Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle.
Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle.
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纳米孔和 Illumina 测序的综合分析揭示了猪背最长肌的选择性剪接复杂性
DOI：
10.3389/fgene.2022.877646
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发表时间：
2022
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
--
作者：
选择性剪接（AS）是影响肌内脂肪（IMF）的基因表达转录后调控的关键步骤。在这项研究中，使用来自高和低IMF组中的30头猪的背最长肌进行Oxford Nanopore Technologies（ONT）全长测序和Illumina链特异性RNA-seq。共鉴定了43,688个全长转录本，其中4,322个新基因和30,795个新转录本。使用Astalavista，在背最长肌中共检测到14，728起AS事件。约17.79%的基因产生剪接亚型，其中外显子跳跃是最常见的AS事件。通过分析mRNA和剪接异构体的表达差异，发现具有剪接异构体的差异表达的mRNA可能参与骨骼肌发育和脂肪酸代谢，可能决定肌肉相关性状。SERBP 1、MYL 1、TNNT 3和TNNT 1被鉴定为具有多个剪接异构体，在表达上具有显著差异。在IFI 6和GADD 45 G中发生的AS事件可能导致基因表达的显著差异。其他AS事件，如ONT. 15153. 3，可能通过调节不同转录物的表达来调节ART 1的功能。此外，共表达和蛋白质-蛋白质相互作用（PPI）分析表明，几个基因（MRPL 27，AAR 2，PYGM，PSMD 4，SCNM 1和HNRNPDL）可能与肌内脂肪有关。本研究所研究的剪接异构体为肌内脂肪沉积的选择性剪接调控研究提供了参考。
Alternative splicing (AS) is a key step in the post-transcriptional regulation of gene expression that can affect intramuscular fat (IMF). In this study, longissimus dorsi muscles from 30 pigs in high- and low- IMF groups were used to perform Oxford Nanopore Technologies (ONT) full-length sequencing and Illumina strand-specific RNA-seq. A total of 43,688 full-length transcripts were identified, with 4,322 novel genes and 30,795 novel transcripts. Using AStalavista, a total of 14,728 AS events were detected in the longissimus dorsi muscle. About 17.79% of the genes produced splicing isoforms, in which exon skipping was the most frequent AS event. By analyzing the expression differences of mRNAs and splicing isoforms, we found that differentially expressed mRNAs with splicing isoforms could participate in skeletal muscle development and fatty acid metabolism, which might determine muscle-related traits. SERBP1, MYL1, TNNT3, and TNNT1 were identified with multiple splicing isoforms, with significant differences in expression. AS events occurring in IFI6 and GADD45G may cause significant differences in gene expression. Other AS events, such as ONT.15153.3, may regulate the function of ART1 by regulating the expression of different transcripts. Moreover, co-expression and protein-protein interaction (PPI) analysis indicated that several genes (MRPL27, AAR2, PYGM, PSMD4, SCNM1, and HNRNPDL) may be related to intramuscular fat. The splicing isoforms investigated in our research provide a reference for the study of alternative splicing regulation of intramuscular fat deposition.
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DOI：
10.3390/foods9091180
发表时间：
2020-08-26
期刊：
Foods (Basel, Switzerland)
影响因子：
--
作者：
Gagaoua M;Bonnet M;Picard B
通讯作者：
Picard B
影响因子：
3.5
作者：
Kelemen O;Convertini P;Zhang Z;Wen Y;Shen M;Falaleeva M;Stamm S
通讯作者：
Stamm S
影响因子：
2.8
作者：
Chen Z;Li XY;Guo P;Wang DL
通讯作者：
Wang DL
DOI：
10.1016/bs.afnr.2019.03.006
发表时间：
2019-01-01
期刊：
ADVANCES IN FOOD AND NUTRITION RESEARCH, VOL 89
影响因子：
--
作者：
Alfaia, C. M.;Lopes, P. A.;Prates, J. A. M.
通讯作者：
Prates, J. A. M.
影响因子：
7
作者：
Cole, Charles;Byrne, Ashley;Vollmers, Christopher
通讯作者：
Vollmers, Christopher