title: Simultaneous deletion of the methylcytosine oxidases Tet1 and Tet3 increases transcriptome variability in early embryogenesis.
abstract: Dioxygenases of the TET (Ten-Eleven Translocation) family produce oxidized methylcytosines, intermediates in DNA demethylation, as well as new epigenetic marks. Here we show data suggesting that TET proteins maintain the consistency of gene transcription. Embryos lacking Tet1 and Tet3 (Tet1/3 DKO) displayed a strong loss of 5-hydroxymethylcytosine (5hmC) and a concurrent increase in 5-methylcytosine (5mC) at the eight-cell stage. Single cells from eight-cell embryos and individual embryonic day 3.5 blastocysts showed unexpectedly variable gene expression compared with controls, and this variability correlated in blastocysts with variably increased 5mC/5hmC in gene bodies and repetitive elements. Despite the variability, genes encoding regulators of cholesterol biosynthesis were reproducibly down-regulated in Tet1/3 DKO blastocysts, resulting in a characteristic phenotype of holoprosencephaly in the few embryos that survived to later stages. Thus, TET enzymes and DNA cytosine modifications could directly or indirectly modulate transcriptional noise, resulting in the selective susceptibility of certain intracellular pathways to regulation by TET proteins.
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037;
authors.forename: Jinsuk
authors.initials: J
authors.lastname: Kang
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;
authors.forename: Matthias
authors.initials: M
authors.lastname: Lienhard
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037;
authors.forename: William A
authors.initials: WA
authors.lastname: Pastor
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037;
authors.forename: Ashu
authors.initials: A
authors.lastname: Chawla
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037;
authors.forename: Mark
authors.initials: M
authors.lastname: Novotny
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037;
authors.forename: Ageliki
authors.initials: A
authors.lastname: Tsagaratou
authors.affiliation: J. Craig Venter Institute, La Jolla, CA 92037;
authors.forename: Roger S
authors.initials: RS
authors.lastname: Lasken
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037;
authors.forename: Elizabeth C
authors.initials: EC
authors.lastname: Thompson
authors.affiliation: Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom;
authors.forename: M Azim
authors.initials: MA
authors.lastname: Surani
authors.affiliation: Department of Pathology, New York University School of Medicine, New York, NY 10016;
authors.forename: Sergei B
authors.initials: SB
authors.lastname: Koralov
authors.affiliation: Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109;
authors.forename: Sundeep
authors.initials: S
authors.lastname: Kalantry
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037; arao@liai.org l.chavez@dkfz-heidelberg.de.
authors.forename: Lukas
authors.initials: L
authors.lastname: Chavez
authors.affiliation: Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, CA 92037; Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093; Moores Cancer Center, University of California at San Diego, La Jolla, CA 92093; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 arao@liai.org l.chavez@dkfz-heidelberg.de.
authors.forename: Anjana
authors.initials: A
authors.lastname: Rao
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism*; D000818:Animals; D015415:Biomarkers / Q000378:metabolism; D001755:Blastocyst / Q000378:metabolism; D001757:Blastomeres / Q000378:metabolism / Q000473:pathology; D019070:Cell Lineage; D002784:Cholesterol / Q000096:biosynthesis; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D049308:Dioxygenases; D015536:Down-Regulation / Q000235:genetics; D020964:Embryo Loss / Q000378:metabolism / Q000473:pathology; D004622:Embryo, Mammalian / Q000473:pathology; D047108:Embryonic Development / Q000235:genetics*; D017353:Gene Deletion; D018507:Gene Expression Regulation, Developmental; D018392:Genomic Imprinting; D053823:Hedgehog Proteins / Q000378:metabolism; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D011518:Proto-Oncogene Proteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D015415:Biomarkers; D004268:DNA-Binding Proteins; D053823:Hedgehog Proteins; D011518:Proto-Oncogene Proteins; C465570:Shh protein, mouse; C540839:TET1 protein, mouse; D044503:5-Methylcytosine; D004247:DNA; D002784:Cholesterol; D049308:Dioxygenases; C551915:Tet3 protein, mouse
keywords: 5-hydroxymethylcytosine; 5hmC; DNA methylation; TET methylcytosine oxidases; cholesterol biosynthesis