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Doctoral thesis, 2019

Comparative bioinformatics analyses of transcriptome and epigenome data using bovine model systems

Jhamat, Naveed ;


Bioinformatics methodology is used to understand complex biological processes in molecular biology, genetics and epigenetics. This thesis performed analysis of the complex biological processes controlling reproduction in mammals including dairy cattle. Successful fertility in dairy cattle is required for farm sustainability as it supports milk productivity and longevity. Disorder in metabolism due to higher levels of insulin during pregnancy and disturbance of immune response due to bacterial infections after calving are detrimental in reproduction. Determinants controlling these molecular mechanisms are poorly understood. To investigate these mechanisms, we performed bioinformatics analyses on data obtained from two experimental studies: Insulin is a regulator of metabolism and conditions such as hyperinsulinemia is known to impair fertility especially during embryonic development. This study investigates the potential effect of insulin treatment on gene expression and DNA methylation patterns of bovine embryos during in vitro oocyte maturation by using the EmbryoGENE DNA Methylation Array. The results of Paper I revealed that the identified differentially methylated regions (DMRs) were correlated with differentially expressed genes involved in metabolic regulation. Uterine diseases impair fertility in dairy cattle and Lipopolysaccharide (LPS) from gram-negative Escherichia coli, is a major source of uterine diseases by activating proinflammatory pathways. This study investigates in vitro the effects of infection by LPS on bovine endometrial epithelial cells (bEEC) mimicking in vivo processes. In Paper II, RNA Sequencing analysis revealed that LPS has significantly affected the transcriptome of bEEC, identifying more than 2000 differentially expressed genes, involved in immune response, proliferation, cell adhesion, and implantation. In Paper III, Bisulfite sequencing revealed that LPS has profoundly affected the DNA methylation pattern of bEEC. 1291 DMRs were found and their associated genes were involved in molecular processes related to proliferation, apoptosis and embryo development. In Paper IV, the enrichment of motifs within these DMRs revealed transcription factor binding sites for immunologically important transcription factors. Thus, the transcriptomics, epigenomics and bioinformatics results obtained from these analyses revealed the complexity of the regulatory transcriptional network activated during inflammation.


Insulin; Metabolic imbalance; RNA-Seq; LPS; Endometritis; Implantation; Epigenetics; RRBS; Differential methylation; TFBS

Published in

Acta Universitatis Agriculturae Sueciae

2019, number: 2019:15
ISBN: 978-91-7760-348-1, eISBN: 978-91-7760-349-8
Publisher: Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences

Authors' information

Jhamat, Naveed (Jhamat, Naveed )
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics

UKÄ Subject classification

Clinical Science
Bioinformatics and Systems Biology

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