, Function, and Translation

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Characterization of a Human-Specific Tandem Repeat Associated with Bipolar Disorder and Schizophrenia

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A One-Penny Imputed Genome from Next-Generation Reference Panels

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An Atomic Model of the Interferon-β Enhanceosome

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Genomic Nucleosome Organization Reconstituted with Pure Proteins

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

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Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

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Co-optation of Tandem DNA Repeats for the Maintenance of Mesenchymal Identity

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Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

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

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Antisense Oligonucleotides Reduce RNA Foci in Spinocerebellar Ataxia 36 Patient iPSCs

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Poly(dA:dT) tracts: major determinants of nucleosome organization

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Mediator and human disease

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Tandem repeat polymorphisms: modulators of disease susceptibility and candidates for ‘missing heritability’

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The overdue promise of short tandem repeat variation for heritability

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Shortened microsatellite d(CA)21 sequence down‐regulates promoter activity of matrix metalloproteinase 9 gene

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Dodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy

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Pharmacogenetic association between ALOX5 promoter genotype and the response to anti-asthma treatment

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Expandable DNA repeats and human disease

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An integrated encyclopedia of DNA elements in the human genome

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Transcriptome and genome sequencing uncovers functional variation in humans

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Biological insights from 108 schizophrenia-associated genetic loci

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A global reference for human genetic variation

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Schizophrenia risk from complex variation of complement component 4

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Fine-mapping inflammatory bowel disease loci to single-variant resolution

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Genetic effects on gene expression across human tissues

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Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast

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A direct characterization of human mutation based on microsatellites

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

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Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite

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A gene-based association method for mapping traits using reference transcriptome data

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Abundant contribution of short tandem repeats to gene expression variation in humans

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Integrative approaches for large-scale transcriptome-wide association studies

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Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels

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Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

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G-quadruplex structures mark human regulatory chromatin

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The impact of structural variation on human gene expression

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Principal components analysis corrects for stratification in genome-wide association studies

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A polymorphic microsatellite that mediates induction of PIG3 by p53

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Genome-wide profiling of heritable and de novo STR variations

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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

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Tandem repeats mediating genetic plasticity in health and disease

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Nucleosome positioning and gene regulation: advances through genomics

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DNA secondary structures: stability and function of G-quadruplex structures

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DNA methylation dynamics in health and disease

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A reference haplotype panel for genome-wide imputation of short tandem repeats

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Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

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Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

inferredcites →https://doi.org/10.1073/pnas.0400182101openalex-snapshot

A variable dinucleotide repeat in the CFTR gene contributes to phenotype diversity by forming RNA secondary structures that alter splicing

inferredcites →https://doi.org/10.1073/pnas.0510310103openalex-snapshot

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

inferredcites →https://doi.org/10.1073/pnas.0909740107openalex-snapshot

R loops stimulate genetic instability of CTG·CAG repeats

inferredcites →https://doi.org/10.1073/pnas.0912629107openalex-snapshot

Rate, molecular spectrum, and consequences of human mutation

inferredcites →https://doi.org/10.1073/pnas.121176998openalex-snapshot

A polymorphic dinucleotide repeat in the rat nucleolin gene forms Z-DNA and inhibits promoter activity

inferredcites →https://doi.org/10.1073/pnas.1410569111openalex-snapshot

Protein−DNA binding in the absence of specific base-pair recognition

inferredcites →https://doi.org/10.1073/pnas.82.24.8419openalex-snapshot

Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast.

inferredcites →https://doi.org/10.1073/pnas.96.4.1504openalex-snapshot

Triplet repeats form secondary structures that escape DNA repair in yeast

inferredcites →https://doi.org/10.1074/jbc.274.19.13176openalex-snapshot

Modulation of Epidermal Growth Factor Receptor Gene Transcription by a Polymorphic Dinucleotide Repeat in Intron 1

inferredcites →https://doi.org/10.1074/jbc.m806514200openalex-snapshot

MED19 and MED26 Are Synergistic Functional Targets of the RE1 Silencing Transcription Factor in Epigenetic Silencing of Neuronal Gene Expression

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

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BEDTools: a flexible suite of utilities for comparing genomic features

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Toward better understanding of artifacts in variant calling from high-coverage samples

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Genome-wide association meta-analysis for total serum bilirubin levels

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Functional analysis of 5-lipoxygenase promoter repeat variants

inferredcites →https://doi.org/10.1093/hmg/ddr538openalex-snapshot

Differential effects of a polyalanine tract expansion in Arx on neural development and gene expression

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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/ddy271openalex-snapshot

Meta-analysis of genome-wide association studies for height and body mass index in ∼700000 individuals of European ancestry

inferredcites →https://doi.org/10.1093/nar/28.21.4083openalex-snapshot

Poly(dAmiddle dotdT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo

inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot

dbSNP: the NCBI database of genetic variation

inferredcites →https://doi.org/10.1093/nar/6.5.1805openalex-snapshot

Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones

inferredcites →https://doi.org/10.1093/nar/gkg595openalex-snapshot

Mfold web server for nucleic acid folding and hybridization prediction

inferredcites →https://doi.org/10.1093/nar/gki553openalex-snapshot

Highly prevalent putative quadruplex sequence motifs in human DNA

inferredcites →https://doi.org/10.1093/nar/gkl706openalex-snapshot

Alu elements as regulators of gene expression

inferredcites →https://doi.org/10.1093/nar/gks557openalex-snapshot

Crystallographic characterization of CCG repeats

inferredcites →https://doi.org/10.1093/nar/gkt685openalex-snapshot

Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins

inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

inferredcites →https://doi.org/10.1093/nar/gkw219openalex-snapshot

Polymorphic tandem repeats within gene promoters act as modifiers of gene expression and DNA methylation in humans

inferredcites →https://doi.org/10.1101/gad.1200804openalex-snapshot

Intracellular transcription of G-rich DNAs induces formation of G-loops, novel structures containing G4 DNA

inferredcites →https://doi.org/10.1101/gad.2037511openalex-snapshot

CpG islands and the regulation of transcription

inferredcites →https://doi.org/10.1101/gr.169243.113openalex-snapshot

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

inferredcites →https://doi.org/10.1101/gr.177774.114openalex-snapshot

The landscape of human STR variation

inferredcites →https://doi.org/10.1101/gr.229102openalex-snapshot

The Human Genome Browser at UCSC

inferredcites →https://doi.org/10.1111/cea.12076openalex-snapshot

ALOX 5 Polymorphism associates with increased leukotriene production and reduced lung function and asthma control in children with poorly controlled asthma

inferredcites →https://doi.org/10.1126/science.1170097openalex-snapshot

Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability

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Resistance to malaria through structural variation of red blood cell invasion receptors

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Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

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Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human

inferredcites →https://doi.org/10.1186/s13059-018-1519-9openalex-snapshot

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

inferredcites →https://doi.org/10.1194/jlr.p012864openalex-snapshot

ALOX5 gene variants affect eicosanoid production and response to fish oil supplementation

inferredcites →https://doi.org/10.1371/journal.pgen.0020190openalex-snapshot

Population Structure and Eigenanalysis

inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

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GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

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Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies

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The Use of Genome-Wide eQTL Associations in Lymphoblastoid Cell Lines to Identify Novel Genetic Pathways Involved in Complex Traits

inferredcites →https://doi.org/10.1371/journal.pone.0054710openalex-snapshot

Microsatellite Tandem Repeats Are Abundant in Human Promoters and Are Associated with Regulatory Elements

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Identifying Causal Variants at Loci with Multiple Signals of Association

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Integration of Enhancer-Promoter Interactions with GWAS Summary Results Identifies Novel Schizophrenia-Associated Genes and Pathways

inferredcites →https://doi.org/10.25080/majora-92bf1922-011openalex-snapshot

Statsmodels: Econometric and Statistical Modeling with Python

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Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions

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The C9ORF72 GGGGCC expansion forms RNA G-quadruplex inclusions and sequesters hnRNP H to disrupt splicing in ALS brains

What points at this work

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

inferred← citeshttps://doi.org/10.1093/molbev/msz118openalex-snapshot

Intraspecific Variation in Microsatellite Mutation Profiles in Daphnia magna

inferred← citeshttps://doi.org/10.1097/jcp.0000000000001215openalex-snapshot

Special Article: Translational Science Update. Pharmacological Implications of Emerging Schizophrenia Genetics

inferred← citeshttps://doi.org/10.1101/634261openalex-snapshot

Evidence of transcription at polyT short tandem repeats

inferred← citeshttps://doi.org/10.1534/g3.119.400771openalex-snapshot

Challenges and Approaches to Genotyping Repetitive DNA

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