Cell Pluripotency Levels Associated with Imprinted Genes in Human

Pluripotent stem cells are exhibited similarly in the morphology, gene expression, growth properties, and epigenetic modification with embryonic stem cells (ESCs). However, it is still controversial that the pluripotency of induced pluripotent stem cell (iPSC) is much inferior to ESC, and the differentiation capacity of iPSC and ESC can also be separated by transcriptome and epigenetics. miRNAs, which act in posttranscriptional regulation of gene expression and are involved in many basic cellular processes, may reveal the answer. In this paper, we focused on identifying the hidden relationship between miRNAs and imprinted genes in cell pluripotency. Total miRNA expression patterns in iPSC and ES cells were comprehensively analysed and linked with human imprinted genes, which show a global picture of their potential function in pluripotent level. A new CPA4-KLF14 region which locates in chromosomal homologous segments (CHSs) within mammals and include both imprinted genes and significantly expressed miRNAs was first identified. Molecular network analysis showed genes interacted with imprinted genes closely and enriched in modules such as cancer, cell death and survival, and tumor morphology. This imprinted region may provide a new look for those who are interested in cell pluripotency of hiPSCs and hESCs

TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency.

Transition from primed to naive pluripotency is associated with dynamic changes in transposable element (TE) expression and demethylation of imprinting control regions (ICRs). In mouse, ICR methylation and TE expression are each regulated by TRIM28; however, the role of TRIM28 in humans is less clear. Here, we show that a null mutation in TRIM28 causes significant alterations in TE expression in both the naive and primed states of human pluripotency, and phenotypically this has limited effects on self-renewal, instead causing a loss of germline competency. Furthermore, we discovered that TRIM28 regulates paternal ICR methylation and chromatin accessibility in the primed state, with no effects on maternal ICRs. Taken together, our study shows that abnormal TE expression is tolerated by self-renewing human pluripotent cells, whereas germline competency is not

Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells.

In the mammalian genome, the clustered protocadherin (cPCDH) locus provides a paradigm for stochastic gene expression with the potential to generate a unique cPCDH combination in every neuron. Here we report a chromatin-based mechanism that emerges during the transition from the naive to the primed states of cell pluripotency and reduces, by orders of magnitude, the combinatorial potential in the human cPCDH locus. This mechanism selectively increases the frequency of stochastic selection of a small subset of cPCDH genes after neuronal differentiation in monolayers, 10-month-old cortical organoids and engrafted cells in the spinal cords of rats. Signs of these frequent selections can be observed in the brain throughout fetal development and disappear after birth, except in conditions of delayed maturation such as Down's syndrome. We therefore propose that a pattern of limited cPCDH-gene expression diversity is maintained while human neurons still retain fetal-like levels of maturation

Epigenetic regulation of Mash1 expression

Mash1 is a proneural gene important for specifying the neural fate. The Mash1 locus undergoes specific epigenetic changes in ES cells following neural induction. These include the loss of repressive H3K27 trimethylation and acquisition of H3K9 acetylation at the promoter, switch to an early replication timing and repositioning of the locus away from the nuclear periphery. Here I examine the relationship between nuclear localization and gene expression during neural differentiation and the role of the neuronal repressor REST in silencing Mash1 expression in ES cells. Following neural induction of ES cells, I observed that relocation of the Mash1 locus occurs from day 4-6 whereas overt expression begins at day 6. Mash1 expression was unaffected by REST removal in ES cells as well as the locus localization at the nuclear periphery. In contrast bona fide REST target genes were upregulated in REST -/- cells. Interestingly, among REST targets, loci that were more derepressed upon REST removal showed an interior location (Sthatmin, Synaptophysin), while those more resistant to REST withdrawal, showed a peripheral location (BDNF, Calbidin, Complexin). To ask whether the insulator protein CTCF together with the cohesin complex might be involved in regulating Mash1 in ES cells, I performed ChIP analysis of CTCF and cohesin binding across the Mash1 locus in ES cells and used RNAi to deplete CTCF and cohesin expression. A slight increase in the transcription of Mash1 was seen in cells upon Rad21 knock down, although it was not possible to exclude this was a consequence of delayed cell cycle progression. Finally ES cell lines that carried a Mash1 transgene were created as a tool to look at whether activation of Mash1 can affect the epigenetic properties of neighbouring genes

The role of NLRP7 in maternal imprinting and early embryonic development

NLRP7 is a maternal effect gene in humans whose mutations are responsible for a rare abnormal pregnancy with familial predisposition, biparental complete hydatidiform mole (BiCHM). Given BiCHM exhibits a similar pathology to androgenetic CHM, including overgrowth of trophoblast tissues and dysregulated maternal imprinting, NLRP7 is thought to play an important role in meditating maternal imprinting and early embryonic development in humans. However, due to the lack of rodent models and limited human materials, it has not been possible to reveal the mechanistic function of NLRP7 in maternal imprinting. In this project, hESCs are used as a model system, to investigate the role of NLRP7 in maternal imprinting and its potential relationship with other imprinting modulators, particularly DNMT3L. Firstly, SNPs were identified in selected imprinted genes in hESCs, so that it was feasible to distinguish their two alleles in imprinting studies. In addition, naïve conversion of hESC was achieved to mimic, at least partly, the process of global DNA demethylation, which would enable them to be used to investigate the possible role of NLRP7 in maintaining maternal imprinting during this process. When NLRP7 was overexpressed in hESCs, it showed partial protection of maternal imprinting from global demethylation after naïve conversion, indicating that NLRP7 may be involved in protecting maternally imprinted genes from global demethylation. Furthermore, by analysing gene expression profiles of imprinting related genes, the expression of NLRP7 and DNMT3L were found to be correlated during early embryonic development and the naïve conversion process; and overexpression of NLRP7 can upregulate DNMT3L mRNA expression, which implies a potential link between them. Consequently, my findings demonstrate the possibility of employing hESCs as an alternative and unlimited resource to study NLRP7 in future. More importantly, this is the first time NLRP7 has been shown to directly protect maternally imprinted genes from global demethylation.Open Acces

Effects of Methyl Cycle Substrate Availability on Epigenetic Stability of Human Embryonic Stem Cells

A link has been hypothesised to occur between suboptimal maternal nutrition and impaired foetal development leading to a predisposition to a range of adult pathologies. As a clear connection between dietary intake of methyl group donors and epigenetic defects has been demonstrated both *in vivo* and *in vitro*, this project had the purpose of generating a disruption into the methyl/folate cycle to investigate DNA methylation alterations during human preimplantation embryo development, using human embryonic stem cells (hESCs) as an in vitro model. In particular, HUES-7 stem cells were employed and cultured using either standard or methyl deficient media to test this hypothesis. After the treatments, that included an inhibitor of a key enzyme of the cycle, Differentially Methylated Regions (DMRs) of six imprinted genes were analysed and assessed for their methylation status at Cytosine-phospho-Guanosine (CpG) sites. As a consistent decrease of methylation was observed for the gene *H19* in treated cultures, its allelic expression was then investigated and an initial process of Loss Of Imprinting (LOI) was found. Additionally, global DNA MethylTransferase (DNMT) activity was examined and a statistically significant decrease in treated samples was detected. Finally, hESCs were differentiated into Embryoid Bodies(hEBs), which were compared and stained for pluripotency and germ-layer specific markers. Consistently different expression of *OCT-4* and *NANOG* was noticed for treated-culture derived hEBs