Identification of Differentially Methylated Regions (DMR) in the genome of bovine endometrial epithelial cells (bEEC)challenged by E.Coli LPS and its effect on transcription

Abstract

Lipopolysaccharide (LPS) from Gram-negative bacteria induces the activation of pro-inflammatory pathways in the endometrium and such reactions potentially affect fertility and more specifically the implantation process. Gene expression studies based on RNA sequencing [Guo et al., Epiconcept Conference 2015, Abstract O-23, 34p] have shown that more than 2000 genes were differentially expressed (DEGs) in bEEC exposed to LPS. This study aimed to identify epigenetic correlates of these DEGs by detecting Differentially Methylated Regions (DMRs) in same cells. bEEC were exposed in vitro to 0, 2, and 8 μg/ml LPS for 24 hours. DNA libraries were prepared at The Babraham Institute, UK for reduced representation bisulfite sequencing (RRBS) using MspI digestion followed by end-repair/A-tailing and 5mC adaptor ligation and bisulfite conversion plus PCR. Sequences were analyzed using BS-Seeker2 for alignment of reads and MethylKit v0.9.5 for finding significant DMRs. AliBaba2 was used to predict potential transcription factor binding sites (TFBS) at DMRs using the TRANSFAC database. Analysis of RRBS data revealed 78 DMRs with q-value

Published in

Title: Epigenetics and Periconception Environment : Proceedings of the EPICONCEPT Conference 2016 : Giardini Naxos, Italy 26 - 29 September 2016
Publisher: University of Milan & COST Action FA1201

Conference

EPICONCEPT Conference 2016, Epigenetics and Periconception

SLU Authors

• Jhamat, Naveed

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Guo, Yongzhi

  • Department of Clinical Sciences, Swedish University of Agricultural Sciences
    

• Niazi, Adnan

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Bongcam Rudloff, Erik

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Andersson, Göran

  • Department of Animal Biosciences, Swedish University of Agricultural Sciences
    

• Humblot, Patrice

  • Department of Clinical Sciences, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Genetics and Breeding in Agricultural Sciences
Bioinformatics and Computational Biology (Methods development to be 10203)

Publication identifier

• ISBN: 978-88-6705-504-3

Permanent link to this page (URI)

https://res.slu.se/id/publ/79662