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牛乳腺中长链基因间非编码RNA的鉴定与特征分析

Identification and characterization of long intergenic noncoding RNAs in bovine mammary glands.

作者信息

Tong Chao, Chen Qiaoling, Zhao Lili, Ma Junfei, Ibeagha-Awemu Eveline M, Zhao Xin

机构信息

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.

Agriculture and Agri-Food Canada, Research and Development Centre, Sherbrooke, QC, J1M 0C8, Canada.

出版信息

BMC Genomics. 2017 Jun 19;18(1):468. doi: 10.1186/s12864-017-3858-4.

DOI:10.1186/s12864-017-3858-4
PMID:28629368
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5477121/
Abstract

BACKGROUND

Mammary glands of dairy cattle produce milk for the newborn offspring and for human consumption. Long intergenic noncoding RNAs (lincRNAs) play various functions in eukaryotic cells. However, types and roles of lincRNAs in bovine mammary glands are still poorly understood.

RESULTS

Using computational methods, 886 unknown intergenic transcripts (UITs) were identified from five RNA-seq datasets from bovine mammary glands. Their non-coding potentials were predicted by using the combination of four software programs (CPAT, CNCI, CPC and hmmscan), with 184 lincRNAs identified. By comparison to the NONCODE2016 database and a domestic-animal long noncoding RNA database (ALDB), 112 novel lincRNAs were revealed in bovine mammary glands. Many lincRNAs were found to be located in quantitative trait loci (QTL). In particular, 36 lincRNAs were found in 172 milk related QTLs, whereas one lincRNA was within clinical mastitis QTL region. In addition, targeted genes for 10 lincRNAs with the highest fragments per kilobase of transcript per million fragments mapped (FPKM) were predicted by LncTar for forecasting potential biological functions of these lincRNAs. Further analyses indicate involvement of lincRNAs in several biological functions and different pathways.

CONCLUSION

Our study has provided a panoramic view of lincRNAs in bovine mammary glands and suggested their involvement in many biological functions including susceptibility to clinical mastitis as well as milk quality and production. This integrative annotation of mammary gland lincRNAs broadens and deepens our understanding of bovine mammary gland biology.

摘要

背景

奶牛的乳腺为新生后代生产牛奶以供人类消费。长链基因间非编码RNA（lincRNA）在真核细胞中发挥多种功能。然而，lincRNA在牛乳腺中的类型和作用仍知之甚少。

结果

利用计算方法，从牛乳腺的五个RNA测序数据集中鉴定出886个未知基因间转录本（UIT）。通过结合四种软件程序（CPAT、CNCI、CPC和hmmscan）预测它们的非编码潜力，共鉴定出184个lincRNA。与NONCODE2016数据库和家畜长链非编码RNA数据库（ALDB）相比，在牛乳腺中发现了112个新的lincRNA。许多lincRNA位于数量性状基因座（QTL）中。特别是，在172个与牛奶相关的QTL中发现了36个lincRNA，而在临床乳腺炎QTL区域内有一个lincRNA。此外，通过LncTar预测了每百万映射片段中每千碱基转录本片段数（FPKM）最高的10个lincRNA的靶向基因，以预测这些lincRNA的潜在生物学功能。进一步分析表明lincRNA参与了多种生物学功能和不同途径。

结论

我们的研究提供了牛乳腺中lincRNA的全景视图，并表明它们参与了许多生物学功能，包括对临床乳腺炎的易感性以及牛奶质量和产量。乳腺lincRNA的这种综合注释拓宽和加深了我们对牛乳腺生物学的理解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/8e17d4db86cc/12864_2017_3858_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/394641f5e4e9/12864_2017_3858_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/cabec5df7231/12864_2017_3858_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/6d6a150c7e9c/12864_2017_3858_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/ffa4c2fde61f/12864_2017_3858_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/9f35651c6326/12864_2017_3858_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/8e17d4db86cc/12864_2017_3858_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/394641f5e4e9/12864_2017_3858_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/cabec5df7231/12864_2017_3858_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/6d6a150c7e9c/12864_2017_3858_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/ffa4c2fde61f/12864_2017_3858_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/9f35651c6326/12864_2017_3858_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/abf9/5477121/8e17d4db86cc/12864_2017_3858_Fig6_HTML.jpg

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