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: Jinsuk Kang, Matthias Lienhard, William A Pastor, Ashu Chawla, Mark Novotny, Ageliki Tsagaratou, Roger S Lasken, Elizabeth C Thompson, M Azim Surani, Sergei B Koralov, Sundeep Kalantry, Lukas Chavez, Anjana Rao
• Journal: Proceedings of the National Academy of Sciences of the United States of America (Proc Natl Acad Sci U S A) Vol. 112 Issue 31 Pg. E4236-45 (Aug 04 2015) ISSN: 1091-6490 [Electronic] United States
• PMID: 26199412 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.)

Chemical References

• Biomarkers
• DNA-Binding Proteins
• Hedgehog Proteins
• Proto-Oncogene Proteins
• Shh protein, mouse
• TET1 protein, mouse
• 5-Methylcytosine
• DNA
• Cholesterol
• Dioxygenases
• Tet3 protein, mouse

Topics

• 5-Methylcytosine (metabolism)
• Animals
• Biomarkers (metabolism)
• Blastocyst (metabolism)
• Blastomeres (metabolism, pathology)
• Cell Lineage
• Cholesterol (biosynthesis)
• DNA (metabolism)
• DNA-Binding Proteins (deficiency, genetics, metabolism)
• Dioxygenases
• Down-Regulation (genetics)
• Embryo Loss (metabolism, pathology)
• Embryo, Mammalian (pathology)
• Embryonic Development (genetics)
• Gene Deletion
• Gene Expression Regulation, Developmental
• Genomic Imprinting
• Hedgehog Proteins (metabolism)
• Mice, Inbred C57BL
• Mice, Knockout
• Proto-Oncogene Proteins (deficiency, genetics, metabolism)
• Repetitive Sequences, Nucleic Acid (genetics)
• Sequence Analysis, RNA
• Signal Transduction (genetics)
• Transcriptome (genetics)