Genome-scale identification of nucleosome organization by using 1000 porcine oocytes at different developmental stages.
The nucleosome is the basic structural unit of chromosomes, and its occupancy and distribution in promoters are crucial for the regulation of gene expression. During the growth process of porcine oocytes, the "growing" oocytes (SF) have a much higher transcriptional activity than the "fully grown" oocytes (BF). However, the chromosome status of the two kinds of oocytes remains poorly understood. In this study, we profiled the nucleosome distributions of SF and BF with as few as 1000 oocytes. By comparing the altered regions, we found that SF tended toward nucleosome loss and more open chromosome architecture than BF did. BF had decreased nucleosome occupancy in the coding region and increased nucleosome occupancy in the promoter compared to SF. The nucleosome occupancy of SF was higher than that of BF in the GC-poor regions, but lower than that of BF in the GC-rich regions. The nucleosome distribution around the transcriptional start site (TSS) of all the genes of the two samples was basically the same, but the nucleosome occupancy around the TSS of SF was lower than that of BF. GO functional annotation of genes with different nucleosome occupancy in promoter showed the genes were mainly involved in cell, cellular process, and metabolic process biological process. The results of this study revealed the dynamic reorganization of porcine oocytes in different developmental stages and the critical role of nucleosome arrangement during the oocyte growth process.
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Chenyu
C
Tao
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Juan
J
Li
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Baobao
B
Chen
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Daming
D
Chi
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Yaqiong
Y
Zeng
College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Honglin
http://orcid.org/0000-0002-0858-8713
H
Liu
D000818:Animals; D002478:Cells, Cultured; D033481:Chromosomes, Mammalian / Q000648:ultrastructure*; D020862:GC Rich Sequence; D016678:Genome / Q000235:genetics; D009707:Nucleosomes / Q000648:ultrastructure*; D009865:Oocytes / Q000254:growth & development / Q000648:ultrastructure*; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment; D013552:Swine
D009707:Nucleosomes