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Deciphering the transcriptome of prepubertal buffalo mammary glands using RNA sequencing

  • Ratan K. ChoudharyEmail author
  • Shanti Choudhary
  • C. S. Mukhopadhyay
  • Devendra Pathak
  • Ramneek Verma
Original Article

Abstract

Although water buffaloes are the main milk-producing animals in Indian subcontinent, only limited attempts have been made to identify canonical pathways and gene regulatory networks operating within the mammary glands of these animals. Such information is important for identifying unique transcriptome signatures in the mammary glands of diseased animals. In this report, we analyzed the transcription profile of 3 prepubertal buffalo mammary glands and identified common genes (mean FPKM > 0.2 in all samples) operating in the glands. Among 19,994 protein coding genes, 14,678 genes expressed and 5316 unique genes did not express in prepubertal buffalo mammary glands. Of these 14,678 expressed genes, 79% comprised a ubiquitous transcriptome that was dominated by very lowly expressed genes (51%). The percentage of rarely, moderately, and abundantly expressed genes was 25%, 2%, and 1%, respectively. Gene Ontology (GO) terms reflected in the expression of common genes (mean FPKM > 5.0) for molecular function were related to binding and catalytic activity. Products of these genes were involved in metabolic and cellular processes and belong to nucleic acid binding proteins. The canonical pathways for growth of mammary glands included integrin signaling, inflammation, GnRH and Wnt pathways. KEGG enriched pathways revealed many pathways of cancer including ribosome, splisosome, endocytosis, and ubiquitin-mediated proteolysis, pathways for viral infection, and bacterial invasion of epithelial. Highly expressed genes (mean FPKM > 500 included beta-actin (ACTB), beta-2 microglobulin (B2M), caseins (CSN2, CNS3), collagens (COL1A1, COL3A1), translation elongation factors (EEF1A1, EEF1G, EEF2), keratins (KRT15, KRT19), major histocompatibility complex genes (CD74, JSP.1), vimentin (VIM), and osteopontin (SPP1). Interestingly, expression of milk protein genes in prepubertal glands opens possible roles of these genes in development of mammary glands. We report the whole transcriptomic signature of prepubertal buffalo mammary gland and indicated its molecular signature is similar to cancer type.

Keywords

Buffalo mammary gland Prepubertal RNA-seq Immunohistochemistry RT-qPCR 

Notes

Acknowledgements

The authors also would like to thank Drs. Anthony Capuco and Kristy Daniels for scientific discussion and Dr. Capuco for grammatical usage and language correction. The authors would also like to thank Dr. Kuldeep Gupta, Professor of Veterinary Pathology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana in identifying pathology of these mammary tissues.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10142_2018_645_MOESM1_ESM.xlsx (5 mb)
ESM 1 Ubiquitous gene list and their mean FPKM values (>0.2 in all three samples), identified in prepubertal buffalo mammary tissue (XLSX 5093 kb)
10142_2018_645_MOESM2_ESM.xlsx (100 kb)
ESM 2 Enrichment of functional annotations using Gene Ontology (GO) terms for Biological Process, Molecular Function and Cellular Component of ubiquitous genes (XLSX 99 kb)
10142_2018_645_MOESM3_ESM.xlsx (33 kb)
ESM 3 Significant KEGG pathways of all the ubiquitous genes having mean FPKM >5.0 (XLSX 32 kb)
10142_2018_645_MOESM4_ESM.xlsx (15 kb)
ESM 4 Pathways that were not expressed in prepubertal buffalo mammary gland. (XLSX 14 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Animal BiotechnologyGuru Angad Dev Veterinary and Animal Sciences UniversityLudhianaIndia
  2. 2.Department of Animal and Veterinary SciencesUniversity of VermontBurlingtonUSA
  3. 3.Department of Veterinary Anatomy, College of Veterinary ScienceGuru Angad Dev Veterinary and Animal Science UniversityLudhianaIndia

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