牛骨骼肌卫星细胞发育过程中的转录组和翻译组联合分析

Joint Analysis of Transcriptome and Translatome During the Development of Bovine Skeletal Muscle Satellite Cells

【目的】利用转录组测序(transcriptome sequencing,RNA-Seq)和全长翻译组测序(ribosome-nascent-chain-complex sequencing,RNC-Seq)分析比对转录和翻译两个不同水平上牛骨骼肌的生长发育过程,解析其发育特征和规律,并筛选出可能在转录组和翻译组共同参与牛肌肉生长发育过程的关键基因,为后续功能基因的筛选和利用提供目标靶点。【方法】采集4月龄牛胚胎的骨骼肌卫星细胞的增殖期(proliferative period,GM)和分化期第2天(the second day of differentiation,DM2)的样品进行RNA-Seq和RNC-Seq分析,对其差异表达基因进行生物信息学分析,从翻译调控的角度分析与骨骼肌发育相关的差异基因。【结果】BSMSCs的DM2期相较于GM期差异基因筛选表明,转录组共筛选获得2808个差异基因(上调基因1749个,下调基因1059个),翻译组共筛选获得3740个差异基因(上调基因1769个,下调基因1971个),转录组和翻译组共有的差异表达基因725个,其中表达趋势相同的基因618个,表达趋势相反的基因107个。功能富集分析获得103个与骨骼肌发育相关的基因。进一步深入分析发现,转录水平的调控和翻译水平的调控具有相对独立性,且翻译调控对转录调控具有一定的回调作用,筛选获得了22个与牛肌肉的生长发育密切相关的标靶基因(CDK1、SERPINE1、THBS1、IGFBP3、CNB1、GADD45A、CYCS、CDK2、CCND1、CCNE2、ZMAT3、ACTB、ACTA1、TNNT1、MYH7、ACTG1、TUBA1C、TNNC1、KIF20A、TUBB4B、MYL3、TUBB3)及13个存在翻译回调现象的关键基因(GREM1、EGR1、SFRP4、NKD2、DKK3、IGFBP3、CTSK、ITGAV、CTSV、CDKN1A、SESN3、GADD45A、ZMAT3)。【结论】本研究筛选获得了22个可能与牛肌肉的生长发育密切相关的关键基因和13个存在翻译回调的关键基因,为进一步利用分子手段调节牛肌肉生长发育过程及进行新品种培育提供了重要的靶点。

【Objective】The aim of this study was to analyze and compare the growth and development process of bovine skeletal muscle at two different levels of transcription and translation using transcriptome sequencing(RNA-Seq)and ribosome-nascent-chain-complex sequencing(RNC-Seq),analyze the developmental characteristics and patterns,and screen out key genes that might be involved in the growth and development process of bovine muscle in the transcriptome and translatome,in order to provide a target for the subsequent screening and utilization of functional genes.【Method】Samples of the proliferative period(GM)and the second day of differentiation(DM2)of skeletal muscle satellite cells from 4-month-old bovine embryos were collected for RNA-Seq and RNC-Seq analysis.The differentially expressed genes were analyzed using bioinformatics,and the differentially expressed genes related to skeletal muscle development were analyzed from the perspective of translational regulation.【Result】The differential gene screening of BSMSCs in DM2 phase compared to GM phase showed that a total of 2808 differential genes(1749 up-regulated genes and 1059 down-regulated genes)were obtained from transcriptome screening,and 3740 differential genes(1769 up-regulated genes and 1971 down-regulated genes)were obtained from translatome screening.There were 725 differentially expressed genes shared between transcriptome and translatome,including 618 genes with similar expression trends and 107 genes with opposite expression trends.The functional enrichment analysis results showed that 103 genes related to skeletal muscle development were obtained.Further in-depth analysis showed that the transcriptional and translational regulation were relatively independent and the translational regulation had a certain effect of retrogression on the transcriptional regulation,22 target genes closely related to the growth and development of bovine muscle(CDK1,SERPINE1,THBS1,IGFBP3,CNB1,GADD45A,CYCS,CDK2,CCND1,CCNE2,ZMAT3,ACTB,ACTA1,TNNT1,MYH7,ACTG1,TUBA1C,TNNC1,KIF20A,TUBB4B,MYL3 and TUBB3)and 13 key genes with translation retrogression(GREM1,EGR1,SFRP4,NKD2,DKK3,IGFBP3,CTSK,ITGAV,CTSV,CDKN1A,SESN3,GADD45A and ZMAT3)were obtained.【Conclusion】In this study,22 key genes that might be closely related to the growth and development of bovine muscles and 13 key genes with translation callbacks were screened,providing important targets for further regulating the process of bovine muscle growth and development through molecular means for new breed cultivation.