Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs

PLOS ONE, Dec 2019

The giant panda (Ailuropoda melanoleuca) is one of the world’s most beloved endangered mammals. Although the draft genome of this species had been assembled, little was known about the composition of its microRNAs (miRNAs) or their functional profiles. Recent studies demonstrated that changes in the expression of miRNAs are associated with immunity. In this study, miRNAs were extracted from the blood of four healthy giant pandas and sequenced by Illumina next generation sequencing technology. As determined by miRNA screening, a total of 276 conserved miRNAs and 51 novel putative miRNAs candidates were detected. After differential expression analysis, we noticed that the expressions of 7 miRNAs were significantly up-regulated in young giant pandas compared with that of adults. Moreover, 2 miRNAs were up-regulated in female giant pandas and 1 in the male individuals. Target gene prediction suggested that the miRNAs of giant panda might be relevant to the expressions of 4,602 downstream genes. Subseuqently, the predicted target genes were conducted to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis and we found that these genes were mainly involved in host immunity, including the Ras signaling pathway, the PI3K-Akt signaling pathway, and the MAPK signaling pathway. In conclusion, our results provide the first miRNA profiles of giant panda blood, and the predicted functional analyses may open an avenue for further study of giant panda immunity.

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Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs

November Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs Mingyu Yang 0 1 Lianming Du 0 1 Wujiao Li 0 1 Fujun Shen 0 1 Zhenxin Fan 0 1 Zuoyi Jian 0 1 Rong Hou 0 1 Yongmei Shen 0 1 Bisong Yue 0 1 Xiuyue Zhang 0 1 0 1 Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University , Chengdu, Sichuan, 610064 , P.R. China , 2 The Key Laboratory for Conservation Biology of Endangered Wildlife, Sichuan Province, Chengdu Research Base of Giant Panda Breeding , Chengdu, Sichuan, 610081, China, 3 Gooddoctor pharmaceutical Group, NO.88 Yingkou Road, Chengdu, Sichuan, 610000 , China 1 Editor: Yun Zheng, Kunming University of Science and Technology , CHINA The giant panda (Ailuropoda melanoleuca) is one of the world's most beloved endangered mammals. Although the draft genome of this species had been assembled, little was known about the composition of its microRNAs (miRNAs) or their functional profiles. Recent studies demonstrated that changes in the expression of miRNAs are associated with immunity. In this study, miRNAs were extracted from the blood of four healthy giant pandas and sequenced by Illumina next generation sequencing technology. As determined by miRNA screening, a total of 276 conserved miRNAs and 51 novel putative miRNAs candidates were detected. After differential expression analysis, we noticed that the expressions of 7 miRNAs were significantly up-regulated in young giant pandas compared with that of adults. Moreover, 2 miRNAs were up-regulated in female giant pandas and 1 in the male individuals. Target gene prediction suggested that the miRNAs of giant panda might be relevant to the expressions of 4,602 downstream genes. Subseuqently, the predicted target genes were conducted to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis and we found that these genes were mainly involved in host immunity, including the Ras signaling pathway, the PI3K-Akt signaling pathway, and the MAPK signaling pathway. In conclusion, our results provide the first miRNA profiles of giant panda blood, and the predicted functional analyses may open an avenue for further study of giant panda immunity. Introduction MicroRNAs (miRNAs), as small non-coding (~22nt) RNAs, are key regulators of gene expression [ 1,2 ]. Precursor miRNA would form the mature functional miRNA after its stems loop structure is cut by two RNase III enzymes, Drosha and Dicer. The mature miRNAs are incorporated into the RNA-induced silencing complex (RISC), which binds to the 3’UTR proteincompany did not have any additional role in the study design, data collection and decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section. Competing Interests: Yongmei Shen is employed by Gooddoctor pharmaceutical group. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors. coding transcripts and represses the transcript translation or degrades the mRNA in mammals [ 3 ]. This leads many biological processes to be regulated, including development, reproduction, apoptosis, proliferation, pathogenesis, and lipometabolism [ 4–6 ]. It means that the abnormal expression of miRNAs may cause many diseases such as cardiac disease and cancer [ 7 ]. For example, the miR-150 was down-regulated in serum of arterial fibrillation patients, while the expression of miR-1, miR-134, miR-186, miR-208, miR-233, and miR-499 increased in serum of acute myocardial infarction patients [ 8–10 ]. Meanwhile, many diseases are related to immunity regulation, and several miRNAs have been shown to be important in immune functions [ 11,12 ]. For example, MiR-146 is implicated in numerous cancers and inflammatory diseases and has been confirmed to regulate inflammatory responses in several different cell types [ 13,14 ]. Thus, miRNAs represent an important target for potential therapeutic and diagnostic agents [ 15 ]. The giant panda, Ailuropoda melanoleuca, is an endangered mammal, which was once widespread in southern China but is now found only in Western China in Sichuan, Shanxi, and Gansu provinces of China [ 16, 17 ]. This species has received widespread attention and its draft genome has been assembled [17]. Although many miRNAs have been identified in mammals, there have been not yet been any reports about miRNAs of the giant panda [ 18, 19 ]. Blood, as a relatively easy tissue to isolate, is the main part of the immune system, and many diseases can be discovered through blood [14]. Therefore, it is more suitable and convenient to use blood to identify miRNAs related to immune and diseases. In this study, we sequenced the small RNA of four giant pandas blood through the next generation sequencing (NGS) te (...truncated)


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Mingyu Yang, Lianming Du, Wujiao Li, Fujun Shen, Zhenxin Fan, Zuoyi Jian, Rong Hou, Yongmei Shen, Bisong Yue, Xiuyue Zhang. Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs, PLOS ONE, 2015, Volume 10, Issue 11, DOI: 10.1371/journal.pone.0143242