Decoding the non-coding genome: elucidating genetic risk outside the coding genome

Combined Whole Methylome and Genomewide Association Study ImplicatesCNTN4in Alcohol Use

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Polymorphisms in a Putative Enhancer at the 10q21.2 Breast Cancer Risk Locus Regulate NRBF2 Expression

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Age-Dependent Levels of 5-Methyl-, 5-Hydroxymethyl-, and 5-Formylcytosine in Human and Mouse Brain Tissues

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Non-CG Methylation in the Human Genome

(2015) Yupeng He et al.   Annual Review of Genomics and Human Genetics

A structure-based Multiple-Instance Learning approach to predicting in vitro transcription factor-DNA interaction

(2015) Zhen Gao et al.   BMC GENOMICS

Generation of neuropeptidergic hypothalamic neurons from human pluripotent stem cells

(2015) F. T. Merkle et al.   DEVELOPMENT

Enhancer-associated RNAs as therapeutic targets

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Methylomic trajectories across human fetal brain development

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Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases

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Biological factors underlying sex differences in neurological disorders

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Behavioral, cognitive, and adaptive development in infants with autism spectrum disorder in the first 2 years of life

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Noncoding RNAs and neurobehavioral mechanisms in psychiatric disease

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Characterization of bipolar disorder patient-specific induced pluripotent stem cells from a family reveals neurodevelopmental and mRNA expression abnormalities

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Integrative analysis of 111 reference human epigenomes

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Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

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Human body epigenome maps reveal noncanonical DNA methylation variation

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

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Rett syndrome: a complex disorder with simple roots

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The selection and function of cell type-specific enhancers

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Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

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Quantitative modeling of transcription factor binding specificities using DNA shape

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Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

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MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome

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The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Advances in Reprogramming-Based Study of Neurologic Disorders

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Genome-wide assays that identify and quantify modified cytosines in human disease studies

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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

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An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs

(2014) René Luijk et al.   BIOINFORMATICS

Integrative modeling of multiple genomic data from different types of genetic association studies

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PD_NGSAtlas: a reference database combining next-generation sequencing epigenomic and transcriptomic data for psychiatric disorders

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Evolving insights on how cytosine methylation affects protein-DNA binding

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Modeling a Genetic Risk for Schizophrenia in iPSCs and Mice Reveals Neural Stem Cell Deficits Associated with Adherens Junctions and Polarity

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Genomic patterns and context specific interpretation of DNA methylation

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Identification of schizophrenia-associated loci by combining DNA methylation and gene expression data from whole blood

(2014) Kristel R van Eijk et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

TET enzymes and DNA hydroxymethylation in neural development and function — How critical are they?

(2014) Mafalda Santiago et al.   GENOMICS

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From development to diseases: The role of 5hmC in brain

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Refinement of schizophrenia GWAS loci using methylome-wide association data

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Brain-specific noncoding RNAs are likely to originate in repeats and may play a role in up-regulating genes in cis

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Integrating the roles of long and small non-coding RNA in brain function and disease

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Genome-wide association study in obsessive-compulsive disorder: results from the OCGAS

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Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia

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An atlas of active enhancers across human cell types and tissues

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Synaptic dysregulation in a human iPS cell model of mental disorders

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Genetic and epigenetic fine mapping of causal autoimmune disease variants

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Biological insights from 108 schizophrenia-associated genetic loci

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Combinatorial analysis of developmental cues efficiently converts human pluripotent stem cells into multiple neuronal subtypes

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Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

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Predicting the human epigenome from DNA motifs

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Genetic variability in the regulation of gene expression in ten regions of the human brain

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Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

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X chromosome regulation: diverse patterns in development, tissues and disease

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Advances in the profiling of DNA modifications: cytosine methylation and beyond

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CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells

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Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation

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Genome-wide association study reveals two new risk loci for bipolar disorder

(2014) Thomas W. Mühleisen et al.   Nature Communications

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

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Enhancing Induced Pluripotent Stem Cell Models of Schizophrenia

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Transcripts involved in calcium signaling and telencephalic neuronal fate are altered in induced pluripotent stem cells from bipolar disorder patients

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Label-free, live optical imaging of reprogrammed bipolar disorder patient-derived cells reveals a functional correlate of lithium responsiveness

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Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients

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Mapping of Immune-Mediated Disease Genes

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The Genome in Three Dimensions: A New Frontier in Human Brain Research

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Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers

(2013) Ulf Andersson Ørom et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

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Super-Enhancers in the Control of Cell Identity and Disease

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Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

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Long Noncoding RNAs: Cellular Address Codes in Development and Disease

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Functional Maturation of hPSC-Derived Forebrain Interneurons Requires an Extended Timeline and Mimics Human Neural Development

(2013) Cory R. Nicholas et al.   Cell Stem Cell

SNPs located at CpG sites modulate genome-epigenome interaction

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Methylomics of gene expression in human monocytes

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Epigenetic Mechanisms may Underlie the Aetiology of Sex Differences in Mental Health Risk and Resilience

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Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis

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Abnormal neuronal differentiation and mitochondrial dysfunction in hair follicle-derived induced pluripotent stem cells of schizophrenia patients

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Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

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Evaluation of methods for modeling transcription factor sequence specificity

(2013) Matthew T Weirauch et al.   NATURE BIOTECHNOLOGY

Identification of multiple risk variants for ankylosing spondylitis through high-density genotyping of immune-related loci

(2013) Adrian Cortes et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

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Genome engineering using the CRISPR-Cas9 system

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Pyramidal Neurons Derived from Human Pluripotent Stem Cells Integrate Efficiently into Mouse Brain Circuits In Vivo

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Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA

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Predicting Cell Types and Genetic Variations Contributing to Disease by Combining GWAS and Epigenetic Data

(2013) Anna Gerasimova et al.   PLoS One

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

(2013) S. C. J. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

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Sex differences in the structural connectome of the human brain

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Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

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

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Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Widespread sex differences in gene expression and splicing in the adult human brain

(2013) Daniah Trabzuni et al.   Nature Communications

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

(2013) Maria A. Hahn et al.   Cell Reports

Combined Analysis of Genome-wide Association Studies for Crohn Disease and Psoriasis Identifies Seven Shared Susceptibility Loci

(2012) David Ellinghaus et al.   AMERICAN JOURNAL OF HUMAN GENETICS

In vitro and in vivo analysis of a JAK inhibitor in rheumatoid arthritis

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Methods for Identifying Higher-Order Chromatin Structure

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Association Between Common Variants Near the Melanocortin 4 Receptor Gene and Severe Antipsychotic Drug–Induced Weight Gain

(2012) Anil K. Malhotra   ARCHIVES OF GENERAL PSYCHIATRY

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

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5-Hydroxymethylcytosine – the elusive epigenetic mark in mammalian DNA

(2012) Edita Kriukienė et al.   CHEMICAL SOCIETY REVIEWS

Activity-Dependent Human Brain Coding/Noncoding Gene Regulatory Networks

(2012) L. Lipovich et al.   GENETICS

HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter

(2012) M. Visser et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Hormonal Programming Across the Lifespan

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Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum

(2012) Tao Wang et al.   HUMAN MOLECULAR GENETICS

Individual common variants exert weak effects on the risk for autism spectrum disorders

(2012) Richard Anney et al.   HUMAN MOLECULAR GENETICS

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

Genome-wide association study of obsessive-compulsive disorder

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Genome-wide association study of Tourette's syndrome

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Replication of bipolar disorder susceptibility alleles and identification of two novel genome-wide significant associations in a new bipolar disorder case–control sample

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Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants

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Genome-wide significant associations in schizophrenia to ITIH3/4, CACNA1C and SDCCAG8, and extensive replication of associations reported by the Schizophrenia PGC

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A mega-analysis of genome-wide association studies for major depressive disorder

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The long-range interaction landscape of gene promoters

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(2012) Sarah Djebali et al.   NATURE

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

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Library-free methylation sequencing with bisulfite padlock probes

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Robust 4C-seq data analysis to screen for regulatory DNA interactions

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Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip

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Tofacitinib, an Oral Janus Kinase Inhibitor, in Active Ulcerative Colitis

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Improved predictions of transcription factor binding sites using physicochemical features of DNA

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Epigenetic Studies of Schizophrenia: Progress, Predicaments, and Promises for the Future

(2012) Emma Dempster et al.   SCHIZOPHRENIA BULLETIN

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Epigenetics of major psychosis: progress, problems and perspectives

(2012) Viviane Labrie et al.   TRENDS IN GENETICS

Brain Expression Genome-Wide Association Study (eGWAS) Identifies Human Disease-Associated Variants

(2012) Fanggeng Zou et al.   PLoS Genetics

Genome-wide association study in German patients with attention deficit/hyperactivity disorder

(2011) Anke Hinney et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Investigating the Contribution of Common Genetic Variants to the Risk and Pathogenesis of ADHD

(2011) Evangelia Stergiakouli et al.   AMERICAN JOURNAL OF PSYCHIATRY

Genetic Variation in the KIAA0319 5′ Region as a Possible Contributor to Dyslexia

(2011) Adrienne Elbert et al.   BEHAVIOR GENETICS

Neurodevelopmental hypothesis of schizophrenia

(2011) Michael J. Owen et al.   BRITISH JOURNAL OF PSYCHIATRY

Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes

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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes

(2011) C. E. Nestor et al.   GENOME RESEARCH

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder

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Development of Patient-Specific Neurons in Schizophrenia Using Induced Pluripotent Stem Cells

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Case-Control Genome-Wide Association Study of Attention-Deficit/Hyperactivity Disorder

(2011) Benjamin M. Neale et al.   JOURNAL OF THE AMERICAN ACADEMY OF CHILD AND ADOLESCENT PSYCHIATRY

Meta-Analysis of Genome-Wide Association Studies of Attention-Deficit/Hyperactivity Disorder

(2011) Benjamin M. Neale et al.   JOURNAL OF THE AMERICAN ACADEMY OF CHILD AND ADOLESCENT PSYCHIATRY

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

(2011) Carlo Colantuoni et al.   NATURE

Modelling schizophrenia using human induced pluripotent stem cells

(2011) Kristen J. Brennand et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Psoriasis: from bed to bench and back

(2011) Ken Garber   NATURE BIOTECHNOLOGY

Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder

(2011) Josephine Elia et al.   NATURE GENETICS

Genome-wide association study identifies five new schizophrenia loci

(2011)   NATURE GENETICS

Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4

(2011)   NATURE GENETICS

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

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Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Imaging brain development: The adolescent brain

(2011) Sarah-Jayne Blakemore   NEUROIMAGE

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

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Lessons from genome-wide association studies findings in Alzheimer's disease

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Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Why Are Autism Spectrum Conditions More Prevalent in Males?

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On Genome-wide Association Studies for Family-Based Designs: An Integrative Analysis Approach Combining Ascertained Family Samples with Unselected Controls

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No evidence that rare coding variants in ZNF804A confer risk of schizophrenia

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Quantification of the Sixth DNA Base Hydroxymethylcytosine in the Brain

(2010) Martin Münzel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Disease-specific, neurosphere-derived cells as models for brain disorders

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The genetics of sex differences in brain and behavior

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Multiple enhancers located in a 1-Mb region upstream of POU3F4 promote expression during inner ear development and may be required for hearing

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Widespread transcription at neuronal activity-regulated enhancers

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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

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The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells Determined by Methylation-Enriched Bisulfite Sequencing

(2010) Jeong-Hyeon Choi et al.   PLoS One

A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder

(2010) Ke-Sheng Wang et al.   SCHIZOPHRENIA RESEARCH

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes

(2010) Hua Zhong et al.   PLoS Genetics

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Duplications Involving a Conserved Regulatory Element Downstream of BMP2 Are Associated with Brachydactyly Type A2

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Allele-Specific Chromatin Remodeling in the ZPBP2/GSDMB/ORMDL3 Locus Associated with the Risk of Asthma and Autoimmune Disease

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Association of reading disabilities with regions marked by acetylated H3 histones in KIAA0319

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Genetics of psychosis; insights from views across the genome

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Genome-wide association studies in ADHD

(2009) Barbara Franke et al.   HUMAN GENETICS

Transcriptome analysis of male–female differences in prefrontal cortical development

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An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

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Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

A rapid simple approach to quantify chromosome conformation capture

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Genome-wide association scan of attention deficit hyperactivity disorder

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Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations

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Disorders of Childhood and Adolescence: Gender and Psychopathology

(2008) Carolyn Zahn-Waxler et al.   Annual Review of Clinical Psychology

Early androgen influences on human neural and behavioural development

(2008) Melissa Hines   EARLY HUMAN DEVELOPMENT

A variant in the sonic hedgehog regulatory sequence (ZRS) is associated with triphalangeal thumb and deregulates expression in the developing limb

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Collaborative genome-wide association analysis supports a role for ANK3 and CACNA1C in bipolar disorder

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The chromatin-remodeling enzyme BRG1 coordinates CIITA induction through many interdependent distal enhancers

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