Global transcriptome analysis and enhancer landscape of human primary T follicular helper and T effector lymphocytes

Helper T-Cell Differentiation in Graft-Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation

(2014) Jianing Fu et al.   ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

(2014) C. Schmidl et al.   BLOOD

How I treat the peripheral T-cell lymphomas

(2014) A. J. Moskowitz et al.   BLOOD

Gene expression signatures delineate biological and prognostic subgroups in peripheral T-cell lymphoma

(2014) J. Iqbal et al.   BLOOD

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma

(2014) Hae Yong Yoo et al.   NATURE GENETICS

Somatic RHOA mutation in angioimmunoblastic T cell lymphoma

(2014) Mamiko Sakata-Yanagimoto et al.   NATURE GENETICS

Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas

(2014) Teresa Palomero et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Mapping of Immune-Mediated Disease Genes

(2013) Isis Ricaño-Ponce et al.   Annual Review of Genomics and Human Genetics

Applications of high-throughput DNA sequencing to benign hematology

(2013) V. G. Sankaran et al.   BLOOD

A targeted mutational landscape of angioimmunoblastic T-cell lymphoma

(2013) O. Odejide et al.   BLOOD

Dynamic regulation of epigenomic landscapes during hematopoiesis

(2013) Brian J Abraham et al.   BMC GENOMICS

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

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Genetic Variants Regulating Immune Cell Levels in Health and Disease

(2013) Valeria Orrù et al.   CELL

The unique features of follicular T cell subsets

(2013) Julie Tellier et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Dynamic regulation of Bcl6 in follicular helper CD4 T (Tfh) cells

(2013) Youn Soo Choi et al.   CURRENT OPINION IN IMMUNOLOGY

New effector functions and regulatory mechanisms of BCL6 in normal and malignant lymphocytes

(2013) Karen L Bunting et al.   CURRENT OPINION IN IMMUNOLOGY

Global Chromatin State Analysis Reveals Lineage-Specific Enhancers during the Initiation of Human T helper 1 and T helper 2 Cell Polarization

(2013) R. David Hawkins et al.   IMMUNITY

Helper T-cell identity and evolution of differential transcriptomes and epigenomes

(2013) Golnaz Vahedi et al.   IMMUNOLOGICAL REVIEWS

T-cell subsets in the germinal center

(2013) Roybel R. Ramiscal et al.   IMMUNOLOGICAL REVIEWS

Regulatory mechanisms that control T-follicular helper and T-helper 1 cell flexibility

(2013) Amy S Weinmann   IMMUNOLOGY AND CELL BIOLOGY

Human T follicular helper (Tfh) cells and disease

(2013) Cindy S Ma et al.   IMMUNOLOGY AND CELL BIOLOGY

Identification of Biologically Relevant Enhancers in Human Erythroid Cells

(2013) Mack Y. Su et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

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

Follicular Peripheral T-cell Lymphoma Expands the Spectrum of Classical Hodgkin Lymphoma Mimics

(2012) Julien Moroch et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

Primary Cutaneous Follicular Helper T-cell Lymphoma

(2012) Maxime Battistella et al.   ARCHIVES OF DERMATOLOGY

Recurrent TET2 mutations in peripheral T-cell lymphomas correlate with TFH-like features and adverse clinical parameters

(2012) F. Lemonnier et al.   BLOOD

IDH2 mutations are frequent in angioimmunoblastic T-cell lymphoma

(2012) R. A. Cairns et al.   BLOOD

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

Enhancers: emerging roles in cell fate specification

(2012) Chin-Tong Ong et al.   EMBO REPORTS

Linking disease associations with regulatory information in the human genome

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

The 1-1-1 fallacy

(2012) Shane Crotty   IMMUNOLOGICAL REVIEWS

T-follicular helper cell differentiation and the co-option of this pathway by non-helper cells

(2012) Michelle A. Linterman et al.   IMMUNOLOGICAL REVIEWS

The Chromatin Fingerprint of Gene Enhancer Elements

(2012) Gabriel E. Zentner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An RNA-Independent Linkage of Noncoding Transcription to Long-Range Enhancer Function

(2012) E. J. Yoo et al.   MOLECULAR AND CELLULAR BIOLOGY

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

Molecular mechanisms that control the expression and activity of Bcl-6 in TH1 cells to regulate flexibility with a TFH-like gene profile

(2012) Kenneth J Oestreich et al.   NATURE IMMUNOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Follicular Helper CD4 T Cells (TFH)

(2011) Shane Crotty   Annual Review of Immunology

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Long non-coding RNAs and enhancers

(2011) Ulf Andersson Ørom et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Enhancer and promoter interactions—long distance calls

(2011) Ivan Krivega et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Human Blood CXCR5+CD4+ T Cells Are Counterparts of T Follicular Cells and Contain Specific Subsets that Differentially Support Antibody Secretion

(2011) Rimpei Morita et al.   IMMUNITY

Functional and Epigenetic Studies Reveal Multistep Differentiation and Plasticity of In Vitro-Generated and In Vivo-Derived Follicular T Helper Cells

(2011) Kristina T. Lu et al.   IMMUNITY

CXCR5 Expressing Human Central Memory CD4 T Cells and Their Relevance for Humoral Immune Responses

(2011) N. Chevalier et al.   JOURNAL OF IMMUNOLOGY

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

(2011) Jason Ernst et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions

(2011) Yeonseok Chung et al.   NATURE MEDICINE

Foxp3+ follicular regulatory T cells control the germinal center response

(2011) Michelle A Linterman et al.   NATURE MEDICINE

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Follicular helper T cells: implications in neoplastic hematopathology

(2011) Philippe Gaulard et al.   SEMINARS IN DIAGNOSTIC PATHOLOGY

Noncoding RNAs and enhancers: complications of a long-distance relationship

(2011) Ulf Andersson Ørom et al.   TRENDS IN GENETICS

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Multiple checkpoints keep follicular helper T cells under control to prevent autoimmunity

(2010) Di Yu et al.   Cellular & Molecular Immunology

Linc-ing Long Noncoding RNAs and Enhancer Function

(2010) John S. Mattick   DEVELOPMENTAL CELL

A novel subset of T-helper cells: follicular T-helper cells and their markers

(2010) C. Laurent et al.   HAEMATOLOGICA

IL-21 acts directly on B cells to regulate Bcl-6 expression and germinal center responses

(2010) Michelle A. Linterman et al.   JOURNAL OF EXPERIMENTAL MEDICINE

IL-21 regulates germinal center B cell differentiation and proliferation through a B cell–intrinsic mechanism

(2010) Dimitra Zotos et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

PD-1 regulates germinal center B cell survival and the formation and affinity of long-lived plasma cells

(2010) Kim L Good-Jacobson et al.   NATURE IMMUNOLOGY

Peripheral T-cell Lymphomas With a Follicular Growth Pattern are Derived From Follicular Helper T Cells (TFH) and may Show Overlapping Features With Angioimmunoblastic T-cell Lymphomas

(2009) Yenlin Huang et al.   AMERICAN JOURNAL OF SURGICAL PATHOLOGY

A spectrum of gene regulatory phenomena at mammalian β-globin gene lociThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

(2009) George Fromm et al.   Biochemistry and Cell Biology

Molecular signatures to improve diagnosis in peripheral T-cell lymphoma and prognostication in angioimmunoblastic T-cell lymphoma

(2009) J. Iqbal et al.   BLOOD

Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila

(2009) M. J. Borok et al.   DEVELOPMENT

Secondary enhancers synergise with primary enhancers to guarantee fine-tuned muscle gene expression

(2009) Lucia Guerrero et al.   DEVELOPMENTAL BIOLOGY

Enhancers: The abundance and function of regulatory sequences beyond promoters

(2009) Michael Bulger et al.   DEVELOPMENTAL BIOLOGY

Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells

(2009) J. Xu et al.   GENES & DEVELOPMENT

Paused Pol II captures enhancer activity and acts as a potent insulator

(2009) L. J. Core et al.   GENES & DEVELOPMENT

Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells

(2009) Gang Wei et al.   IMMUNITY

The Transcriptional Repressor Bcl-6 Directs T Follicular Helper Cell Lineage Commitment

(2009) Di Yu et al.   IMMUNITY

Follicular helper T cells are required for systemic autoimmunity

(2009) Michelle A. Linterman et al.   JOURNAL OF EXPERIMENTAL MEDICINE

T follicular helper cells differentiate from Th2 cells in response to helminth antigens

(2009) Arielle Glatman Zaretsky et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Chromatin Architecture and Transcription Factor Binding Regulate Expression of Erythrocyte Membrane Protein Genes

(2009) L. A. Steiner et al.   MOLECULAR AND CELLULAR BIOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Revisiting the follicular helper T cell paradigm

(2009) Bernard Malissen   NATURE IMMUNOLOGY

Cytokine-secreting follicular T cells shape the antibody repertoire

(2009) R Lee Reinhardt et al.   NATURE IMMUNOLOGY

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bcl6 and Blimp-1 Are Reciprocal and Antagonistic Regulators of T Follicular Helper Cell Differentiation

(2009) R. J. Johnston et al.   SCIENCE

Bcl6 Mediates the Development of T Follicular Helper Cells

(2009) R. I. Nurieva et al.   SCIENCE

T Follicular Helper (TFH) Cells in Normal and Dysregulated Immune Responses

(2008) Cecile King et al.   Annual Review of Immunology

Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus

(2008) O. Maksimenko et al.   MOLECULAR AND CELLULAR BIOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

The costimulatory molecule ICOS regulates the expression of c-Maf and IL-21 in the development of follicular T helper cells and TH-17 cells

(2008) Aurelie T Bauquet et al.   NATURE IMMUNOLOGY

Detecting shared pathogenesis from the shared genetics of immune-related diseases

(2008) Alexandra Zhernakova et al.   NATURE REVIEWS GENETICS

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY