Watson Hannah, Powell Daniel, Salmón Pablo, Jacobs Arne, Isaksson Caroline
Evolutionary Ecology, Biology Department Lund University Lund Sweden.
Global Change Ecology, School of Science, Technology and Engineering University of the Sunshine Coast Sippy Downs QLD Australia.
Evol Appl. 2020 Nov 13;14(1):85-98. doi: 10.1111/eva.13160. eCollection 2021 Jan.
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 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.
城市化是表型变化的强大驱动力，然而，导致所观察到的表型模式的分子机制却鲜为人知。与基因序列的缓慢变化相比，表观遗传变化有望促进对不断变化的或新的环境（如我们的城镇）更快地适应。对来自城市和森林地区的大山雀的肝脏和血液组织进行比较后发现，城市化与全基因组DNA甲基化模式的变化有关。结合简化代表性亚硫酸氢盐测序和转录组数据，我们揭示了DNA甲基化模式中的栖息地差异，这表明对城市环境有调节和协调的反应。在肝脏中，城市和森林栖息鸟类之间差异甲基化的基因组位点在基因组的调控区域中过度富集，并且更有可能出现在表达基因中。DNA甲基化水平在转录起始位点也与基因表达呈负相关。此外，肝脏中差异甲基化的CpG位点在以下途径中过度富集：（i）类固醇生物合成、（ii）超氧化物代谢、（iii）仲醇代谢、（iv）乳糜微粒重塑、（v）胆固醇运输、（vi）活性氧（ROS）代谢过程和（vii）上皮细胞增殖。这与早期的研究结果一致，早期研究确定饮食和接触ROS是城市和非城市环境中生物差异的两个主要驱动因素。相反，在血液中，城市和森林栖息鸟类之间差异甲基化的位点在调控区域中代表性不足，更有可能出现在非表达基因中，并且在特定生物途径中没有过度富集。DNA甲基化的不同模式是否代表适应性进化反应，以及这些结论是否能更广泛地归因于城市化，仍有待确定。
