Global DNA methylation changes and differential gene expression in Anaplasma phagocytophilum-infected human neutrophils

Sara H G Sinclair,Srinivasan Yegnasubramanian,J Stephen Dumler

doi:10.1186/s13148-015-0105-1

Abstract

BackgroundAnaplasma phagocytophilum is an obligate intracellular prokaryotic pathogen that both infects and replicates within human neutrophils. The bacterium represses multiple antimicrobial functions while simultaneously increasing proinflammatory functions by reprogramming the neutrophil genome. Previous reports show that many observed phenotypic changes are in part explained by altered gene transcription. We recently identified that large chromosomal regions of the neutrophil genome are differentially expressed during A. phagocytophilum infection. Because of this, we sought to determine whether gene expression programs altered by infection were the result of changes in the host neutrophil DNA methylome.ResultsWithin 24 h of infection, marked increases in DNA methylation were observed genome-wide as compared with mock-infected controls and pharmacologic inhibition of DNA methyltransferases resulted in decreased bacterial growth. New regions of DNA methylation were enriched at intron and exon junctions; however, intragenic methylation did not correlate with altered gene expression. In contrast, intergenic DNA methylation was associated with A. phagocytophilum-induced gene expression changes. Within the major histocompatibility complex locus on chromosome 6, a region with marked changes in infection-induced differential gene expression, new regions of methylation were localized to boundaries of active and inactive chromatin.ConclusionsThese data strongly suggest that A. phagocytophilum infection, in addition to altering histone structure, alters DNA methylation and the epigenome of its host cell to promote survival and replication, providing evidence that such bacterial infection can radically alter the epigenome of its host cell.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0105-1) contains supplementary material, which is available to authorized users.

Highlights

Anaplasma phagocytophilum is an obligate intracellular prokaryotic pathogen that both infects and replicates within human neutrophils
Using peaks called by Model-based analysis of ChIP-Seq software (MACS), the majority of methylated regions (~84 %) across the genome were maintained between uninfected and infected neutrophils; there were a significant number of newly methylated regions (~30,000 or 16 %) in the infected neutrophils as compared to uninfected samples (Fig. 1a)
Luminometric methylation assay (LUMA) analysis of the same DNA samples further confirmed an increase in the percentage of DNA methylation with A. phagocytophilum infection of human neutrophils

Summary

Introduction

Anaplasma phagocytophilum is an obligate intracellular prokaryotic pathogen that both infects and replicates within human neutrophils. We sought to determine whether gene expression programs altered by infection were the result of changes in the host neutrophil DNA methylome. The observed changes in host cell function are partially explained by alterations in granulocyte gene transcription [9,10,11]. Transcription of BCL2 family member genes are maintained during A. phagocytophilum infection which results in delayed neutrophil apoptosis [7, 13] and increased transcript levels of cytokines and chemokines such as IL-1α and IL-8 contribute to exaggerated inflammatory responses that recruit new neutrophil hosts [14,15,16]

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Conclusion