AIRE in context: Leveraging chromatin plasticity to trigger ectopic gene expression*

Distinct kinetic mechanisms of H3K4 methylation catalyzed by MLL3 and MLL4 core complexes

(2021) Yongxin Zheng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mechanistic dissection of dominant AIRE mutations in mouse models reveals AIRE autoregulation

(2021) Yael Goldfarb et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions

(2020) Kanishk Jain et al.   Epigenetics & Chromatin

Evaluating Enhancer Function and Transcription

(2020) Andrew Field et al.   Annual Review of Biochemistry

Dual functions of Aire CARD multimerization in the transcriptional regulation of T cell tolerance

(2020) Yu-San Huoh et al.   Nature Communications

Chd4 choreographs self-antigen expression for central immune tolerance

(2020) Yoshihiko Tomofuji et al.   NATURE IMMUNOLOGY

Pioneer Transcription Factors Initiating Gene Network Changes

(2020) Kenneth S. Zaret   Annual Review of Genetics

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

(2020) Liguo Zhang et al.   GENOME RESEARCH

Aire-expressing ILC3-like cells in the lymph node display potent APC features

(2019) Tomoyoshi Yamano et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Understanding histone H3 lysine 36 methylation and its deregulation in disease

(2019) Jie Li et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Phase separation of 53 BP 1 determines liquid‐like behavior of DNA repair compartments

(2019) Sinan Kilic et al.   EMBO JOURNAL

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells

(2019) Fatima Dhalla et al.   EMBO JOURNAL

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Rapid chromatin repression by Aire provides precise control of immune tolerance

(2018) Andrew S. Koh et al.   NATURE IMMUNOLOGY

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

(2018) Shasha Chong et al.   SCIENCE

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells

(2018) Chamutal Bornstein et al.   NATURE

Thymic tuft cells promote an IL-4-enriched medulla and shape thymocyte development

(2018) Corey N. Miller et al.   NATURE

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

(2018) Seychelle M. Vos et al.   NATURE

Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes

(2018) Caroline Bouchard et al.   Cell Reports

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

Transcription and DNA Damage: Holding Hands or Crossing Swords?

(2017) Giuseppina D'Alessandro et al.   JOURNAL OF MOLECULAR BIOLOGY

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability

(2017) Ryan Rickels et al.   NATURE GENETICS

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Physiological functions of programmed DNA breaks in signal-induced transcription

(2017) Janusz Puc et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Understanding nucleosome dynamics and their links to gene expression and DNA replication

(2017) William K. M. Lai et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Histone chaperone networks shaping chromatin function

(2017) Colin M. Hammond et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

(2016) Laura Baranello et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

AIRE-mutations and autoimmune disease

(2016) Øyvind Bruserud et al.   CURRENT OPINION IN IMMUNOLOGY

The NF-κB family: Key players during embryonic development and HSC emergence

(2016) Raquel Espín-Palazón et al.   EXPERIMENTAL HEMATOLOGY

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

(2016) Manuel Beltran et al.   GENOME RESEARCH

Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin

(2016) Benjamin Z Stanton et al.   NATURE GENETICS

Dynamics of BAF–Polycomb complex opposition on heterochromatin in normal and oncogenic states

(2016) Cigall Kadoch et al.   NATURE GENETICS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Ligand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity

(2015) Janusz Puc et al.   CELL

Fezf2 Orchestrates a Thymic Program of Self-Antigen Expression for Immune Tolerance

(2015) Hiroyuki Takaba et al.   CELL

A highly conserved NF-κB-responsive enhancer is critical for thymic expression of Aire in mice

(2015) Uku Haljasorg et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Dominant Mutations in the Autoimmune Regulator AIRE Are Associated with Common Organ-Specific Autoimmune Diseases

(2015) Bergithe E. Oftedal et al.   IMMUNITY

Identification of a novel cis-regulatory element essential for immune tolerance

(2015) Taylor N. LaFlam et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Ectopic Aire Expression in the Thymic Cortex Reveals Inherent Properties of Aire as a Tolerogenic Factor within the Medulla

(2015) Hitoshi Nishijima et al.   JOURNAL OF IMMUNOLOGY

Aire controls gene expression in the thymic epithelium with ordered stochasticity

(2015) Matthew Meredith et al.   NATURE IMMUNOLOGY

Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells

(2015) Philip Brennecke et al.   NATURE IMMUNOLOGY

Brd4 bridges the transcriptional regulators, Aire and P-TEFb, to promote elongation of peripheral-tissue antigen transcripts in thymic stromal cells

(2015) Hideyuki Yoshida et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Cancer Tissue Procoagulant Mechanisms and the Hypercoagulable State of Patients with Cancer

(2015) Francesca Schieppati et al.   SEMINARS IN THROMBOSIS AND HEMOSTASIS

Transcriptional elongation requires DNA break-induced signalling

(2015) Heeyoun Bunch et al.   Nature Communications

Homeodomain-Interacting Protein Kinase 2, a Novel Autoimmune Regulator Interaction Partner, Modulates Promiscuous Gene Expression in Medullary Thymic Epithelial Cells

(2015) Kristin Rattay et al.   JOURNAL OF IMMUNOLOGY

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

MANAGEMENT OF ENDOCRINE DISEASE: A clinical update on tumor-induced hypoglycemia

(2014) Pedro Iglesias et al.   EUROPEAN JOURNAL OF ENDOCRINOLOGY

Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

(2014) Stephen N. Sansom et al.   GENOME RESEARCH

A Specific Anti-Aire Antibody Reveals Aire Expression Is Restricted to Medullary Thymic Epithelial Cells and Not Expressed in Periphery

(2014) F.-X. Hubert et al.   JOURNAL OF IMMUNOLOGY

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotolerance

(2014) Michael Waterfield et al.   NATURE IMMUNOLOGY

Histone core modifications regulating nucleosome structure and dynamics

(2014) Peter Tessarz et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Brd4 activates P-TEFb for RNA polymerase II CTD phosphorylation

(2014) Friederike Itzen et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Warren A. Whyte et al.   CELL

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

(2013) D. Hu et al.   MOLECULAR AND CELLULAR BIOLOGY

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

Deterministic direct reprogramming of somatic cells to pluripotency

(2013) Yoach Rais et al.   NATURE

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells

(2013) Bruno Di Stefano et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

BAF complexes facilitate decatenation of DNA by topoisomerase IIα

(2013) Emily C. Dykhuizen et al.   NATURE

Differential roles for MBD2 and MBD3 at methylated CpG islands, active promoters and binding to exon sequences

(2013) Katharina Günther et al.   NUCLEIC ACIDS RESEARCH

Overlapping gene coexpression patterns in human medullary thymic epithelial cells generate self-antigen diversity

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

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

A quantitative atlas of histone modification signatures from human cancer cells

(2013) Gary LeRoy et al.   Epigenetics & Chromatin

RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

Aire mediates thymic expression and tolerance of pancreatic antigens via an unconventional transcriptional mechanism

(2012) Dina Danso-Abeam et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Trans-tail regulation of MLL4-catalyzed H3K4 methylation by H4R3 symmetric dimethylation is mediated by a tandem PHD of MLL4

(2012) S. S. Dhar et al.   GENES & DEVELOPMENT

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

New insights into nucleosome and chromatin structure: an ordered state or a disordered affair?

(2012) Karolin Luger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons

(2011) Samuele Marro et al.   Cell Stem Cell

Two-pronged Binding with Bromodomain-containing Protein 4 Liberates Positive Transcription Elongation Factor b from Inactive Ribonucleoprotein Complexes

(2011) Sebastian Schröder et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MicroRNA-mediated conversion of human fibroblasts to neurons

(2011) Andrew S. Yoo et al.   NATURE

Patient mutation in AIRE disrupts P-TEFb binding and target gene transcription

(2011) Kristina Žumer et al.   NUCLEIC ACIDS RESEARCH

Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells

(2011) M. Giraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aire's Partners in the Molecular Control of Immunological Tolerance

(2010) Jakub Abramson et al.   CELL

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis

(2010) A. El Hage et al.   GENES & DEVELOPMENT

Chromatin remodelling during development

(2010) Lena Ho et al.   NATURE

The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation

(2010) Sohail Malik et al.   NATURE REVIEWS GENETICS

RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation

(2010) Iván D'Orso et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells

(2010) L.-O. Tykocinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global relevance of Aire binding to hypomethylated lysine-4 of histone-3

(2010) A. S. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Determination of enriched histone modifications in non-genic portions of the human genome

(2009) Jeffrey A Rosenfeld et al.   BMC GENOMICS

Differentiation between Thyroidal and Ectopic Calcitonin Secretion in patients with Coincidental Thyroid Nodules and Pancreatic Tumors – A Report of Two Cases

(2009) R. Schneider et al.   EXPERIMENTAL AND CLINICAL ENDOCRINOLOGY & DIABETES

AIRE activated tissue specific genes have histone modifications associated with inactive chromatin

(2009) Tõnis Org et al.   HUMAN MOLECULAR GENETICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation

(2009) Francesca Chignola et al.   NUCLEIC ACIDS RESEARCH

Structure and Site-Specific Recognition of Histone H3 by the PHD Finger of Human Autoimmune Regulator

(2009) Suvobrata Chakravarty et al.   STRUCTURE

The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression

(2008) Tõnis Org et al.   EMBO REPORTS

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

The Cytokine RANKL Produced by Positively Selected Thymocytes Fosters Medullary Thymic Epithelial Cells that Express Autoimmune Regulator

(2008) Yu Hikosaka et al.   IMMUNITY

The Tumor Necrosis Factor Family Receptors RANK and CD40 Cooperatively Establish the Thymic Medullary Microenvironment and Self-Tolerance

(2008) Taishin Akiyama et al.   IMMUNITY

Evolutionarily conserved and divergent regions of the Autoimmune Regulator (Aire) gene: a comparative analysis

(2008) Mark Saltis et al.   IMMUNOGENETICS

Mechanisms of an autoimmunity syndrome in mice caused by a dominant mutation in Aire

(2008) Maureen A. Su et al.   JOURNAL OF CLINICAL INVESTIGATION

Aire controls the differentiation program of thymic epithelial cells in the medulla for the establishment of self-tolerance

(2008) Masashi Yano et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcriptional impact of Aire varies with cell type

(2008) M. Guerau-de-Arellano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variable immunological self: Genetic variation and nongenetic noise in Aire-regulated transcription

(2008) E. S. Venanzi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ectopic expression of peripheral-tissue antigens in the thymic epithelium: Probabilistic, monoallelic, misinitiated

(2008) J. Villasenor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity

(2008) A. S. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promiscuous gene expression patterns in single medullary thymic epithelial cells argue for a stochastic mechanism

(2008) J. Derbinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells

(2008) J. M. Gardner et al.   SCIENCE

DNA-PK contributes to the phosphorylation of AIRE: Importance in transcriptional activity

(2007) Ingrid Liiv et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH