IDEAS home Printed from https://ideas.repec.org/a/gam/jagris/v13y2022i1p108-d1020590.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2077-0472/13/1/108/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/2077-0472/13/1/108/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Qiwen Deng & Huiling Sun & Bangshun He & Yuqin Pan & Tianyi Gao & Jie Chen & Houqun Ying & Xian Liu & Feng Wang & Yong Xu & Shukui Wang, 2014. "Prognostic Value of Long Non-Coding RNA HOTAIR in Various Cancers," PLOS ONE, Public Library of Science, vol. 9(10), pages 1-9, October.
    2. Zhanwei Zhuang & Shaoyun Li & Rongrong Ding & Ming Yang & Enqin Zheng & Huaqiang Yang & Ting Gu & Zheng Xu & Gengyuan Cai & Zhenfang Wu & Jie Yang, 2019. "Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations," PLOS ONE, Public Library of Science, vol. 14(6), pages 1-21, June.
    3. Lei Sun & Hui Liu & Lin Zhang & Jia Meng, 2015. "lncRScan-SVM: A Tool for Predicting Long Non-Coding RNAs Using Support Vector Machine," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-16, October.
    4. Siddharth Sethi & David Zhang & Sebastian Guelfi & Zhongbo Chen & Sonia Garcia-Ruiz & Emmanuel O. Olagbaju & Mina Ryten & Harpreet Saini & Juan A. Botia, 2022. "Leveraging omic features with F3UTER enables identification of unannotated 3’UTRs for synaptic genes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Yanchun Li & Cintia M Coelho & Tian Liu & Song Wu & Jiasheng Wu & Yanru Zeng & Youchun Li & Brenda Hunter & Ricardo A Dante & Brian A Larkins & Rongling Wu, 2008. "A Statistical Model for Estimating Maternal-Zygotic Interactions and Parent-of-Origin Effects of QTLs for Seed Development," PLOS ONE, Public Library of Science, vol. 3(9), pages 1-12, September.
    6. A. C. Cattáneo & M. S. Trigo & L. O. Perez & C. A. Cordiviola & A. G. Antonini, 2017. "Detection of Three Allelic Variants in the Rabbit Growth Hormone Gene," International Journal of Sciences, Office ijSciences, vol. 6(03), pages 48-50, March.
    7. Kroll, K.M. & Ferrantini, A. & Domany, E., 2010. "Introduction to biology and chromosomal instabilities in cancer," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 389(20), pages 4374-4388.
    8. L. Zwierzchowski & E. Siadkowska & J. Oprządek & K. Flisikowski & E. Dymnicki, 2010. "An association of C/T polymorphism in exon 2 of the bovine insulin-like growth factor 2 gene with meat production traits in Polish Holstein-Friesian cattle," Czech Journal of Animal Science, Czech Academy of Agricultural Sciences, vol. 55(6), pages 227-233.

    More about this item

    Keywords

    mRNAs; lncRNA; spleen growth; ZBED6 KO Chinese Bama pigs;
    All these keywords.

    JEL classification:

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jagris:v:13:y:2022:i:1:p:108-:d:1020590. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.