title: Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape.
abstract: BACKGROUND
  Previously, a role was demonstrated for transcription in the acquisition of DNA methylation at imprinted control regions in oocytes. Definition of the oocyte DNA methylome by whole genome approaches revealed that the majority of methylated CpG islands are intragenic and gene bodies are hypermethylated. Yet, the mechanisms by which transcription regulates DNA methylation in oocytes remain unclear. Here, we systematically test the link between transcription and the methylome.
  
  
  RESULTS
  We perform deep RNA-Seq and de novo transcriptome assembly at different stages of mouse oogenesis. This reveals thousands of novel non-annotated genes, as well as alternative promoters, for approximately 10 % of reference genes expressed in oocytes. In addition, a large fraction of novel promoters coincide with MaLR and ERVK transposable elements. Integration with our transcriptome assembly reveals that transcription correlates accurately with DNA methylation and accounts for approximately 85-90 % of the methylome. We generate a mouse model in which transcription across the Zac1/Plagl1 locus is abrogated in oocytes, resulting in failure of DNA methylation establishment at all CpGs of this locus. ChIP analysis in oocytes reveals H3K4me2 enrichment at the Zac1 imprinted control region when transcription is ablated, establishing a connection between transcription and chromatin remodeling at CpG islands by histone demethylases.
  
  
  CONCLUSIONS
  By precisely defining the mouse oocyte transcriptome, this work not only highlights transcription as a cornerstone of DNA methylation establishment in female germ cells, but also provides an important resource for developmental biology research.
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge, UK. lenka.veselovska@babraham.ac.uk.
authors.forename: Lenka
authors.initials: L
authors.lastname: Veselovska
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge, UK. sebastien.smallwood@babraham.ac.uk.
authors.forename: Sebastien A
authors.initials: SA
authors.lastname: Smallwood
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge, UK. heba.saadeh@babraham.ac.uk.|Bioinformatics Group, Babraham Institute, Cambridge, UK. heba.saadeh@babraham.ac.uk.
authors.forename: Heba
authors.initials: H
authors.lastname: Saadeh
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge, UK. kathleen.stewart@babraham.ac.uk.
authors.forename: Kathleen R
authors.initials: KR
authors.lastname: Stewart
authors.affiliation: Bioinformatics Group, Babraham Institute, Cambridge, UK. felix.krueger@babraham.ac.uk.
authors.forename: Felix
authors.initials: F
authors.lastname: Krueger
authors.affiliation: GReD, CNRS, INSERM, and Clermont University, 63001, Clermont-Ferrand, France. stephanie.maupetit_mehouas@udamail.fr.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Maupetit-Méhouas
authors.affiliation: GReD, CNRS, INSERM, and Clermont University, 63001, Clermont-Ferrand, France. philippe.arnaud@udamail.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Arnaud
authors.affiliation: Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, Japan. tomizawa@yokohama-cu.ac.jp.
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Tomizawa
authors.affiliation: Bioinformatics Group, Babraham Institute, Cambridge, UK. simon.andrews@babraham.ac.uk.
authors.forename: Simon
authors.initials: S
authors.lastname: Andrews
authors.affiliation: Epigenetics Programme, Babraham Institute, Cambridge, UK. gavin.kelsey@babraham.ac.uk.|Centre for Trophoblast Research, University of Cambridge, Cambridge, UK. gavin.kelsey@babraham.ac.uk.
authors.forename: Gavin
authors.initials: G
authors.lastname: Kelsey
mesh_terms: D000818:Animals; D018797:Cell Cycle Proteins / Q000235:genetics; D042002:Chromatin Assembly and Disassembly; D018899:CpG Islands; D019175:DNA Methylation; D004251:DNA Transposable Elements; D005260:Female; D020869:Gene Expression Profiling; D016147:Genes, Tumor Suppressor; D018392:Genomic Imprinting; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D008822:Mice, Transgenic; D009865:Oocytes / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics; D024363:Transcription Initiation Site; D059467:Transcriptome
chemical_list: D018797:Cell Cycle Proteins; D004251:DNA Transposable Elements; C498423:Plagl1 protein, mouse; D014157:Transcription Factors