Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Identification and Functional Analysis of Transcriptome Profiles, Long Non-coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing

Zi Jing Zhang
,
Qiao ting Shi
,
Xiao ting Zhu
,
Lei Jin
,
Li min Lang
,
Shi jie Lyv
,
Xiao ling Xin
,
Yong zhen Huang
ORCID logo ,
Xiang Yu
,
Zhi ming Li
,
Su Juan Chen
,
Zhao xue Xu
,
Wei Zhang
* ,
Er yao Wang
*
Version 1 : Received: 22 April 2023 / Approved: 23 April 2023 / Online: 23 April 2023 (04:57:02 CEST)

A peer-reviewed article of this Preprint also exists.

Zhang, Z.; Shi, Q.; Zhu, X.; Jin, L.; Lang, L.; Lyu, S.; Xin, X.; Huang, Y.; Yu, X.; Li, Z.; Chen, S.; Xu, Z.; Zhang, W.; Wang, E. Identification and Functional Analysis of Transcriptome Profiles, Long Non-Coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing. Genes 2023, 14, 1145. Zhang, Z.; Shi, Q.; Zhu, X.; Jin, L.; Lang, L.; Lyu, S.; Xin, X.; Huang, Y.; Yu, X.; Li, Z.; Chen, S.; Xu, Z.; Zhang, W.; Wang, E. Identification and Functional Analysis of Transcriptome Profiles, Long Non-Coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing. Genes 2023, 14, 1145.

Abstract

Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development have not been studied. Here, we conducted a scRNA-seq survey of cells from sheep from the oocyte to the blastocyst developmental stages. We then carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS). We founded that between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis.

Keywords

Key words: transcriptome profiles; long non-coding RNAs; single-nucleotide polymorphisms; alternative splicing; sheep; preimplantation; Single-cell RNA sequencing

Subject

Biology and Life Sciences, Animal Science, Veterinary Science and Zoology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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