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Comprehensive Analysis of lncRNA and mRNA Reveals the Effect of ZBED6 on Spleen Growth in Pigs

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  • Dandan Wang

    (Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
    National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China)

  • Shengnan Wang

    (Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
    National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China)

  • Wenjie Tian

    (Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
    National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China)

  • Yuehui Ma

    (National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China)

  • Lin Jiang

    (Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China)

Abstract

Transcription factor zinc-finger BED domain-containing protein 6 ( ZBED6 ) is unique to placental mammals and regulates insulin-like growth factor 2 ( IGF2 ) expression, which lead to muscle growth. However, the effect of ZBED6 on the growth of spleen is still elusive. In this study, we explored the regulation of ZBED6 on spleen growth, and the results showed ZBED6 knockout ( ZBED6 KO) pigs had heavier spleens than wild-type (WT) pigs. To analyze the mechanism of increased spleen weight in ZBED6 KO pigs, long noncoding RNAs (lncRNAs) and mRNAs in the spleen samples (WT: ZBED6 KO pigs = 3:3) were analyzed to identify differentially expressed lncRNAs (DE-lncRNAs) and genes (DEGs) based on the RNA sequencing (RNA-seq) method. Then, 142 DEGs and 82 DE-lncRNAs were obtained. The qRT-PCR results were consistent with those of the RNA-seq, indicating that the data were reliable. The heavier spleen weight of ZBED6 KO pigs coincided with the significantly upregulated IGF2 mRNA. Functional enrichment analysis of DEGs showed enrichment mainly in myofibril assembly and sarcomere. In addition, 252 cis- and 109 trans-acting target genes of 82 DE-lncRNAs were predicted. By conjoint analysis of lncRNA and mRNA revealed that IGF2 , DE-lnRNAs ( XLOC_113021 , XLOC_078852 , NONSUSG004057.1 , NONSUSG014354.1 , and NONSUSG009750.1 ), and their target gene ACTN2 may be the key candidate genes in promoting spleen growth in ZBED6 KO pigs. This study provides new directions to understand the global functions of ZBED6 and lncRNAs in spleen growth in pigs.

Suggested Citation

  • Dandan Wang & Shengnan Wang & Wenjie Tian & Yuehui Ma & Lin Jiang, 2022. "Comprehensive Analysis of lncRNA and mRNA Reveals the Effect of ZBED6 on Spleen Growth in Pigs," Agriculture, MDPI, vol. 13(1), pages 1-13, December.
  • Handle: RePEc:gam:jagris:v:13:y:2022:i:1:p:108-:d:1020590
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    1. Mitchell Guttman & Ido Amit & Manuel Garber & Courtney French & Michael F. Lin & David Feldser & Maite Huarte & Or Zuk & Bryce W. Carey & John P. Cassady & Moran N. Cabili & Rudolf Jaenisch & Tarjei S, 2009. "Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals," Nature, Nature, vol. 458(7235), pages 223-227, March.
    2. Anne-Sophie Van Laere & Minh Nguyen & Martin Braunschweig & Carine Nezer & Catherine Collette & Laurence Moreau & Alan L. Archibald & Chris S. Haley & Nadine Buys & Michael Tally & Göran Andersson & M, 2003. "A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig," Nature, Nature, vol. 425(6960), pages 832-836, October.
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    Keywords

    mRNAs; lncRNA; spleen growth; ZBED6 KO Chinese Bama pigs;
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