Urbanization is associated with modifications in DNA methylation in a small passerine bird

Watson, H., Powell, D., Salmón, P. , Jacobs, A. and Isaksson, C. (2021) Urbanization is associated with modifications in DNA methylation in a small passerine bird. Evolutionary Applications, 14(1), pp. 85-98. (doi: 10.1111/eva.13160) (PMID:33519958) (PMCID:PMC7819559)

Abstract

Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome‐wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban‐ and forest‐dwelling birds were over‐represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over‐represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban‐ and forest‐dwelling birds were under‐represented in regulatory regions, more likely to occur in nonexpressed genes and not over‐represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.

• Item Type: Articles
• Additional Information: Funding Information: FP7 People: Marie‐Curie Actions. Grant Number: CIG322217. H2020 Marie Skłodowska‐Curie Actions. Grant Number: 659643. Kungliga Fysiografiska Sällskapet i Lund. Grant Number: 36781. Vetenskapsrådet. Grant Number: C0361301.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Watson, Miss Hannah and Jacobs, Mr Arne and Salmon, Dr Pablo
• Authors: Watson, H., Powell, D., Salmón, P., Jacobs, A., and Isaksson, C.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Evolutionary Applications
• Publisher: Wiley
• ISSN: 1752-4563
• ISSN (Online): 1752-4571
• Published Online: 29 October 2020
• Copyright Holders: Copyright © 2020 The Authors
• First Published: First published in Evolutionary Applications 14(1): 85-98
• Publisher Policy: Reproduced under a Creative Commons License