In addition to OCT4, SOX2, KLF4 and cMYC, enucleated oocytes contain many regulators of chromatin modification, cell cycle and DNA damage response [40], which may be responsible for their robust reprogramming ability.
Of the 23 functional categories of genes, 20 were included in the comparison (Figure 3), because none of the absent or duplicated genes belonged to the categories of RNA processing and modification, cell cycle control and chromatin structure and dynamics.
However, no DEGs were found for "RNA processing and modification", "cell cycle control", "cell division", "chromosome partitioning", "nuclear structure", "defense mechanisms", "extracellular structures and intracellular trafficking", "secretion", and "vesicular transport".
In the susceptible Tugela and the tolerant Tugela- Dn2, genes related to stress, proton pumps and Ca2+ transport, protein biosynthesis and modification, cell cycle regulation, and cellular respiration were differentially regulated.
The common binding of genes involved in chromatin modification, cell cycle, DNA repair and replication by RB family members suggests that they represent deeply conserved functions of this family of proteins.
Biological function analysis shows that the candidate synthetic lethal genes to p53 are mostly relevant to post-translational modification, cell cycle, cell development, cancer etc. (p-value<10-8, Figure 2).
A handful of DUBs have been studied, and their function has been linked to various cellular processes, including ubiquitin processing, histone modification, cell-cycle regulation, and developmental signaling (Nijman et al. 2005; Reyes-Turcu et al. 2009; Sowa et al. 2009).
A well-studied function of ubiquitin is its role in selective proteolysis by the ubiquitin-proteasome system (UPS), which serves as a mechanism to modify cellular functions and protein function such as cell signaling, protein trafficking, DNA repair, chromatin modifications, cell-cycle progression, and cell death.
The most affected gene networks include post-translational modification, cancer, cell cycle, cell morphology, cellular assembly and organization, RNA post-transcriptional modification, DNA replication, recombination and repair, and embryonic development (additional file 3).
The pathways associated with RNA post-transcriptional modification, DNA replication, recombination, and repair, protein synthesis, lipid metabolism, post-translational modification and cell cycle were down-regulated, whereas pathways linked to gene expression displayed altered regulation.
Some of these modifications are cell cycle specific, with modification at S1354, S1357, S1364 and T1366 being increased during mitosis, and modification at positions T1259, S1273, S1270 and S1267 increasing in G1 [7].
