Genome-wide census of ATF4 binding sites and functional profiling of trait-associated genetic variants overlapping ATF4 binding motifs

A stay of execution: ATF4 regulation and potential outcomes for the integrated stress response

(2023) Graham Neill et al.   Frontiers in Molecular Neuroscience

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

(2022) Miguel Martinez-Ara et al.   MOLECULAR CELL

A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression

(2022) Ioannis I. Verginadis et al.   NATURE CELL BIOLOGY

Compatibility rules of human enhancer and promoter sequences

(2022) Drew T. Bergman et al.   NATURE

Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome

(2021) Denis A. Baird et al.   PLoS Genetics

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

LocusZoom.js: interactive and embeddable visualization of genetic association study results

(2021) Andrew P Boughton et al.   BIOINFORMATICS

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

FIVEx: an interactive eQTL browser across public datasets

(2021) Alan Kwong et al.   BIOINFORMATICS

A functional genomics pipeline identifies pleiotropy and cross-tissue effects within obesity-associated GWAS loci

(2021) Amelia C. Joslin et al.   Nature Communications

Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation

(2021) Shubham Khetan et al.   Nature Communications

A single-cell atlas of chromatin accessibility in the human genome

(2021) Kai Zhang et al.   CELL

Biology of Activating Transcription Factor 4 (ATF4) and Its Role in Skeletal Muscle Atrophy

(2021) Scott M Ebert et al.   JOURNAL OF NUTRITION

An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

(2021) Edward Mountjoy et al.   NATURE GENETICS

A cross-population atlas of genetic associations for 220 human phenotypes

(2021) Saori Sakaue et al.   NATURE GENETICS

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

HRI-regulated transcription factor ATF4 activates BCL11A transcription to silence fetal hemoglobin expression

(2020) Peng Huang et al.   BLOOD

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma

(2020) Jiyeon Choi et al.   Nature Communications

Occupancy maps of 208 chromatin-associated proteins in one human cell type

(2020) E. Christopher Partridge et al.   NATURE

A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals

(2020) Tiit Örd et al.   PLoS Genetics

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

(2020) Ming-Huei Chen et al.   CELL

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics

(2020) Maya Ghoussaini et al.   NUCLEIC ACIDS RESEARCH

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Genome-wide analysis identifies novel susceptibility loci for myocardial infarction

(2020) Jaana A Hartiala et al.   EUROPEAN HEART JOURNAL

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

ATF4 couples MYC-dependent translational activity to bioenergetic demands during tumour progression

(2019) Feven Tameire et al.   NATURE CELL BIOLOGY

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

(2019) Jason C. Klein et al.   Nature Communications

Comparative genetic architectures of schizophrenia in East Asian and European populations

(2019) Max Lam et al.   NATURE GENETICS

Genomic Relationships, Novel Loci, and Pleiotropic Mechanisms across Eight Psychiatric Disorders

(2019) Phil H. Lee et al.   CELL

TRIB3 limits FGF21 induction during in vitro and in vivo nutrient deficiencies by inhibiting C/EBP–ATF response elements in the Fgf21 promoter

(2018) Tiit Örd et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Chemical stresses fail to mimic the unfolded protein response resulting from luminal load with unfolded polypeptides

(2018) Timothy J. Bergmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Activating Transcription Factor 4 (ATF4) regulates neuronal activity by controlling GABABR trafficking

(2018) Carlo Corona et al.   JOURNAL OF NEUROSCIENCE

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

(2018) James J. Lee et al.   NATURE GENETICS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

(2018) Gail Davies et al.   Nature Communications

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Genome-wide association analysis identifies novel blood pressure loci and offers biological insights into cardiovascular risk

(2017) Helen R Warren et al.   NATURE GENETICS

Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

(2017) José A Rodríguez-Martínez et al.   eLife

TRIB3 increases cell resistance to arsenite toxicity by limiting the expression of the glutathione-degrading enzyme CHAC1

(2016) Daima Örd et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

The integrated stress response

(2016) Karolina Pakos‐Zebrucka et al.   EMBO REPORTS

Transcription factor ATF4 directs basal and stress-induced gene expression in the unfolded protein response and cholesterol metabolism in the liver

(2016) Michael E. Fusakio et al.   MOLECULAR BIOLOGY OF THE CELL

DNA-damage response gene GADD45A induces differentiation in hematopoietic stem cells without inhibiting cell cycle or survival

(2016) Susanne Wingert et al.   STEM CELLS

TRIB3 enhances cell viability during glucose deprivation in HEK293-derived cells by upregulating IGFBP2, a novel nutrient deficiency survival factor

(2015) Tiit Örd et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

(2015) Daniel Savic et al.   GENOME RESEARCH

The gene expression signature of anagrelide provides an insight into its mechanism of action and uncovers new regulators of megakaryopoiesis

(2015) M. Ahluwalia et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Specific Downregulation of Hippocampal ATF4 Reveals a Necessary Role in Synaptic Plasticity and Memory

(2015) Silvia Pasini et al.   Cell Reports

ATF4 licenses C/EBPβ activity in human mesenchymal stem cells primed for adipogenesis

(2015) Daniel M Cohen et al.   eLife

A forward genetic screen reveals novel independent regulators of ULBP1, an activating ligand for natural killer cells

(2015) Benjamin G Gowen et al.   eLife

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

(2014) Alfonso Buil et al.   NATURE GENETICS

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Massively Parallel Reporter Assays in Cultured Mammalian Cells

(2014) Alexandre Melnikov et al.   Jove-Journal of Visualized Experiments

Gadd45a regulates hematopoietic stem cell stress responses in mice

(2013) Y. Chen et al.   BLOOD

Macrophage lipoprotein lipase modulates the development of atherosclerosis but not adiposity

(2013) Manabu Takahashi et al.   JOURNAL OF LIPID RESEARCH

DISC1–ATF4 transcriptional repression complex: dual regulation of the cAMP-PDE4 cascade by DISC1

(2013) T Soda et al.   MOLECULAR PSYCHIATRY

ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death

(2013) Jaeseok Han et al.   NATURE CELL BIOLOGY

The UPR in atherosclerosis

(2013) Alex X. Zhou et al.   Seminars in Immunopathology

Heme-regulated eIF2  kinase activated Atf4 signaling pathway in oxidative stress and erythropoiesis

(2012) R. N. V. S. Suragani et al.   BLOOD

Trib3 is regulated by IL-3 and affects bone marrow-derived mast cell survival and function

(2012) Tiit Örd et al.   CELLULAR IMMUNOLOGY

Targeting the ATF4 pathway in cancer therapy

(2012) Dean C Singleton et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Brain-Specific Disruption of the eIF2α Kinase PERK Decreases ATF4 Expression and Impairs Behavioral Flexibility

(2012) Mimi A. Trinh et al.   Cell Reports

Role of ATF4 in regulation of autophagy and resistance to drugs and hypoxia

(2011) Tomasz Rzymski et al.   CELL CYCLE

The eIF2 kinase PERK and the integrated stress response facilitate activation of ATF6 during endoplasmic reticulum stress

(2011) Brian F. Teske et al.   MOLECULAR BIOLOGY OF THE CELL

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The GCN2-ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation

(2010) Jiangbin Ye et al.   EMBO JOURNAL

The transcription factor Znf219 regulates chondrocyte differentiation by assembling a transcription factory with Sox9

(2010) Y. Takigawa et al.   JOURNAL OF CELL SCIENCE

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

(2010) Sven Heinz et al.   MOLECULAR CELL

Atf4 Regulates Obesity, Glucose Homeostasis, and Energy Expenditure

(2009) J. Seo et al.   DIABETES

Elevated ATF4 Expression, in the Absence of Other Signals, Is Sufficient for Transcriptional Induction via CCAAT Enhancer-binding Protein-activating Transcription Factor Response Elements

(2009) Jixiu Shan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Activating transcription factor 4

(2007) Kurosh Ameri et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY