Dynamic Switching of Active Promoter and Enhancer Domains Regulates Tet1 and Tet2 Expression during Cell State Transitions between Pluripotency and Differentiation

ABSTRACT The Tet 5-methylcytosine dioxygenases catalyze DNA demethylation by producing 5-hydroxymethylcytosine and further oxidized products. Tet1 and Tet2 are highly expressed in mouse pluripotent cells and downregulated to different extents in somatic cells, but the transcriptional mechanisms are unclear. Here we defined the promoter and enhancer domains in Tet1 and Tet2. Within a 15-kb “superenhancer” of Tet1, there are two transcription start sites (TSSs) with different activation patterns during development. A 6-kb promoter region upstream of the distal TSS is highly active in naive pluripotent cells, autonomously reports Tet1 expression in a transgenic system, and rapidly undergoes DNA methylation and silencing upon differentiation in cultured cells and native epiblast. A second TSS downstream, associated with a constitutively weak CpG-rich promoter, is activated by a neighboring enhancer in naive embryonic stem cells (ESCs) and primed epiblast-like cells (EpiLCs). Tet2 has a CpG island promoter with pluripotency-independent activity and an ESC-specific distal intragenic enhancer; the latter is rapidly downregulated in EpiLCs. Our study reveals distinct modes of transcriptional regulation at Tet1 and Tet2 during cell state transitions of early development. New transgenic reporters using Tet1 and Tet2 cis-regulatory domains may serve to distinguish nuanced changes in pluripotent states and the underlying epigenetic variations.

[1]  J. Nichols,et al.  Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human , 2014, Cell.

[2]  E. Solary,et al.  TET2 Deficiency Inhibits Mesoderm and Hematopoietic Differentiation in Human Embryonic Stem Cells , 2014, Stem cells.

[3]  Daniel C. Factor,et al.  Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency. , 2014, Cell stem cell.

[4]  A. Simeone,et al.  Reorganization of enhancer patterns in transition from naive to primed pluripotency. , 2014, Cell stem cell.

[5]  J. Issa,et al.  TET1 is a maintenance DNA demethylase that prevents methylation spreading in differentiated cells , 2014, Nucleic acids research.

[6]  W. Liu,et al.  Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. , 2014, Cell stem cell.

[7]  Erdahl T. Teber,et al.  The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. , 2014, Cell stem cell.

[8]  T. Down,et al.  Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency , 2013, Stem cell reports.

[9]  Yuting Liu,et al.  Role of Tet1 in erasure of genomic imprinting , 2013, Nature.

[10]  A. Sidow,et al.  Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines , 2013, BMC Genomics.

[11]  Luca Pinello,et al.  Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions , 2013, Epigenetics.

[12]  M. Gut,et al.  Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. , 2013, Cell stem cell.

[13]  Li-Huei Tsai,et al.  Tet1 Is Critical for Neuronal Activity-Regulated Gene Expression and Memory Extinction , 2013, Neuron.

[14]  W. Reik,et al.  FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency , 2013, Clinical Epigenetics.

[15]  Zachary D. Smith,et al.  Tet1 regulates adult hippocampal neurogenesis and cognition. , 2013, Cell stem cell.

[16]  T. Cai,et al.  Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. , 2013, Cell stem cell.

[17]  M. Pellegrini,et al.  Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. , 2013, Cell stem cell.

[18]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[19]  Yongyan Wu,et al.  Oct4 and the small molecule inhibitor, SC1, regulates Tet2 expression in mouse embryonic stem cells , 2013, Molecular Biology Reports.

[20]  R. Shiekhattar,et al.  Activating RNAs associate with Mediator to enhance chromatin architecture and transcription , 2013, Nature.

[21]  R. Jaenisch,et al.  Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. , 2013, Developmental cell.

[22]  W. Reik,et al.  Nanog-dependent function of Tet1 and Tet2 in establishment of pluripotency , 2013, Nature.

[23]  T. Down,et al.  Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine , 2013, Science.

[24]  E. Ballestar,et al.  Tet2 facilitates the derepression of myeloid target genes during CEBPα-induced transdifferentiation of pre-B cells. , 2012, Molecular cell.

[25]  Alexander R. Pico,et al.  Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage , 2012, Cell.

[26]  Hsien-Da Huang,et al.  TET1 suppresses cancer invasion by activating the tissue inhibitors of metalloproteinases. , 2012, Cell reports.

[27]  Abraham J. Khorasani,et al.  Loss of 5-Hydroxymethylcytosine Is an Epigenetic Hallmark of Melanoma , 2012, Cell.

[28]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[29]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[30]  E. Furlong,et al.  Transcription factors: from enhancer binding to developmental control , 2012, Nature Reviews Genetics.

[31]  Lee E. Edsall,et al.  A map of the cis-regulatory sequences in the mouse genome , 2012, Nature.

[32]  G. Hon,et al.  Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome , 2012, Cell.

[33]  Barry J Dickson,et al.  HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. , 2012, Genes & development.

[34]  Zachary D. Smith,et al.  A unique regulatory phase of DNA methylation in the early mammalian embryo , 2012, Nature.

[35]  Vijay K. Tiwari,et al.  DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.

[36]  Z. Deng,et al.  The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes , 2011, Nature.

[37]  Yang Wang,et al.  Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA , 2011, Science.

[38]  Chuan He,et al.  Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine , 2011, Science.

[39]  H. Ohta,et al.  Reconstitution of the Mouse Germ Cell Specification Pathway in Culture by Pluripotent Stem Cells , 2011, Cell.

[40]  Juri Rappsilber,et al.  TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity , 2011, Nature.

[41]  W. Reik,et al.  Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation , 2011, Nature.

[42]  Keji Zhao,et al.  Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells , 2011, Nature.

[43]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[44]  Riitta Lahesmaa,et al.  Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. , 2011, Cell stem cell.

[45]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[46]  Yi Zhang,et al.  Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification , 2010, Nature.

[47]  H. Leonhardt,et al.  Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA , 2010, Nucleic acids research.

[48]  Catalin C. Barbacioru,et al.  Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis , 2010, Cell stem cell.

[49]  Christopher B. Burge,et al.  c-Myc Regulates Transcriptional Pause Release , 2010, Cell.

[50]  David R. Liu,et al.  The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing , 2010, PloS one.

[51]  David R. Liu,et al.  Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1 , 2009, Science.

[52]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[53]  T. Mikkelsen,et al.  Genome-scale DNA methylation maps of pluripotent and differentiated cells , 2008, Nature.

[54]  N. D. Clarke,et al.  Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells , 2008, Cell.

[55]  B. Doble,et al.  The ground state of embryonic stem cell self-renewal , 2008, Nature.

[56]  Masaaki Oda,et al.  QUMA: quantification tool for methylation analysis , 2008, Nucleic Acids Res..

[57]  S. Orkin,et al.  An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells , 2008, Cell.

[58]  R. Jaenisch,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[59]  R. McKay,et al.  New cell lines from mouse epiblast share defining features with human embryonic stem cells , 2007, Nature.

[60]  W. Reik.  Stability and flexibility of epigenetic gene regulation in mammalian development , 2007, Nature.

[61]  X. Chen,et al.  Reciprocal Transcriptional Regulation of Pou5f1 and Sox2 via the Oct4/Sox2 Complex in Embryonic Stem Cells , 2005, Molecular and Cellular Biology.

[62]  S. Mathew,et al.  TET1, a member of a novel protein family, is fused to MLL in acute myeloid leukemia containing the t(10;11)(q22;q23) , 2003, Leukemia.

[63]  Akihiko Okuda,et al.  The Gene for the Embryonic Stem Cell Coactivator UTF1 Carries a Regulatory Element Which Selectively Interacts with a Complex Composed of Oct-3/4 and Sox-2 , 1999, Molecular and Cellular Biology.

[64]  H. Schöler,et al.  Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells. , 1996, Development.

[65]  A. Rao,et al.  TET proteins and 5-methylcytosine oxidation in the immune system. , 2013, Cold Spring Harbor symposia on quantitative biology.

[66]  T. Misteli,et al.  Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. , 2006, Developmental cell.