A DNA Repair Complex Functions as an Oct4/Sox2 Coactivator in Embryonic Stem Cells

SummaryThe transcriptional activators Oct4, Sox2, and Nanog cooperate with a wide array of cofactors to orchestrate an embryonic stem (ES) cell-specific gene expression program that forms the molecular basis of pluripotency. Here, we report using an unbiased in vitro transcription-biochemical complementation assay to discover a multisubunit stem cell coactivator complex (SCC) that is selectively required for the synergistic activation of the Nanog gene by Oct4 and Sox2. Purification, identification, and reconstitution of SCC revealed this coactivator to be the trimeric XPC-nucleotide excision repair complex. SCC interacts directly with Oct4 and Sox2 and is recruited to the Nanog and Oct4 promoters as well as a majority of genomic regions that are occupied by Oct4 and Sox2. Depletion of SCC/XPC compromised both pluripotency in ES cells and somatic cell reprogramming of fibroblasts to induced pluripotent stem (iPS) cells. This study identifies a transcriptional coactivator with diversified functions in maintaining ES cell pluripotency and safeguarding genome integrity.PaperCli

Evaluating Transcriptional Regulation Through Multiple Lenses

Scientific research, especially within the space of translational research is becoming increasingly multidisciplinary. With the development of each new method there is not only a need for a broad fundamental understanding of all the sciences and mathematics, but also an acute awareness of how errors propagate across methods, the limitation of the methods and what contextual frameworks need to be used for the interpretation. The ability to understand transcriptional mechanisms and the affect that subtle changes in equilibrium may have on cell fate decisions has been greatly advanced by next generation sequencing and subsequent tools that have been developed. Bioinformatic techniques can serve multiple roles. They fundamentally provide a global picture of what is happening within an experimental condition which can then be used to either confirm individual experimental findings as globally relevant, or to discover new insights to inform the next iteration of experiments. Many of the experiments are done in in vitro conditions and therefore I have also focused energy on trying to understand how the mechanical inputs, largely not representative of what is occurring in vivo, from these methods affect transcriptional regulation. Much of this research requires the switching of frameworks to understand how results from disparate data sources can be correlated. I then applied a similar thought process to the development of Lens. Without an effective means of communicating research findings in an elegant and streamline mannered, we are slowing down the ability for researchers to learn new frame- works to efficiently approach the next research questions. In addition to better methods of communicating, we also need more modular and simplified tools that can be applied to various experimental systems to increase the speed and efficiency of translational research

Evaluating Transcriptional Regulation Through Multiple Lenses

Scientific research, especially within the space of translational research is becoming increasingly multidisciplinary. With the development of each new method there is not only a need for a broad fundamental understanding of all the sciences and mathematics, but also an acute awareness of how errors propagate across methods, the limitation of the methods and what contextual frameworks need to be used for the interpretation. The ability to understand transcriptional mechanisms and the affect that subtle changes in equilibrium may have on cell fate decisions has been greatly advanced by next generation sequencing and subsequent tools that have been developed. Bioinformatic techniques can serve multiple roles. They fundamentally provide a global picture of what is happening within an experimental condition which can then be used to either confirm individual experimental findings as globally relevant, or to discover new insights to inform the next iteration of experiments. Many of the experiments are done in in vitro conditions and therefore I have also focused energy on trying to understand how the mechanical inputs, largely not representative of what is occurring in vivo, from these methods affect transcriptional regulation. Much of this research requires the switching of frameworks to understand how results from disparate data sources can be correlated. I then applied a similar thought process to the development of Lens. Without an effective means of communicating research findings in an elegant and streamline mannered, we are slowing down the ability for researchers to learn new frame- works to efficiently approach the next research questions. In addition to better methods of communicating, we also need more modular and simplified tools that can be applied to various experimental systems to increase the speed and efficiency of translational research

Fas receptor is required for estrogen deficiency-induced bone loss in mice

Bone mass is determined by bone cell differentiation, activity, and death, which mainly occur through apoptosis. Apoptosis can be triggered by death receptor Fas (CD95), expressed on osteoblasts and osteoclasts and may be regulated by estrogen. We have previously shown that signaling through Fas inhibits osteoblast differentiation. In this study we analyzed Fas as a possible mediator of bone loss induced by estrogen withdrawal. At 4 weeks after ovariectomy (OVX), Fas gene expression was greater in osteoblasts and lower in osteoclasts in ovariectomized C57BL/6J (wild type (wt)) mice compared with sham-operated animals. OVX was unable to induce bone loss in mice with a gene knockout for Fas (Fas -/- mice). The number of osteoclasts increased in wt mice after OVX, whereas it remained unchanged in Fas -/- mice. OVX induced greater stimulation of osteoblastogenesis in Fas -/- than in wt mice, with higher expression of osteoblast-specific genes. Direct effects on bone cell differentiation and apoptosis in vivo were confirmed in vitro, in which addition of estradiol decreased Fas expression and partially abrogated the apoptotic and differentiation-inhibitory effect of Fas in osteoblast lineage cells, while having no effect on Fas-induced apoptosis in osteoclast lineage cells. In conclusion, the Fas receptor has an important role in the pathogenesis of postmenopausal osteoporosis by mediating apoptosis and inhibiting differentiation of osteoblast lineage cells. Modulation of Fas effects on bone cells may be used as a therapeutic target in the treatment of osteoresorptive disorders