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A novel lincRNA identified in buffalo oocytes with protein binding characteristics could hold the key for oocyte competence

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Abstract

Studying the maternal oocyte-specific genes, in farm animals is a significant step towards delineating the underlying mechanisms that regulate oocyte quality, early embryonic development and survival. With the creation of buffalo oocyte-specific subtracted cDNA library, it has raised new questions which need to be answered. The present study has characterized one of the ESTs selected from the library and highlighted its importance in the oocyte quality. The selected EST was made full length by RLM-RACE and four transcript variants were identified. Bioinformatics analysis indicated the novelty of full-length transcript along with conserved intergenic nature. The largest transcript was identified as long intergenic noncoding RNA based upon coding potential calculator output. The expression analysis at different hours of oocyte maturation showed a significant variation in developmentally competent oocytes to that of incompetent ones. Along with this, the transcript was also found to have protein binding ability which was confirmed by RNA electrophoretic mobility shift assay. The protein used in the experiment was isolated from oocyte and cumulus cells via sonication. A novel lincRNA has been reported here that might have an important role in maturation of oocytes, inferred from its relative gene expression study and protein binding characteristics.

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Abbreviations

ESTs:

Expressed sequence tags

RLM:

RNA ligase mediated

RACE:

Rapid amplification of cDNA ends

COC:

Cumulus oocyte complex

μg:

Micro gram

ml:

Millilitre

PBS:

Phosphate buffer saline

NCBI:

National Centre for Biotechnology Information

BLAST:

Basic local alignment search tool

RPS:

Ribosomal protein S

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Acknowledgements

SD acknowledge NDRI, Karnal for providing infrastructure and facility and Council of Scientific and Industrial Research (CSIR), Govt. of India for his JRF and SRF Grant.

Funding

This work was supported by the National Fund under Grant No. NF2049/3040 of Indian Council of Agricultural Research, New Delhi, India.

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Authors and Affiliations

  1. Department of Life Science, Sharda University, Greater Noida, India

    Sunny Dholpuria

  2. Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India

    Sandeep Kumar, Manish Kumar, Parul Sarwalia, Rakesh Kumar & Tirtha Kumar Datta

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  1. Sunny Dholpuria
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  2. Sandeep Kumar
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  3. Manish Kumar
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  4. Parul Sarwalia
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  5. Rakesh Kumar
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  6. Tirtha Kumar Datta
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Contributions

SD performed experiments, interpreted results and wrote the manuscript, SK in data interpretation and manuscript revision, MK helped in real time expression study and result analysis, PS in data interpretation, RK provided vital inputs to this study, TKD conceived the work, designed, supervised the final manuscript.

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Correspondence to Sunny Dholpuria or Tirtha Kumar Datta.

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Dholpuria, S., Kumar, S., Kumar, M. et al. A novel lincRNA identified in buffalo oocytes with protein binding characteristics could hold the key for oocyte competence. Mol Biol Rep 48, 3925–3934 (2021). https://doi.org/10.1007/s11033-021-06388-9

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