Research Article: Genome-scale identification of nucleosome organization by using 1000 porcine oocytes at different developmental stages

Date Published: March 23, 2017

Publisher: Public Library of Science

Author(s): Chenyu Tao, Juan Li, Baobao Chen, Daming Chi, Yaqiong Zeng, Honglin Liu, Wei Shen.

http://doi.org/10.1371/journal.pone.0174225

Abstract

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.

Partial Text

Follicles of mammals are generally categorized into preantral follicles (prior to the accumulation of antral fluid), and antral follicles (after the accumulation of antral fluid) [1–6]. This is a universally applied classification system used by the majority of researchers [7–10], but some important information such as the diameter of oocytes and the number of supporting granulosa cells in each stage are not evaluated in this system [11–12]. Torben [13] established a useful evaluation system of mouse oocytes and follicles according to the following three parameters: 1) the size of oocytes in follicles in different developmental stages, 2) the size of follicles defined by the number of granulosa cells, and 3) the morphology of the follicles. According to this system, there are three types of oocytes. An oocyte with a diameter of less than 20 μm is called a small oocyte. The growing oocyte is a cell which has begun to grow but has not reached its final size; usually, the diameter of a growing oocyte is between 20 μm and 70 μm. This is the stage with active mRNA transcription and high accumulation of energy sources. The large oocyte, also called the fully grown oocyte, is a cell that has almost reached its final size and is approximately 70 μm in diameter. Jeanine [14] had systematically performed statistical analysis of diameters of oocytes, follicles, and granulosa cells in mice, hamsters, pigs, and humans at all stages of maturation. According to the statistics, the diameter of pig oocytes in the primordial, primary, preantral, incipient antral, early antral, and Graafian follicular stages ranges from 20 to 105 μm.

The oocyte growth process is a complex biological process during which there is an accumulation of lipid, proteins, and other energy-providing macromolecules, which leads to an increase in the volume of the oocyte. The growing oocytes show high transcriptional activity, while the fully grown oocytes show low transcriptional activity [31–37]. Therefore, we suspect that there may be a big difference between the chromosome status of the growing and fully grown oocytes, but little research has been carried out to clarify this. Thus, we chose porcine oocytes in two developmental stages and attempted to compare their differences in nucleosome occupancy and distribution. In this study, because the experimental materials are precious and it is difficult to obtain large quantities of porcine oocytes, a total of 1000 oocytes in different stages were chosen. The method of establishing an MNase-seq library with as few as 1000 cells was used successfully.

 

Source:

http://doi.org/10.1371/journal.pone.0174225

 

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