First publication for PhD candidate Jani de Vos in iScience

The abovementioned pig and chicken cell lines are of particular interest because of their untransformed nature and wide use in functional studies.

Annotation of genomic elements

Gene expression is regulated through a network of physical interactions of enhancers, promoters, insulators, epigenetic marks, and chromatin-binding factors. Epigenetic marks such as DNA methylation, noncoding RNAs and histone modifications can be studied to obtain insight into regulation of the epigenome. Some histone modifications are highly informative regarding gene expression and are associated with transcriptional activation, promoters, and enhancers. In addition, DNA methylation is important in identifying gene expression and gene silencing, as methylation and gene expression generally show an inverse correlation. Together these (epi)genetic marks can be used to annotate the functional genomic elements that determine gene expression.

Why the pige IPEC-J2 and chicken SL-29 cell lines?

Jani: “For the study of the genomic architecture and regulatory genome of a specific species, cell lines (particularly primary cell lines) provide an interesting model. Such cells can either continue growing indefinitely or die off after a certain number of cell divisions. Cell lines that can be grown indefinitely often show cell aneuploidy or heteroploidy, which is most pronounced in cancer cell lines. Characterisation of the pig IPEC-J2 cell line and chicken SL-29 cell line holds value for the animal genomics community because of the untransformed nature and wide use of in functional studies in these cells.” The study performed by Jani and her colleagues is the first to describe the molecular characteristics (structure) of the abovementioned cell lines, and the (epi)genetic makeup thereof can provide a better understanding of the limitations and value of these cell lines as a model for in vivo research.

First publication for Jani de Vos

Jani: “This paper was quite fundamental for me in my PhD trajectory. Not only because it was my first paper (an important milestone), but also because it gave me the opportunity to learn how to analyse many different data sets. I also loved making the graphical abstract and the figure 360 video; it was a nice creative touch and I think it really complements the paper. Overall, I think the entire process was good practice for building up my expertise for the remaining research chapters in my PhD.”

It was quite the proverbial Mount Everest for Jani to learn how to analyse all the new data types and, consequently, translate all the information in a descriptive publication. However, it was a good way to learn about writing, which will undoubtedly prove advantageous for her PhD thesis as well.