Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

GWAS for autoimmune Addison’s disease identifies multiple risk loci and highlights AIRE in disease susceptibility

(2021) Daniel Eriksson et al.   Nature Communications

Single-cell transcriptional profiling of human thymic stroma uncovers novel cellular heterogeneity in the thymic medulla

(2021) Jhoanne L. Bautista et al.   Nature Communications

Modular, efficient and constant-memory single-cell RNA-seq preprocessing

(2021) Páll Melsted et al.   NATURE BIOTECHNOLOGY

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

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

(2021) Caroline Kaiser et al.   IMMUNOLOGICAL REVIEWS

Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on superenhancers

(2021) Kushagra Bansal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A cell atlas of human thymic development defines T cell repertoire formation

(2020) Jong-Eun Park et al.   SCIENCE

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

Diversity in medullary thymic epithelial cells controls the activity and availability of iNKT cells

(2020) Beth Lucas et al.   Nature Communications

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

(2020) Jeanette Baran-Gale et al.   eLife

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells

(2020) Kristen L Wells et al.   eLife

Sox8 is essential for M cell maturation to accelerate IgA response at the early stage after weaning in mice

(2019) Shunsuke Kimura et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A reinforcing HNF4–SMAD4 feed-forward module stabilizes enterocyte identity

(2019) Lei Chen et al.   NATURE GENETICS

Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling

(2019) Michael P. Meers et al.   Epigenetics & Chromatin

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

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

(2019) Fatima Dhalla et al.   EMBO JOURNAL

Rapid chromatin repression by Aire provides precise control of immune tolerance

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

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

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development

(2018) Adam E. Handel et al.   Frontiers in Immunology

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Fox transcription factors: from development to disease

(2016) Maria L. Golson et al.   DEVELOPMENT

Two Ancient Gene Families Are Critical for Maintenance of the Mammalian Skin Barrier in Postnatal Life

(2016) Michael Cangkrama et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Tolerance is established in polyclonal CD4+ T cells by distinct mechanisms, according to self-peptide expression patterns

(2016) Deepali Malhotra et al.   NATURE IMMUNOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity

(2016) Simon Joost et al.   Cell Systems

Alternative NF-κB signaling regulates mTEC differentiation from podoplanin-expressing precursors in the cortico-medullary junction

(2015) Lucas Onder 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

More tricks with tetramers: a practical guide to staining T cells with peptide-MHC multimers

(2015) Garry Dolton et al.   IMMUNOLOGY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Aire controls gene expression in the thymic epithelium with ordered stochasticity

(2015) Matthew Meredith et al.   NATURE IMMUNOLOGY

The deacetylase Sirt1 is an essential regulator of Aire-mediated induction of central immunological tolerance

(2015) Anna Chuprin 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

Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance

(2015) S. Yang et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging

(2014) Nicolas Renier et al.   CELL

Cholinergic epithelial cell with chemosensory traits in murine thymic medulla

(2014) Alexandra Regina Panneck et al.   CELL AND TISSUE RESEARCH

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

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao 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

Lineage Tracing and Cell Ablation Identify a Post-Aire-Expressing Thymic Epithelial Cell Population

(2013) Todd C. Metzger et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Spi-B is critical for plasmacytoid dendritic cell function and development

(2012) I. Sasaki et al.   BLOOD

The Ets transcription factor Spi-B is essential for the differentiation of intestinal microfold cells

(2012) Takashi Kanaya et al.   NATURE IMMUNOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The human AIRE gene at chromosome 21q22 is a genetic determinant for the predisposition to rheumatoid arthritis in Japanese population

(2011) Chikashi Terao et al.   HUMAN MOLECULAR GENETICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Aire's Partners in the Molecular Control of Immunological Tolerance

(2010) Jakub Abramson et al.   CELL

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

Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis

(2010) Xiangdong Liu et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) M. D. Robinson et al.   BIOINFORMATICS

Neonatal tolerance revisited: a perinatal window for Aire control of autoimmunity

(2009) Mireia Guerau-de-Arellano et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region

(2009) Jeffrey C Barrett et al.   NATURE GENETICS

Tracking epitope-specific T cells

(2009) James J Moon et al.   Nature Protocols

Sox8 is a critical regulator of adult Sertoli cell function and male fertility

(2008) Moira K. O'Bryan et al.   DEVELOPMENTAL BIOLOGY

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY