TRF2-independent chromosome end protection during pluripotency.

Mammalian telomeres protect chromosome ends from aberrant DNA repair1. TRF2, a component of the telomere-specific shelterin protein complex, facilitates end protection through sequestration of the terminal telomere repeat sequence within a lariat T-loop structure2,3. Deleting TRF2 (also known as TERF2) in somatic cells abolishes T-loop formation, which coincides with telomere deprotection, chromosome end-to-end fusions and inviability3-9. Here we establish that, by contrast, TRF2 is largely dispensable for telomere protection in mouse pluripotent embryonic stem (ES) and epiblast stem cells. ES cell telomeres devoid of TRF2 instead activate an attenuated telomeric DNA damage response that lacks accompanying telomere fusions, and propagate for multiple generations. The induction of telomere dysfunction in ES cells, consistent with somatic deletion of Trf2 (also known as Terf2), occurs only following the removal of the entire shelterin complex. Consistent with TRF2 being largely dispensable for telomere protection specifically during early embryonic development, cells exiting pluripotency rapidly switch to TRF2-dependent end protection. In addition, Trf2-null embryos arrest before implantation, with evidence of strong DNA damage response signalling and apoptosis specifically in the non-pluripotent compartment. Finally, we show that ES cells form T-loops independently of TRF2, which reveals why TRF2 is dispensable for end protection during pluripotency. Collectively, these data establish that telomere protection is solved by distinct mechanisms in pluripotent and somatic tissues.

Telomere Loop Dynamics in Chromosome End Protection.

Telomeres regulate DNA damage response (DDR) and DNA repair activity at chromosome ends. How telomere macromolecular structure contributes to ATM regulation and its potential dissociation from control over non-homologous end joining (NHEJ)-dependent telomere fusion is of central importance to telomere-dependent cell aging and tumor suppression. Using super-resolution microscopy, we identify that ATM activation at mammalian telomeres with reduced TRF2 or at human telomeres during mitotic arrest occurs specifically with a structural change from telomere loops (t-loops) to linearized telomeres. Additionally, we find the TRFH domain of TRF2 regulates t-loop formation while suppressing ATM activity. Notably, we demonstrate that ATM activation and telomere linearity occur separately from telomere fusion via NHEJ and that linear DDR-positive telomeres can remain resistant to fusion, even during an extended G1 arrest, when NHEJ is most active. Collectively, these results suggest t-loops act as conformational switches that specifically regulate ATM activation independent of telomere mechanisms to inhibit NHEJ.

Small Interfering RNA (siRNA) Transfection in Epiblast Stem Cells.

Lipid-based transfection of siRNA is a technique routinely used to investigate gene function in experiments using mammalian cells cultured in vitro. Due to innate differences in cellular characteristics, the efficiency of lipid-based transfection is variable across cell types. Pluripotent cells which exist in a "primed" state such as human embryonic stem cells (hESCs) and mouse epiblast stem cells (mEpiSCs) are notorious for being refractory to lipid-based transfection systems. Herein we describe a forward transfection protocol which we routinely use to achieve upwards of 70% transfection efficiency rates in mEpiSCs. Our protocol also includes a suggested transfection timeline and details pertaining to the techniques we use to validate transfection success.

BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer.

BACKGROUND: BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised, in a wide range of malignancies. We have probed the functions of BRG1 on a background of prostate cancer to investigate how BRG1 controls gene expression programmes and cancer cell behaviour. RESULTS: Our investigation of SMARCA4 revealed that BRG1 is over-expressed in the majority of the 486 tumours from The Cancer Genome Atlas prostate cohort, as well as in a complementary panel of 21 prostate cell lines. Next, we utilised a temporal model of BRG1 depletion to investigate the molecular effects on global transcription programmes. Depleting BRG1 had no impact on alternative splicing and conferred only modest effect on global expression. However, of the transcriptional changes that occurred, most manifested as down-regulated expression. Deeper examination found the common thread linking down-regulated genes was involvement in proliferation, including several known to increase prostate cancer proliferation (KLK2, PCAT1 and VAV3). Interestingly, the promoters of genes driving proliferation were bound by BRG1 as well as the transcription factors, AR and FOXA1. We also noted that BRG1 depletion repressed genes involved in cell cycle progression and DNA replication, but intriguingly, these pathways operated independently of AR and FOXA1. In agreement with transcriptional changes, depleting BRG1 conferred G1 arrest. CONCLUSIONS: Our data have revealed that BRG1 promotes cell cycle progression and DNA replication, consistent with the increased cell proliferation associated with oncogenesis.

Toxic effects of hyperglycemia are mediated by the hexosamine signaling pathway and o-linked glycosylation in early mouse embryos.

Maternal hyperglycemia is believed to be the metabolic derangement associated with both early pregnancy loss and congenital malformations in a diabetic pregnancy. Using an in vitro model of embryo exposure to hyperglycemia, this study questioned if increased flux through the hexosamine signaling pathway (HSP), which results in increased embryonic O-linked glycosylation (O-GlcNAcylation), underlies the glucotoxic effects of hyperglycemia during early embryogenesis. Mouse zygotes were randomly allocated to culture treatment groups that included no glucose (no flux through HSP), hyperglycemia (27 mM glucose, excess flux), 0.2 mM glucosamine (GlcN) in the absence of glucose (HSP flux alone), and O-GlcNAcylation levels monitored immunohistochemically. The impact of HSP manipulation on the first differentiation in development, blastocyst formation, was assessed, as were apoptosis and cell number in individual embryos. The enzymes regulating O-GlcNAcylation, and therefore hexosamine signaling, are the beta-linked-O-GlcNAc transferase (OGT) and an O-GlcNAc-selective beta-N-acetylglucosaminidase (O-GlcNAcase). Inhibition of these enzymes has a negative impact on blastocyst formation, demonstrating the importance of this signaling system to developmental potential. The ability of the OGT inhibitor benzyl-2-acetamido-2-deoxy-alpha-D-galactopyranoside (BADGP) to reverse the glucotoxic effects of hyperglycemia on these parameters was also sought. Excess HSP flux arising from a hyperglycemic environment or glucosamine supplementation reduced cell proliferation and blastocyst formation, confirming the criticality of this signaling pathway during early embryogenesis. Inhibition of OGT using BADGP blocked the negative impact of hyperglycemia on blastocyst formation, cell number, and apoptosis. Our results suggest that dysregulation of HSP and O-GlcNAcylation is the mechanism by which the embryotoxic effects of hyperglycemia are manifested during preimplantation development.

A Survey of Essential Genome Stability Genes Reveals That Replication Stress Mitigation Is Critical for Peri-Implantation Embryogenesis.

Murine development demands that pluripotent epiblast stem cells in the peri-implantation embryo increase from approximately 120 to 14,000 cells between embryonic days (E) 4.5 and E7.5. This is possible because epiblast stem cells can complete cell cycles in under 3 h in vivo. To ensure conceptus fitness, epiblast cells must undertake this proliferative feat while maintaining genome integrity. How epiblast cells maintain genome health under such an immense proliferation demand remains unclear. To illuminate the contribution of genome stability pathways to early mammalian development we systematically reviewed knockout mouse data from 347 DDR and repair associated genes. Cumulatively, the data indicate that while many DNA repair functions are dispensable in embryogenesis, genes encoding replication stress response and homology directed repair factors are essential specifically during the peri-implantation stage of early development. We discuss the significance of these findings in the context of the unique proliferative demands placed on pluripotent epiblast stem cells.

The histone variant H2A.Z is dynamically expressed in the developing mouse placenta and in differentiating trophoblast stem cells.

The histone variant H2A.Z is important in establishing new chromatin environments necessary for permitting changes in gene expression and thus differentiation in mouse embryonic stem (mES) cells. In this study we show that H2A.Z is highly expressed in the early mouse placenta, and is specifically limited to progenitor-like trophoblast cells. Using in vitro models, we revealed distinct differences in H2A.Z abundance between undifferentiated, differentiating and differentiated mouse trophoblast stem (mTS) cells. Our work supports the hypothesis that in addition to roles in differentiating mES cells, H2A.Z is also involved in the differentiation of extra-embryonic tissues.

In vitro manipulation of mammalian preimplantation embryos can alter transcript abundance of histone variants and associated factors.

Manipulation of mammalian embryos and gametes in vitro reduces viability. Specific causes for these reductions are still largely undetermined. Accumulating evidence suggests that survival rates and developmental competency may be reduced following disruptions in the epigenetic regulation of gene expression. Chromatin-based epigenetics can regulate the transcriptome through the establishment of different transcriptionally permissive and repressive chromatin environments. Recently, support has been gathering for the hypothesis that the in vitro embryo displays reduced viability due to abnormal remodelling of the paternal chromatin, which is hypothesized to result in global transcriptional repression. In this study, we have used quantitative real-time PCR to document the effect of in vitro culture on the transcription of genes that code for proteins that are directly involved in the establishment of chromatin environments. We compare in vitro embryos to embryos generated through parthenogenetic activation to determine how the absence of paternal chromatin remodeling affects transcriptional activity. Through these studies, we show that the expression of many genes encoding for histone proteins and other modifiers involved in chromatin-based epigenetic regulation are perturbed by in vitro culture. In addition, we show that the expression of many candidate genes was reduced in in vitro embryos but not in parthenogenetic embryos. These results support the hypothesis that events linked to remodeling of paternal chromatin may influence transcriptional activity in the in vitro embryo and that chromatin-based reprogramming events in developing embryos are dynamically responsive to prevailing conditions.

Expression of genes coding for histone variants and histone-associated proteins in pluripotent stem cells and mouse preimplantation embryos.

The histone code is an epigenetic regulatory system thought to play a crucial role in cellular events such as development, differentiation and in the maintenance of pluripotency. In order to gain an insight into the role variant histones may play during mammalian development; we studied gene expression of histone variants and remodelling enzymes in mouse embryonic stem (ES) cells and during mouse preimplantation development. Using quantitative reverse-transcription PCR (qRT-PCR) we document the gene expression pattern of 12 histone variants and 2 of their associated remodelling enzymes in undifferentiated ES cells and during preimplantation embryo development. All histone variants were detected in undifferentiated ES cells, with H2AZ showing the highest expression levels of all the histone variants tested. The results also show that H2A variant levels tend to increase later in embryo development whilst H3 variant levels are elevated in early preimplantation stages. In addition, the expression of SWI/SNF, a remodeler protein involved in specifically remodelling H2A-H2B dimers, mirrors the expression of H2B and H2A variants, and the H3-H4 specific chaperone CAF-1 expression mirrors H3 variant expression. These results provide a foundation for further studies on the functions of histone variants during development, differentiation and in pluripotency.