Understanding the molecular mechanisms underlying individual responses to environmental changes is crucial for species conservation and management. Pelagic fishes including Atlantic herring (Clupea harengus) are of particular interest because of their key ecological and economic roles and their susceptibility to a changing ocean from global warming. Temperature and photoperiod have been linked with spawning time and location in adult herring, but no study has thus far investigated the role of environmental factors on gene regulation during the vulnerable early developmental stages. Here we examine DNA methylation patterns of larval herring bred under two temperatures (11°C and 13°C) and photoperiod (6 hr and 12 hr) regimes in a 2X2 factorial design. We found consistently high levels of global methylation across all individuals and a decline in global methylation with increased developmental stage that was more pronounced at 13°C (P ≤ 0.007) than at 11°C (P ≥ 0.21). Most of the differentially methylated sites were in exon and promoter regions for genes linked to metabolism and development, some of which were hypermethylated at higher temperature. These results demonstrate the important role of DNA methylation during larval development and suggest that this molecular mechanism might be key in regulating early-stage responses to environmental stressors in Atlantic herring.

DNA from 53 Atlantic herring larvae (22 from 2019 and 32 from 2020) from different temperatures (11 and 13°C) and photoperiod (6h and 12h) treatments were sent for whole genome bisulfite sequencing (details in paper). Bisulfite conversion was done using NEBNext Ultra II Library Prep Kit for Illumina workflow (New England BioLabs, Oshawa, Canada) and sequencing was conducted on Illumina’s NovaSeq 6000 PE150 at 49X coverage. These are the raw sequencing reads that we use for downstream analyses.

Post processing include quality control of reads using FastQC v0.11.5 (Andrews, 2020) and trimming was done using Trimmomatic (Bolger et al., 2014). Alignment to Clupea harengus reference genome (GCF_900700415.1_Ch_v2.0.2, NCBI) was done using Bismark v0.22.3 (Krueger and Andrews, 2011) and Bowtie2 v2.4.1 (Langmead and Salzberg, 2012) with default settings. Differential methylation analysis was done in methylKit (Akalin et al., 2012).