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Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak

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Abstract

Cattleyaks are the crossbred offspring between cattle and yaks, exhibiting the prominent adaptability to the harsh environment as yaks and much higher growth performances than yaks around Qinghai-Tibet plateau. Unfortunately, cattleyak cannot be effectively used in yak breeding due to its male infertility resulted from spermatogenic arrest. In this study, we performed RNA sequencing (RNA-seq) and bioinformatics analysis to determine the expression profiles of long noncoding RNA (lncRNA) from cattleyak and yak testis. A total of 604 differentially expressed (DE) lncRNAs (135 upregulated and 469 downregulated) were identified in cattleyak with respect to yak. Through gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we identified several DE lncRNAs regulating the mitotic cell cycle processes by targeting the genes significantly associated with the mitotic cell cycle checkpoint and DNA damage checkpoint term and also significantly involved in p53 signaling pathway, mismatch repair and homologous recombination pathway (P < 0.05). The reverse transcription PCR (RT-PCR) and quantitative Real-Time PCR (qRT-PCR) analysis of the randomly selected fourteen DE lncRNAs and the seven target genes validated the RNA-seq data and their true expressions during spermatogenesis in vivo. Molecular cloning and sequencing indicated that the testis lncRNAs NONBTAT012170 and NONBTAT010258 presented higher similarity among different cattleyak and yak individuals. The downregulation of these target genes in cattleyak contributed to the abnormal DNA replication and spermatogenic arrest during the S phase of mitotic cell cycle. This study provided a novel insight into lncRNA expression profile changes associated with spermatogenic arrest of cattleyak.

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Data availability

All analyzed data in this study are included in this published article and all RNA-seq data in this study are available in NCBI under accession numbers: PRJNA509997, PRJNA510216, PRJNA510224, PRJNA510232, PRJNA510475, and PRJNA510552.

Abbreviations

lncRNA:

Long non-coding RNA

RNA-Seq:

RNA sequencing

SSC:

Spermatogonial stem cell

DE:

Differentially expressed

QC:

Quality control

FC:

Fold change

ORF:

Open reading frame

GO:

Gene ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

CPC:

Coding Potential Calculator

CNCI:

Coding-Non-Coding-Index

CPAT:

The Coding Potential Assessment Tool

RT-PCR:

Reverse transcription Polymerase Chain Reaction

qRT-PCR:

Quantitative Real-Time PCR

FPKM:

Fragments per kilobase of transcript per million mapped reads

TMM:

Trimmed mean of M values

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Funding

This work was supported by “the Fundamental Research Funds for the Central Universities,” Southwest Minzu University (2020NZD04); the Key Project of Sichuan Provincial Education Department (16ZA0134); and the Program of National Beef Cattle and Yak Industrial Technology System (No. CARS-37).

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Authors and Affiliations

  1. Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, 610041, Sichuan, China

    Xin Cai, Shixin Wu, TserangDonko Mipam, Hui Luo, Chuanping Yi, Chuanfei Xu & Jincheng Zhong

  2. School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, Sichuan, China

    Shixin Wu, Hui Luo, Chuanping Yi, Chuanfei Xu & Wangsheng Zhao

  3. College of Chemistry&Environment, Southwest Minzu University, Chengdu, 610041, Sichuan, China

    Hongying Wang

Authors
  1. Xin Cai
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  2. Shixin Wu
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  3. TserangDonko Mipam
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  4. Hui Luo
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  7. Wangsheng Zhao
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  8. Hongying Wang
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  9. Jincheng Zhong
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Contributions

Xin Cai, Shixin Wu, and Jincheng Zhong conceived the study; Shixin Wu, TserangDonko Mipam, Hui Luo, and Wangsheng Zhao analyzed data; Shixin Wu, Chuanfei Xu, Chuanping Yi, and Hongying Wang prepared and performed experiments under the supervision of Xin Cai; Shixin Wu wrote and revised the manuscript with the help of Hui Luo, Xin Cai, and Jincheng Zhong. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Xin Cai or Jincheng Zhong.

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Ethical approval

The experimental animal procedures were followed in accordance with the approved protocols of Sichuan Province, PR China, for the Biological Studies Animal Care and Use Committee, and all protocols were approved by the Institutional Review Board of Southwest Minzu University.

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The authors declare no competing interests.

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Supplementary Information

Below is the link to the electronic supplementary material.

10142_2021_806_MOESM1_ESM.docx

Supplementary file1 (DOCX 17 KB) Table S1: Primer sequences used for RT-PCR and Q-PCR validation of the target genes for lncRNAs involved in mitotic cell cycle processes.

10142_2021_806_MOESM2_ESM.docx

Supplementary file2 (DOCX 18 KB) Table S2: Primer sequences used for RT-PCR and Q-PCR of the lncRNAs involved in mitotic cell cycle processes.

10142_2021_806_MOESM3_ESM.docx

Supplementary file3 (DOCX 17 KB) Table S3: Primer sequences used for molecular cloning of the lncRNAs NONBTAT012170 and NONBTAT010258.

10142_2021_806_MOESM4_ESM.xlsx

Supplementary file4 (XLSX 11 KB) Table S4: Sequencing statistics summary of the lncRNA library and database alignment generated by RNA-seq.

Supplementary file5 (XLSX 60 KB) Table S5: DE lncRNAs between testis transcriptome of cattleyak and yak.

Supplementary file6 (XLS 1371 KB) Table S6: Target genes of LncRNA in cis-prediction

Supplementary file7 (XLS 3421 KB) Table S7: Target genes of LncRNA in trans-prediction

10142_2021_806_MOESM8_ESM.xlsx

Supplementary file8 (XLSX 21 KB) Table S8: Summary of the significantly enriched GO items for the target genes of DE lncRNAs and the list of genes involved in each item.

Supplementary file9 (DOCX 46 KB) Table S9: Top listed Go enrichments of target genes and the corresponding lncRNAs.

10142_2021_806_MOESM10_ESM.xlsx

Supplementary file10 (XLSX 12 KB) Table S10: Summary of the significantly enriched KEGG pathways for the target genes of DE lncRNAs and the list of genes involved in each pathway.

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Cai, X., Wu, S., Mipam, T. et al. Testis transcriptome profiling identified lncRNAs involved in spermatogenic arrest of cattleyak. Funct Integr Genomics 21, 665–678 (2021). https://doi.org/10.1007/s10142-021-00806-8

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