Purdue University Graduate School
Innis_dissertation_Final.pdf (9.1 MB)

Investigating epigenetic mechanisms in early porcine development

Download (9.1 MB)
posted on 2024-03-22, 19:02 authored by Sarah M InnisSarah M Innis

Epigenetics involves the study of mechanisms that influence gene expression. These mechanisms are heritable and dynamic, and despite altering gene transcriptional activity, they do not change the underlying DNA sequence. While epigenetic mechanisms govern gene expression throughout the lifetime of an organism, the dynamic nature and precision of the transcriptional control afforded by processes such as histone modifications and chromatin architecture remodeling are exemplified in early mammalian development. Perhaps unsurprisingly, perturbations to the epigenetic status of a cell can alter its function, and widespread epigenome disruptions due to changes in the developmental environment can compromise the growth, and even viability, of an embryo or fetus. By studying epigenetic mechanisms and the patterns they impart, we can better understand not only how developmental progression is regulated during embryonic development and beyond, but also what the consequences of aberrant epigenetic disturbances may be to developing organisms.

Many gaps remain in our knowledge concerning epigenetic mechanisms in domestic livestock species, particularly regarding early development. Pigs represent a compelling model organism for study in this area, as they are increasingly being used as a biomedical model for human-oriented research due to their physiological similarities to humans, and they remain a staple meat species in many parts of the world. Chapter 2 investigates the presence and transcriptional dynamics of the SWI/SNF chromatin remodeling complex GBAF in porcine trophectoderm (PTr2) and fetal fibroblast (PFF) cells. These cell lines represent two discrete developmental stages during early swine development, with the PTr2 cells originally obtained from the trophectoderm of a gestation day 12 elongating porcine conceptus, and the fetal fibroblast cells were collected from a fetus on day 40 of gestation. Using immunocytochemistry and Western blotting techniques, GBAF was identified in both cell lines. Further, co-immunoprecipitation of GBAF constituent subunits and other BAF family subcomplex subunits revealed a previously undescribed interaction between the GBAF subunit GLTSCR1 and the BAF subunit BAF170, the latter of which has not been shown to be present in human and mouse GBAF. This may suggest a species-specific GBAF composition in swine. Analysis of RNA-seq data from porcine embryos, PTr2 cells, and PFF cells showed that while transcription of GBAF-specific subunits BRD9 and GLTSCR1 was detectable, expression levels were lower compared to other BAF family subunits. Taken together these results suggest that, while GBAF is detectable in swine early development contexts, it may have a comparatively minor contribution as an epigenetic mechanism during the represented developmental timepoints.

Details in the literature about the epigenetic landscape and the resulting chromatin state during porcine early development are also limited at present. Chapter 3 involves the global epigenetic profiling of the histone marks H3K4me3, H3K27ac, and H3K27me3 and the SWI/SNF central ATPase BRG1 in PTr2 and PFF cells using CUT&RUN. The enrichment patterns observed for these features were consistent with known patterns described in the literature. H3K4me3 was primarily enriched in gene promoter regions, and H3K27ac showed enrichment in both promoter regions and distal intergenic regions, some of which are likely active enhancers. H3K27me3 showed broad genomic localization and was detected at genes known to be transcriptionally inactive in these cell types, as well as in distal intergenic regions. BRG1 showed some co-enrichment with H3K4me3 and H3K27ac in promoter regions, as well as several instances of H3K27ac co-enrichment at intergenic sites. The sequencing files were used to build a chromatin state prediction model for 10 states in each cell line, ranging from TSS to repressed genomic regions. Additionally, the transcriptomes of PTr2 and PFF cells were compared to those of human cells taken from comparable gestational time points to determine if these swine cell lines could potentially serve as translational in vitro models. PTr2 cells and human trophectoderm (TE) cells were relatively dissimilar in their cell-type specific gene identities (~24% overlap) and corresponding transcriptional levels, but the porcine and human fibroblast cells shared around 50% of the same cell type-specific genes, and expression levels were broadly similar among them. Altogether, these findings provide foundational epigenetic landscape information for PTr2 and PFF cells and potential insights regarding similarities and differences in cell identity between human and pig trophectoderm and fetal fibroblast cells.

The placenta is a transient organ that provides essential support to the developing fetus in the form of nutrient and gas exchange. Despite its significance in facilitating fetal development, our understanding of how the placenta is affected by its environment is greatly limited, and only a handful of studies exploring the placental epigenome in swine exist to date. To address these gaps, and building upon the epigenetic profiling methods developed in Chapter 3, Chapter 4 investigated whether, and to what extent, the placental epigenome changes in response to fetal endocrine perturbations. Placental tissue was collected at day 86 of gestation from untreated pregnant gilts and pregnant gilts treated for 21 days with methimazole (MMI) to induce fetal hypothyroidism. CUT&RUN was used to evaluate the enrichment of H3K4me3, H3K27ac, and BRG1 in placental tissue derived from n=6 male and female fetuses in each treatment group (n=12 samples per group). Differential enrichment of all three epigenetic features was seen in placental tissues obtained from MMI-treated fetuses, and, notably, existing sex-specific differences in placental epigenetic features were exacerbated by MMI-induced fetal hypothyroidism. This may suggest that the porcine placenta may be impacted by fetal endocrine status during late gestation. Together, these findings show that sex-specific differences in placental chromatin state exist and that a fetal hypothyroid state is sufficient to perturb the placental epigenome, ultimately providing novel insights into the intricate interplay between fetal endocrine status and regulation of the placental epigenome.


Degree Type

  • Doctor of Philosophy


  • Animal Sciences

Campus location

  • West Lafayette

Advisor/Supervisor/Committee Chair

Ryan Cabot

Additional Committee Member 2

Emily Dykhuizen

Additional Committee Member 3

Shihuan Kuang

Additional Committee Member 4

Zoltan Machaty

Usage metrics



    Ref. manager