Response of the cells with suppressed chromatin repression system to osmotic stress

DNA methylation is implicated in transcription regulation, mostly by repressing initiation of transcription. Such repression often appears as a result of a repressive complex binding to methylated genomic regions. Kaiso, a transcription factor that binds methylated DNA sequence, can form a complex with N-CoR causing histone deacetylation and, therefore, repression of transcription. Osmotic stress has been shown to result in Kaiso translocation to inner surface of nuclear membrane reducing its DNA binding. Also, it is known that hyper-osmosis is critical for the efficiency of somatic cells reprogramming, primarily due to the effect on DNA demethylation processes. Moreover, Kaiso has an effect on the efficiency of reprogramming independent of hyper-osmosis.

In this work we study an interplay between hyper-osmosis, DNA methylation and KAISO binding and their joined effects on the efficiency of reprogramming. To do so we use RRBS (reduced representation bisulfite sequencing) data obtained from wild type (wt) and KAISO-knockout mouse embryonic fibroblasts during reprogramming into iPS (induced pluripotent stem cells). We focus  our analysis of effects of osmotic stress on the DNA methylation of these cells. Using Methpipe pipeline we identified  21230 deferentially methylated regions (DMR) between wild type cells and Kaiso knockout, and 24388 DMR between samples in normal osmotic conditions and under osmosis streess (NaCl). We confirm functionality of methylation change with the data on gene expression.  We also perform functional analysis of the deferentially methylated genes between wt and KAISO-knockout as well as between responses to different osmotic conditions.

 

Студент:
   Полина Липаева
Куратор:
   Юлия Медведева
Время выполнения проекта: Feb 2017 — Jun 2017
Файлы:
   lipaeva_final_2552017.pdf