Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

Abstract

Background: Sunite sheep are a fat-tailed sheep species with a low percentage of intramuscular fat and good quality lean meat, and their tail fat can be used as a source of dietary fat by humans. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6 months, 18 months, and 30 months.Results: A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep (false discovery rate < 0.05, |Fold Change| ≥ 2). Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that fat-related DEGs were mainly expressed at 6 months of age, and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their trans-regulators (53 mRNAs at most). Further, we obtained several fat-related differentially-expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Conclusions: Finally, we conclude that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process, and our findings will provide some basic theoretical data for future studies on tail fat development of fat-tailed sheep.

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

“…Many studies have attempted to identify the candidate gene associated with tail fat and understand the underlying mechanisms of fat deposition ( Ahbara et al, 2018 ; Amane et al, 2020 ; Baazaoui et al, 2021 ; Bakhtiarizadeh & Alamouti, 2020 ; Dong et al, 2020 ; Han et al, 2021 ; Li et al, 2018a ; Mastrangelo et al, 2019a ; Mastrangelo et al, 2019b ; Moioli, Pilla & Ciani, 2015 ; Moradi et al, 2012 ; Wei et al, 2015 ; Xu et al, 2017 ; Yuan et al, 2017 ; Zhang et al, 2019 ; Zhao et al, 2020 ; Zhi et al, 2018 ; Zhu et al, 2016 ). Previous studies suggested that microRNAs ( Miao et al, 2015a ; Pan et al, 2018 ), lncRNAs ( Bakhtiarizadeh & Salami, 2019 ; He et al, 2020 ) and mRNAs ( Bakhtiarizadeh et al, 2019 ; Kang et al, 2017a ; Miao et al, 2015b ; Wang et al, 2014 ) may regulate tail fat deposition in sheep. These results contribute to understanding the underlying mechanisms of fat deposition.…”

Peer Review #2 of "Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat (v0.1)"

“…Many studies have attempted to identify the candidate gene associated with tail fat and understand the underlying mechanisms of fat deposition (Ahbara et al 2018;Amane et al 2020;Baazaoui et al 2021;Bakhtiarizadeh & Alamouti 2020;Dong et al 2020;Han et al 2021;Li et al 2018a;Mastrangelo et al 2019a;Mastrangelo et al 2019b;Moioli et al 2015;Moradi et al 2012;Wei et al 2015;Xu et al 2017;Yuan et al 2017;Zhang et al 2019;Zhao et al 2020;Zhi et al 2018;Zhu et al 2016). Previous studies suggested that microRNAs (Miao et al 2015a;Pan et al 2018), lncRNAs He et al 2020) and mRNAs Kang et al 2017a;Miao et al 2015b;Wang et al 2014) may regulate tail fat deposition in sheep. These results contribute to understanding the underlying mechanisms of fat deposition.…”

Peer Review #3 of "Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat (v0.2)"

“…Many studies have attempted to identify the candidate gene associated with tail fat and understand the underlying mechanisms of fat deposition (Ahbara et al 2018;Amane et al 2020;Baazaoui et al 2021;Bakhtiarizadeh & Alamouti 2020;Dong et al 2020;Han et al 2021;Li et al 2018a;Mastrangelo et al 2019a;Mastrangelo et al 2019b;Moioli et al 2015;Moradi et al 2012;Wei et al 2015;Xu et al 2017;Yuan et al 2017;Zhang et al 2019;Zhao et al 2020;Zhi et al 2018;Zhu et al 2016). Previous studies suggested that microRNAs (Miao et al 2015a;Pan et al 2018), lncRNAs He et al 2020) and mRNAs Kang et al 2017a;Miao et al 2015b;Wang et al 2014) may regulate tail fat deposition in sheep. These results contribute to understanding the underlying mechanisms of fat deposition.…”