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Data released on March 30, 2018

Supporting data for "Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm"

Zhou, Y; Connor, E, E; Bickhart, D, M; Li, C; Baldwin, R, L; Schroeder, S, G; Rosen, B, D; Yang, L; Van Tassell, C, P; Liu, G, E (2018): Supporting data for "Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm" GigaScience Database. http://dx.doi.org/10.5524/100424 RIS BibTeX Text

Compared to somatic cells, sperm cells undergo nearly complete reprogramming of DNA methylation and exchange histones by protamine. Although sperm DNA methylation has been studied in humans and other model species, as the most beneficiary species of artificial insemination, its status in cattle is largely unknown. Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with somatic cells from three bovine tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected and like other species, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in the somatic cells and identified meiosis-related genes like KIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. Besides the common HMRs around gene promoters which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some hypomethylated repeats were enriched in gene promoters with large variations among tissues. For example, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated and could affect the promoter structures by introducing new regulatory elements. Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.

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Accessions (data included in GigaDB):

BioProject: PRJNA417285

Keywords:

cattle sperm somatic cells dna methylation hypomethylated region 

Epigenomic

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Funding:

  • Funding body - National Institute of Food and Agriculture
  • Award ID - 2013-67015-20951
  • Awardee - George Liu
  • Funding body - US-Israel Binational Agricultural Research and Development (BARD) Fund
  • Award ID - US-4997-17
  • Awardee - George Liu

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN079821289913bovinecattleBos taurus Description:Genomic DNA isolated from semen straws...
Sex:male
Tissue:sperm
...
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SAMN079821299913bovinecattleBos taurus Description:Genomic DNA isolated from the mammary ...
Sex:female
Tissue:mammary gland
...
+
SAMN079821309913bovinecattleBos taurus Description:Genomic DNA isolated from the mammary ...
Sex:female
Tissue:mammary gland
...
+
SAMN079821319913bovinecattleBos taurus Description:Genomic DNA isolated from the prefront...
Sex:female
Tissue:prefrontal cortex
...
+
SAMN079821329913bovinecattleBos taurus Description:Genomic DNA isolated from semen straws...
Sex:male
Tissue:sperm
...
+
SAMN079821339913bovinecattleBos taurus Description:Genomic DNA isolated from semen straws...
Sex:male
Tissue:sperm
...
+
SAMN079821349913bovinecattleBos taurus Description:Genomic DNA isolated from semen straws...
Sex:male
Tissue:sperm
...
+
SAMN079821359913bovinecattleBos taurus Description:Genomic DNA isolated from the prefront...
Sex:female
Tissue:prefrontal cortex
...
+
SAMN079821369913bovinecattleBos taurus Description:Genomic DNA isolated from whole blood ...
Sex:female
Tissue:blood
...
+
SAMN079821379913bovinecattleBos taurus Description:Genomic DNA isolated from whole blood ...
Sex:female
Tissue:blood
...
+
Displaying 1-10 of 10 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT3.66 KB2018-03-14
Tabular DataUNKNOWN0.55 KB2018-03-14
Tabular DataUNKNOWN1.48 KB2018-03-14
Tabular DataUNKNOWN0.39 KB2018-03-14
Tabular DataUNKNOWN0.25 KB2018-03-14
Tabular DataUNKNOWN2.05 MB2018-03-14
Tabular DataUNKNOWN1.76 KB2018-03-14
Tabular DataUNKNOWN11.48 KB2018-03-14
Tabular DataUNKNOWN155.03 KB2018-03-14
Tabular DataUNKNOWN4.6 KB2018-03-14
Displaying 1-10 of 11 File(s).

History:

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