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Transcription and chromatin determinants of de novo DNA methylation timing in oocytes
L. Gahurova, SI. Tomizawa, SA. Smallwood, KR. Stewart-Morgan, H. Saadeh, J. Kim, SR. Andrews, T. Chen, G. Kelsey,
Jazyk angličtina Země Anglie, Velká Británie
Typ dokumentu časopisecké články
BioMedCentral Open Access od 2008
Directory of Open Access Journals od 2008
Free Medical Journals od 2008
PubMed Central od 2008
Europe PubMed Central od 2008
ProQuest Central od 2009-01-01
Open Access Digital Library od 2008-01-01
Open Access Digital Library od 2008-01-01
Health & Medicine (ProQuest) od 2009-01-01
ROAD: Directory of Open Access Scholarly Resources od 2008
Springer Journals Complete - Open Access od 2008-12-01
Springer Nature OA/Free Journals od 2008-12-01
Odkazy
PubMed
28507606
DOI
10.1186/s13072-017-0133-5
Knihovny.cz E-zdroje
- MeSH
- chromatin genetika MeSH
- CpG ostrůvky genetika MeSH
- DNA-(cytosin-5-)methyltransferasa genetika MeSH
- genetická transkripce * MeSH
- genomový imprinting genetika MeSH
- histony genetika MeSH
- metylace DNA genetika MeSH
- myši MeSH
- oocyty růst a vývoj metabolismus MeSH
- oogeneze genetika MeSH
- restrukturace chromatinu MeSH
- transkriptom genetika MeSH
- zárodečné buňky MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. RESULTS: Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally, we show that establishment of non-CpG methylation, which is prevalent in fully grown oocytes, and methylation over non-transcribed regions, are later events in oogenesis. CONCLUSIONS: These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation.
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- $a Gahurova, Lenka $u Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK. Laboratory of Developmental Biology and Genetics, Department of Molecular Biology, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic.
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- $a BACKGROUND: Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. RESULTS: Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally, we show that establishment of non-CpG methylation, which is prevalent in fully grown oocytes, and methylation over non-transcribed regions, are later events in oogenesis. CONCLUSIONS: These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation.
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- $a Saadeh, Heba $u Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT UK. Computer Science Department, KASIT, University of Jordan, Amman, Jordan.
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