New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing
Lingwei Peng,
Xiaolian Zhang,
Yuqin Du,
Fan Li,
Jiazheng Han,
Oujin Liu,
Shoulu Dai,
Xiang Zhang,
George E. Liu,
Liguo Yang,
Yang Zhou
Affiliations
Lingwei Peng
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Xiaolian Zhang
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Yuqin Du
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Fan Li
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Jiazheng Han
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Oujin Liu
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Shoulu Dai
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Xiang Zhang
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
George E. Liu
Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
Liguo Yang
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
Yang Zhou
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Corresponding author
Summary: We performed direct RNA sequencing (DRS) together with PCR-amplified cDNA long and short read sequencing for cattle adipocyte at different stages. We proved that the DRS was with advantages to avoid artificial transcripts and questionable exitrons. Totally, we obtained 68,124 transcripts with information of alternative splicing, poly (A) length and mRNA modification. The number of transcripts for adipogenesis was expanded by alternative splicing, which lead regulation mechanisms far more complex than ever known. We detected 891 differentially expressed genes (DEGs). However, 62.78% transcripts of DEGs were not significantly differentially expressed, and 248 transcripts showed opposite changing directions with their genes. The poly (A) tail became globally shorter in differentiated adipocyte than in primary adipocyte, and had a weak negative correlation with gene/transcript expression. Moreover, the study of different mRNA modifications implied their potential roles in gene expression and alternative splicing. Overall, our study promoted better understanding of adipogenesis mechanisms in cattle adipocytes.
