A potential role for epigenetic mechanisms enabling appropriate seasonal reproductive transitions of liver yolk-precursor production
Data files
Oct 14, 2025 version files 7.04 KB
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methylation.junco.combined.DRYAD.withage.csv
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README.md
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Abstract
Animals utilize mechanisms that enable breeding at times that ensure offspring production and growth during periods of abundant resources. DNA methylation is one mechanism by which the expression of genes necessary for reproduction may be regulated so that they are expressed only at appropriate times of the year. To date, much work on seasonal breeding in vertebrates has focused on the neuroendocrine system; however, oviparous vertebrates, including birds, must also rely on the liver for the production of yolk precursor hormones that will provide the nutrients necessary for developing young in ovo. We hypothesized that changes in DNA methylation in the liver may be one mechanism ensuring appropriately timed seasonal breeding. We observed that liver expression of (VTG2) was upregulated in birds sampled during the early breeding compared with those sampled during the pre-breeding period, and also observed changes in liver expression of DNMT1 and DNMT3a between these two periods. Contrary to our predictions, we observed an increase in methylation from pre-breeding to breeding at one of the three CpG sites in the promoter region of the VTG2 gene, with no differences at the other two CpG sites. Finally, we asked if patterns of methylation of VTG2 are similar between the liver and the blood. We observed strong correlations between blood and liver in two sites that did not change between pre-breeding and breeding, while there was only a trend for a significant association between blood and liver DNA methylation at the site that displayed a significant increase in liver CpG methylation between sampling time periods. Together, these findings suggest that changes in DNA methylation in a tissue important for reproduction outside of the reproductive endocrine axis (liver) may play a critical role in appropriate timing of seasonal clutch initiation.
Dataset DOI: 10.5061/dryad.9zw3r22rw
Description of the data and file structure
Each individual was sacrificed during one of two sampling periods as described in the text. All individuals had their DNA bisulfite converted and the percent of methylation at the targeted sites denoted in the text were analyzed using pyrosequencing. Pyrosequencing results that did not meet quality control criteria described in the text were not included in the analysis.
Files and variables
File: methylation.junco.combined.DRYAD.withage.csv
Description:
Variables
- Female No.: Female number was assigned to each bird captured and sampled sequentially. Cells marked 'null' had no age information recorded on the datasheet.
- age: AY are birds determined as young adults (after hatch year) in their first breeding year using plumage to classify age; AO are adult birds determined to be 2 or more years old using plumage characteristics. Cells marked 'null' had no age information recorded on the datasheet.
- age.yr: Converted AY and AO into a numerical variable. AY birds were assigned a 1, and AO birds were assigned a 2.
- Date: this was the calendar day that birds were sacrificed for sampling.
- Sample.tim: This is a categorical variable to denote the two distinct sampling time periods described in the text.
* Pre-breeding were from the sampling dates from 4/25/16 through 4/27/16.
* Early-breeding were from the sampling period of 5/12/16 through 5/14/16 and corresponded to the time period when the earliest females in the population were initiating clutches. - Sample.time: Converted sample.tim to a numeric value. Birds sampled in the pre-breeding period were assigned a 0, and birds sampled during the early breeding period were assigned a 1.
- Time of Capture: This variable denotes the hour and minute that birds were sacrificed.
- Liver_site1_methylation: The percent of methylated cytosinse at CpG site 1 in liver as measured by pyrosequencing. Cells marked 'null' did not pass the QC check.
- Liver_site2_methylation: The percent of methylated cytosinse at CpG site 2 in liver as measured by pyrosequencing. Cells marked 'null' did not pass the QC check.
- Liver_site3_methylation: The percent of methylated cytosinse at CpG site 3 in liver as measured by pyrosequencing. Cells marked 'null' did not pass the QC check.
- Blood_site1_methylation: The percent of methylated cytosinse at CpG site 1 in blood as measured by pyrosequencing. Cells marked 'null' did not pass the QC check.
- Blood_site2_methylation: The percent of methylated cytosinse at CpG site 2 in blood as measured by pyrosequencing. Cells marked 'null' did not pass the QC check.
- Blood_site3_methylation: The percent of methylated cytosinse at CpG site 3 in blood as measured by pyrosequencing. Cells marked 'null' did not pass the QC check.
- Liver_VTG2_expression: Relative expression of VTG2 in liver sample from qPCR.
- LOG10_Liver_VTG2_expression: log10 relative expression of VTG2 in liver sample from qPCR.
- Liver_DNMT1_expressoin: Relative expression of DNMT1 in liver sample from qPCR. Cells marked 'null' did not have enough sample remaining to run.
- Liver_DNMT3A_expressoin: Relative expression of DNMT3a in liver sample from qPCR. Cells marked 'null' did not have enough sample remaining to run.
- F1_size_mm: Size of the largest follicle in the ovary sample. Follicles were only measured during the early breeding period, as no bird sampled during the pre-breeding period displayed developed follicles.