猪皮下和内脏脂肪组织microRNA转录组的鉴定与差异表达分析
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摘要
猪(Sus scrofa)在肉类产业中占有重要地位,随着高通量测序技术(Solexa sequencing)在miRNA测序中的广泛应用,利用niRNA-seq技术挖掘到大量与特定生物学或组织学功能相关的miRNAs。通过比较组织或生物学过程中miRNAs的表达差异,可以为解释脂肪组织中的成脂和脂肪细胞分化差异提供依据,同时,发掘与脂肪沉积调控相关的miRNA,为猪肉质改良提供后备基因。
本文选取3头210日龄的健康长白母猪,测定了猪背部皮下上层脂肪(Upper layer of backfat, ULB)、背部皮下下层脂肪(Inner layer of backfat,ILB)、心脏包膜脂肪(Pericardial adipose, PAD)、腹膜后脂肪(Retroperitoneal adipose, RAD)、肠系膜脂肪(Mesenteric adipose, MAD)和大网膜脂肪(Greater omentum, GOM)的脂肪细胞体积及炎症相关基因的表达差异。采用Solexa测序方法分析了6个文库的miRNAs表达谱。利用IDEG6.0等软件,分析了这6个脂肪组织中miRNA的表达差异。通过组织和基因的聚类分析,探讨6个脂肪组织中miRNAs的表达规律。利用靶基因预测软件MicroCosm,预测了高丰度差异niRNAs调控的靶基因。通过GO (Gene ontology)和Pathway分析,研究了这些靶基因参与的生物学过程,从而解释这些差异表达miRNA在不同部位脂肪组织中的生物学功能差异。
荧光定量结果显示,巨噬细胞标志基因CD14在内脏脂肪中的表达量显著高于皮下脂肪组织(p<0.05),说明在VATs中的巨噬细胞数量高于SATs。组织石蜡切片研究结果显示,长白母猪在210日龄时,SATs (Subcutaneous adipose tissues)的脂肪细胞体积极显著大于VATs (Visceral adipose tissues)(p<0.01)。
通过Solexa测序,在6个脂肪组织小RNA文库中共获得803条miRNAs,其中,199条miRNAs已在miRBase数据库中公布,新发现miRNAs604条。miRNAs表达种类分析结果显示,6个文库两两间的共表达基因数相似(326±9个)。SATs与VATs间的差异基因总数达到398个,这部分差异基因中,在VATs中特异性表达的有303个。
共表达基因的聚类分析结果显示,2个SATs与4个VATs明显的聚为2类。共表达miRNAs表达量差异分析显示,198个基因在、VATs与SATs间存在显著差异。与4个VATs miRNAs表达量比较,49个miRNAs在ULB中上调,81个出现下调；ILB中94个miRNAs出现上调,59个呈现下调。
对SATs和VATs差异表达前10位的miRNAs做靶基因预测及GO和Pathway注释,结果显示,在SATs中上调的miRNAs调控的基因主要富集于能量代谢和脂肪代谢过程中,在VATs中上调的miRNAs主要参与炎症反应和免疫应答过程。
通过本文的研究,不仅增加了猪脂肪组织中表达的候选miRNAs数量,还从miRNAs的角度初步分析了SATs与VATs内的生物学调控通路差异。为猪肉质改良和研究不同部位脂肪组织生物学功能差异提供了依据。
The domestic pig (Sus scrofa) is an important economic animal for meet production, as high-throughput sequencing (Solexa sequencing) technology has been widely used to determine miRNA, which can obtain a large number of miRNAs play the different role in biological processes or organizational functions. Differential expression analysis of these miRNAs in organization or biological processes, can interpretation the miRNAs regulation and function differences in adipogenesis and fat deposition. At the same time, expand the repertoire of porcine miRNAs and further explore potential regulatory miRNAs which involved in adipogenesis and fat deposition, and provided genes for swine meat quality improvement.
In order to identification the differential expression profile in six adipose tissues (i.e. upper layer of backfat (ULB), inner layer of backfat (ILB), pericardial adipose (PAD), retroperitoneal adipose (RAD), mesenteric adipose (MAD) and greater omentum (GOM)) of porcine, we adopted a deep sequencing approach to determine the miRNAs expression in three healthy Landrace female pigs (210-days old). And then analyzed the differential expression miRNAs in six libraries through the IDEG6.0software. Via organization and gene cluster analysis of miRNAs in the six fat to identify the depot expression pattern. At last, the target genes predicted by differential expression miRNAs were made GO term and Pathway enrichment to observe the involvement in biological processes, which may explaining the differential expression miRNA specific functions in different adipose sites. To test our hypothesis that the porcine VATs have higher inflammatory gene expression and adipocyte volume than SATs as previous observations in human studies, the inflammatory gene expression profiles and adipocyte volume of distinct porcine adipose tissues were measured.
Our results indicated that the monocyte/macrophage marker gene (CD14) exhibited a higher expression level in VATs vs. SATs (p<0.05), which indicated a smaller rate of macrophage infiltration in SATs in comparison to VATs, even though there was no significant difference between MAD and ILB. The results showed that two SATs (Subcutaneous adipose tissues)(i.e. ULB, ILB) had a significant higher adipocyte volume than the compartmental VATs (Visceral adipose tissues)(i.e. GOM, RAD, MAD and PAD)(p<0.01). Solexa sequencing identified803unique miRNAs in the six adipose tissue, of which199miRNAs has been released in the database, and604were novel predicted miRNAs. Although six miRNAs libraries had a similar co-expression number (326±9) between each other, we also found a large number of specific expression types (398) among SATs and VATs, of which303specific expression in VATs.
Clustering of co-expression miRNAs results showed that two SATs (i.e. ILB and ULB) were tightly clustered into a subgroup, and other four VATs (i.e. GOM, MAD, RAD and PAD) were clustered together into another subgroup. Differential expression analysis of co-expression miRNAs showed that198genes were significantly different expression between VATs and SATs. Compared with VATs,49miRNAs up-regulated and81miRNAs down-regulated in the ULB. About another SATs,94and59miRNAs significantly raised and declined respectively in ILB versus VATs.
GO and Pathway annotation of target gene of top10most differential expression miRNAs showed that miRNAs highly expressed in the SATs were mainly enriched in the biological process of energy metabolism and fat metabolism, and the miRNAs highly expression in VATs were mainly involved in inflammation and immune response.
This study present that six adipose tissue characteristics significant difference can be classified as SATs and VATs group. From the phenotype, SATs had a significantly big adipocyte volumes than VATs. And expression profiling analysis also indicated that differentially expressed miRNAs cataloged by SATs and VATs were correspond the biological characteristics of SATs and VATs. The miRNAs highly expressed in SATs were involved in the process of lipose synthesis and metabolism, and miRNAs highly expressed in VATs is involved in the immune and inflammatory responses.
Our results predicted many novel candidate miRNAs, which required further experimental validation. In addition, provide new information for biological process regulation different between SATs and VATs of miRNAs. Take together, these studies may help with the genomic analysis of economic traits in the pig that can be used to improve the selection of more efficient and healthier pork production.
本文选取3头210日龄的健康长白母猪,测定了猪背部皮下上层脂肪(Upper layer of backfat, ULB)、背部皮下下层脂肪(Inner layer of backfat,ILB)、心脏包膜脂肪(Pericardial adipose, PAD)、腹膜后脂肪(Retroperitoneal adipose, RAD)、肠系膜脂肪(Mesenteric adipose, MAD)和大网膜脂肪(Greater omentum, GOM)的脂肪细胞体积及炎症相关基因的表达差异。采用Solexa测序方法分析了6个文库的miRNAs表达谱。利用IDEG6.0等软件,分析了这6个脂肪组织中miRNA的表达差异。通过组织和基因的聚类分析,探讨6个脂肪组织中miRNAs的表达规律。利用靶基因预测软件MicroCosm,预测了高丰度差异niRNAs调控的靶基因。通过GO (Gene ontology)和Pathway分析,研究了这些靶基因参与的生物学过程,从而解释这些差异表达miRNA在不同部位脂肪组织中的生物学功能差异。
荧光定量结果显示,巨噬细胞标志基因CD14在内脏脂肪中的表达量显著高于皮下脂肪组织(p<0.05),说明在VATs中的巨噬细胞数量高于SATs。组织石蜡切片研究结果显示,长白母猪在210日龄时,SATs (Subcutaneous adipose tissues)的脂肪细胞体积极显著大于VATs (Visceral adipose tissues)(p<0.01)。
通过Solexa测序,在6个脂肪组织小RNA文库中共获得803条miRNAs,其中,199条miRNAs已在miRBase数据库中公布,新发现miRNAs604条。miRNAs表达种类分析结果显示,6个文库两两间的共表达基因数相似(326±9个)。SATs与VATs间的差异基因总数达到398个,这部分差异基因中,在VATs中特异性表达的有303个。
共表达基因的聚类分析结果显示,2个SATs与4个VATs明显的聚为2类。共表达miRNAs表达量差异分析显示,198个基因在、VATs与SATs间存在显著差异。与4个VATs miRNAs表达量比较,49个miRNAs在ULB中上调,81个出现下调；ILB中94个miRNAs出现上调,59个呈现下调。
对SATs和VATs差异表达前10位的miRNAs做靶基因预测及GO和Pathway注释,结果显示,在SATs中上调的miRNAs调控的基因主要富集于能量代谢和脂肪代谢过程中,在VATs中上调的miRNAs主要参与炎症反应和免疫应答过程。
通过本文的研究,不仅增加了猪脂肪组织中表达的候选miRNAs数量,还从miRNAs的角度初步分析了SATs与VATs内的生物学调控通路差异。为猪肉质改良和研究不同部位脂肪组织生物学功能差异提供了依据。
The domestic pig (Sus scrofa) is an important economic animal for meet production, as high-throughput sequencing (Solexa sequencing) technology has been widely used to determine miRNA, which can obtain a large number of miRNAs play the different role in biological processes or organizational functions. Differential expression analysis of these miRNAs in organization or biological processes, can interpretation the miRNAs regulation and function differences in adipogenesis and fat deposition. At the same time, expand the repertoire of porcine miRNAs and further explore potential regulatory miRNAs which involved in adipogenesis and fat deposition, and provided genes for swine meat quality improvement.
In order to identification the differential expression profile in six adipose tissues (i.e. upper layer of backfat (ULB), inner layer of backfat (ILB), pericardial adipose (PAD), retroperitoneal adipose (RAD), mesenteric adipose (MAD) and greater omentum (GOM)) of porcine, we adopted a deep sequencing approach to determine the miRNAs expression in three healthy Landrace female pigs (210-days old). And then analyzed the differential expression miRNAs in six libraries through the IDEG6.0software. Via organization and gene cluster analysis of miRNAs in the six fat to identify the depot expression pattern. At last, the target genes predicted by differential expression miRNAs were made GO term and Pathway enrichment to observe the involvement in biological processes, which may explaining the differential expression miRNA specific functions in different adipose sites. To test our hypothesis that the porcine VATs have higher inflammatory gene expression and adipocyte volume than SATs as previous observations in human studies, the inflammatory gene expression profiles and adipocyte volume of distinct porcine adipose tissues were measured.
Our results indicated that the monocyte/macrophage marker gene (CD14) exhibited a higher expression level in VATs vs. SATs (p<0.05), which indicated a smaller rate of macrophage infiltration in SATs in comparison to VATs, even though there was no significant difference between MAD and ILB. The results showed that two SATs (Subcutaneous adipose tissues)(i.e. ULB, ILB) had a significant higher adipocyte volume than the compartmental VATs (Visceral adipose tissues)(i.e. GOM, RAD, MAD and PAD)(p<0.01). Solexa sequencing identified803unique miRNAs in the six adipose tissue, of which199miRNAs has been released in the database, and604were novel predicted miRNAs. Although six miRNAs libraries had a similar co-expression number (326±9) between each other, we also found a large number of specific expression types (398) among SATs and VATs, of which303specific expression in VATs.
Clustering of co-expression miRNAs results showed that two SATs (i.e. ILB and ULB) were tightly clustered into a subgroup, and other four VATs (i.e. GOM, MAD, RAD and PAD) were clustered together into another subgroup. Differential expression analysis of co-expression miRNAs showed that198genes were significantly different expression between VATs and SATs. Compared with VATs,49miRNAs up-regulated and81miRNAs down-regulated in the ULB. About another SATs,94and59miRNAs significantly raised and declined respectively in ILB versus VATs.
GO and Pathway annotation of target gene of top10most differential expression miRNAs showed that miRNAs highly expressed in the SATs were mainly enriched in the biological process of energy metabolism and fat metabolism, and the miRNAs highly expression in VATs were mainly involved in inflammation and immune response.
This study present that six adipose tissue characteristics significant difference can be classified as SATs and VATs group. From the phenotype, SATs had a significantly big adipocyte volumes than VATs. And expression profiling analysis also indicated that differentially expressed miRNAs cataloged by SATs and VATs were correspond the biological characteristics of SATs and VATs. The miRNAs highly expressed in SATs were involved in the process of lipose synthesis and metabolism, and miRNAs highly expressed in VATs is involved in the immune and inflammatory responses.
Our results predicted many novel candidate miRNAs, which required further experimental validation. In addition, provide new information for biological process regulation different between SATs and VATs of miRNAs. Take together, these studies may help with the genomic analysis of economic traits in the pig that can be used to improve the selection of more efficient and healthier pork production.
引文
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