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TET enzymes augment AID expression via 5hmC modifications at the Aicda superenhancer

https://doi.org/10.1101/438531
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/bs.ai.2016.11.002openalex-snapshot
Molecular Mechanisms of Somatic Hypermutation and Class Switch Recombination
inferredcites →https://doi.org/10.1016/j.ccr.2011.06.003openalex-snapshot
TET2 Inactivation Results in Pleiotropic Hematopoietic Abnormalities in Mouse and Is a Recurrent Event during Human Lymphomagenesis
inferredcites →https://doi.org/10.1016/j.cell.2013.01.007openalex-snapshot
Mechanisms of Programmed DNA Lesions and Genomic Instability in the Immune System
inferredcites →https://doi.org/10.1016/j.cell.2013.11.039openalex-snapshot
Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation
inferredcites →https://doi.org/10.1016/j.cell.2014.11.014openalex-snapshot
Convergent Transcription at Intragenic Super-Enhancers Targets AID-Initiated Genomic Instability
inferredcites →https://doi.org/10.1016/j.cell.2017.09.027openalex-snapshot
Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma
inferredcites →https://doi.org/10.1016/j.gde.2017.07.011openalex-snapshot
TET proteins in natural and induced differentiation
inferredcites →https://doi.org/10.1016/j.immuni.2006.07.009openalex-snapshot
Graded Expression of Interferon Regulatory Factor-4 Coordinates Isotype Switching with Plasma Cell Differentiation
inferredcites →https://doi.org/10.1016/j.it.2015.07.003openalex-snapshot
AID targeting: old mysteries and new challenges
inferredcites →https://doi.org/10.1016/j.jaci.2007.08.008openalex-snapshot
B-cell receptor cross-linking delays activation-induced cytidine deaminase induction and inhibits class-switch recombination to IgE
inferredcites →https://doi.org/10.1016/j.molcel.2010.05.004openalex-snapshot
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
inferredcites →https://doi.org/10.1016/j.molcel.2013.01.038openalex-snapshot
Modification of Enhancer Chromatin: What, How, and Why?
inferredcites →https://doi.org/10.1016/j.molcel.2017.07.013openalex-snapshot
Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation
inferredcites →https://doi.org/10.1016/j.molcel.2017.11.026openalex-snapshot
AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection
inferredcites →https://doi.org/10.1016/s0092-8674(00)00078-7openalex-snapshot
Class Switch Recombination and Hypermutation Require Activation-Induced Cytidine Deaminase (AID), a Potential RNA Editing Enzyme
inferredcites →https://doi.org/10.1016/s1074-7613(00)80605-6openalex-snapshot
Helper T Cell Differentiation Is Controlled by the Cell Cycle
inferredcites →https://doi.org/10.1038/nature10102openalex-snapshot
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature11530openalex-snapshot
BATF–JUN is critical for IRF4-mediated transcription in T cells
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature21406openalex-snapshot
Phosphatidylinositol 3-kinase δ blockade increases genomic instability in B cells
inferredcites →https://doi.org/10.1038/ng.3522openalex-snapshot
Active DNA demethylation at enhancers during the vertebrate phylotypic period
inferredcites →https://doi.org/10.1038/ni.1829openalex-snapshot
B cell–specific and stimulation-responsive enhancers derepress Aicda by overcoming the effects of silencers
inferredcites →https://doi.org/10.1038/ni.2037openalex-snapshot
The transcription factor BATF controls the global regulators of class-switch recombination in both B cells and T cells
inferredcites →https://doi.org/10.1038/ni.3630openalex-snapshot
TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells
inferredcites →https://doi.org/10.1038/ni1357openalex-snapshot
Transcription factor IRF4 controls plasma cell differentiation and class-switch recombination
inferredcites →https://doi.org/10.1038/nmeth.2688openalex-snapshot
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot
HISAT: a fast spliced aligner with low memory requirements
inferredcites →https://doi.org/10.1038/nprot.2012.103openalex-snapshot
The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine
inferredcites →https://doi.org/10.1038/nprot.2012.104openalex-snapshot
The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine
inferredcites →https://doi.org/10.1038/nprot.2014.006openalex-snapshot
Full-length RNA-seq from single cells using Smart-seq2
inferredcites →https://doi.org/10.1038/nrg.2017.33openalex-snapshot
TET-mediated active DNA demethylation: mechanism, function and beyond
inferredcites →https://doi.org/10.1038/nri.2016.2openalex-snapshot
Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity
inferredcites →https://doi.org/10.1038/nri3470openalex-snapshot
Specificity through cooperation: BATF–IRF interactions control immune-regulatory networks
inferredcites →https://doi.org/10.1038/nri3804openalex-snapshot
Dynamics of B cells in germinal centres
inferredcites →https://doi.org/10.1038/nrm3589openalex-snapshot
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription
inferredcites →https://doi.org/10.1038/s41467-017-01605-1openalex-snapshot
Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB
inferredcites →https://doi.org/10.1042/bst20130028openalex-snapshot
ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection
inferredcites →https://doi.org/10.1056/nejmoa1801445openalex-snapshot
Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma
inferredcites →https://doi.org/10.1073/pnas.0502779102openalex-snapshot
Expression of activation-induced cytidine deaminase is regulated by cell division, providing a mechanistic basis for division-linked class switch recombination
inferredcites →https://doi.org/10.1073/pnas.1112317108openalex-snapshot
Ten-Eleven-Translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice
inferredcites →https://doi.org/10.1073/pnas.1412327111openalex-snapshot
Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation
inferredcites →https://doi.org/10.1073/pnas.1604365113openalex-snapshot
Tissue-specific DNA demethylation is required for proper B-cell differentiation and function
inferredcites →https://doi.org/10.1074/jbc.r115.692020openalex-snapshot
Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300
inferredcites →https://doi.org/10.1084/jem.20051450openalex-snapshot
Regulation of the germinal center gene program by interferon (IFN) regulatory factor 8/IFN consensus sequence-binding protein
inferredcites →https://doi.org/10.1084/jem.20061952openalex-snapshot
Regulation of AID expression in the immune response
inferredcites →https://doi.org/10.1084/jem.20081007openalex-snapshot
AID expression levels determine the extent of cMyc oncogenic translocations and the incidence of B cell tumor development
inferredcites →https://doi.org/10.1084/jem.20091548openalex-snapshot
Batf coordinates multiple aspects of B and T cell function required for normal antibody responses
inferredcites →https://doi.org/10.1084/jem.20151438openalex-snapshot
Control of Foxp3 stability through modulation of TET activity
inferredcites →https://doi.org/10.1084/jem.20152002openalex-snapshot
Molecular functions of the transcription factors E2A and E2-2 in controlling germinal center B cell and plasma cell development
inferredcites →https://doi.org/10.1084/jem.20152003openalex-snapshot
Dynamic changes in Id3 and E-protein activity orchestrate germinal center and plasma cell development
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btt548openalex-snapshot
BSeQC: quality control of bisulfite sequencing experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btw468openalex-snapshot
LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs
inferredcites →https://doi.org/10.1093/nar/gku864openalex-snapshot
svaseq: removing batch effects and other unwanted noise from sequencing data
inferredcites →https://doi.org/10.1093/nar/gkw257openalex-snapshot
deepTools2: a next generation web server for deep-sequencing data analysis
inferredcites →https://doi.org/10.1101/gr.110114.110openalex-snapshot
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
inferredcites →https://doi.org/10.1111/imr.12239openalex-snapshot
TET proteins and 5‐methylcytosine oxidation in hematological cancers
inferredcites →https://doi.org/10.1126/science.1228309openalex-snapshot
A Genomic Regulatory Element That Directs Assembly and Function of Immune-Specific AP-1–IRF Complexes
inferredcites →https://doi.org/10.1146/annurev-pathol-020712-164004openalex-snapshot
Chromosome Translocation, B Cell Lymphoma, and Activation-Induced Cytidine Deaminase
inferredcites →https://doi.org/10.1186/1471-2105-10-232openalex-snapshot
BSMAP: whole genome bisulfite sequence MAPping program
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1371/journal.pone.0003927openalex-snapshot
Haploinsufficiency of Activation-Induced Deaminase for Antibody Diversification and Chromosome Translocations both In Vitro and In Vivo
inferredcites →https://doi.org/10.1371/journal.pone.0008888openalex-snapshot
The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0061433openalex-snapshot
In Vivo Analysis of Aicda Gene Regulation: A Critical Balance between Upstream Enhancers and Intronic Silencers Governs Appropriate Expression
inferredcites →https://doi.org/10.1371/journal.pone.0081148openalex-snapshot
A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics
inferredcites →https://doi.org/10.3389/fgene.2016.00115openalex-snapshot
Modifiers and Readers of DNA Modifications and Their Impact on Genome Structure, Expression, and Stability in Disease
inferredcites →https://doi.org/10.3389/fimmu.2015.00405openalex-snapshot
Epigenetic Codes Programing Class Switch Recombination
inferredcites →https://doi.org/10.3389/fimmu.2015.00631openalex-snapshot
Epigenetics of Peripheral B-Cell Differentiation and the Antibody Response
inferredcites →https://doi.org/10.3389/fimmu.2017.00220openalex-snapshot
TET Methylcytosine Oxidases in T Cell and B Cell Development and Function
inferredcites →https://doi.org/10.7554/elife.18290openalex-snapshot
Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1126/sciadv.aay5872openalex-snapshot
TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis
inferred← citeshttps://doi.org/10.3389/fimmu.2019.00210openalex-snapshot
TET Enzymes and 5hmC in Adaptive and Innate Immune Systems
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.