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DNA methylation subpatterns at distinct regulatory regions in human early embryos

DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic d...

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Autores principales: Luo, Rongsong, Bai, Chunling, Yang, Lei, Zheng, Zhong, Su, Guanghua, Gao, Guangqi, Wei, Zhuying, Zuo, Yongchun, Li, Guangpeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223221/
https://www.ncbi.nlm.nih.gov/pubmed/30381360
http://dx.doi.org/10.1098/rsob.180131
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author Luo, Rongsong
Bai, Chunling
Yang, Lei
Zheng, Zhong
Su, Guanghua
Gao, Guangqi
Wei, Zhuying
Zuo, Yongchun
Li, Guangpeng
author_facet Luo, Rongsong
Bai, Chunling
Yang, Lei
Zheng, Zhong
Su, Guanghua
Gao, Guangqi
Wei, Zhuying
Zuo, Yongchun
Li, Guangpeng
author_sort Luo, Rongsong
collection PubMed
description DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed ‘bins’. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels, and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, the current study finally revealed that the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.
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spelling pubmed-62232212018-11-20 DNA methylation subpatterns at distinct regulatory regions in human early embryos Luo, Rongsong Bai, Chunling Yang, Lei Zheng, Zhong Su, Guanghua Gao, Guangqi Wei, Zhuying Zuo, Yongchun Li, Guangpeng Open Biol Research DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed ‘bins’. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels, and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, the current study finally revealed that the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos. The Royal Society 2018-10-31 /pmc/articles/PMC6223221/ /pubmed/30381360 http://dx.doi.org/10.1098/rsob.180131 Text en © 2018 The Authors. http://creativecommons.org/licenses/by/4.0/ Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
spellingShingle Research
Luo, Rongsong
Bai, Chunling
Yang, Lei
Zheng, Zhong
Su, Guanghua
Gao, Guangqi
Wei, Zhuying
Zuo, Yongchun
Li, Guangpeng
DNA methylation subpatterns at distinct regulatory regions in human early embryos
title DNA methylation subpatterns at distinct regulatory regions in human early embryos
title_full DNA methylation subpatterns at distinct regulatory regions in human early embryos
title_fullStr DNA methylation subpatterns at distinct regulatory regions in human early embryos
title_full_unstemmed DNA methylation subpatterns at distinct regulatory regions in human early embryos
title_short DNA methylation subpatterns at distinct regulatory regions in human early embryos
title_sort dna methylation subpatterns at distinct regulatory regions in human early embryos
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223221/
https://www.ncbi.nlm.nih.gov/pubmed/30381360
http://dx.doi.org/10.1098/rsob.180131
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