Asynchronous Transcriptional Silencing of Individual Retroviral Genomes in Embryonic Cells

Background Retroviral DNAs are profoundly silenced at the transcriptional level in embryonic cell types. The transcriptional profile of pluripotent stem cells has been demonstrated to be extremely heterogeneous from cell to cell, and how the silencing of retroviral DNAs is achieved is not yet well characterized. Results In the current study, we investigated the transcriptional silencing dynamics in stem cells by independently monitoring the expression of two Moloney murine leukemia virus (MMLV) retroviral vectors newly introduced into embryonic carcinoma (EC) cells. Although MMLV is efficiently silenced by epigenetic mechanisms in most such cells, a small number of the doubly-transduced EC cells transiently show double-positive proviral expression. These cells were sorted and their expression patterns were studied over time as silencing is established. Conclusions Our data suggest that retroviral silencing occurs stochastically, in an individual locus-specific fashion, and often without synchronous silencing of both viruses in the same cells. Surprisingly, the chromatin modifications that mark the silenced proviruses are unchanged even in cells that temporarily escape silencing. This local silencing effect is a feature of stem cell epigenomic regulation that has not previously been revealed

Translating Research Into Practice: Speeding the Adoption of Innovative Health Care Programs

Looks at case studies of four innovative clinical programs to determine key factors influencing the diffusion and adoption of innovations in health care

Players in the silencing of retroviral DNAs in embryonic stem cells

Embryonic stem (ES) cells potently repress retroviral infection through transcriptional silencing of the newly established proviral DNAs. We have characterized two distinct types of silencing in embryonic mouse cells infected by the Moloney murine leukemia virus (MLV): a highly efficient one targeted to the proline tRNA primer binding site (PBSpro) on the MLV genome, and a less efficient one occurring independently of the PBS. We determined that the PBS-specific silencing is mediated by TRIM28 (Kap-1), a known transcriptional silencer, tethered to the DNA by ZFP809, one of the dozens of zinc finger proteins encoded in the mammalian genome. At least two more components, HP1gamma and EBP1, are implicated in this silencing. We have also begun characterizing a non-PBS directed silencing complex acting more broadly on incoming viral DNAs in ES cells. We suggest that a major player in this process is Yin Yang1 (YY1), a GLI-Kruppel zinc finger protein, ubiquitously expressed and highly conserved between species. We show by ChIP that YY1 binds the LTR of both exogenous and endogenous retroviruses in ES cells. Deletion of the YY1 binding site from the MLV-LTR increased expression of the provirus at least four fold over that of the wild-type virus. Moreover, in YY1 KD cells the expression of the IAP (class II) endogenous retroviruses was remarkably upregulated

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

Embryonic stem cells (ESCs) repress the expression of exogenous proviruses and endogenous retroviruses (ERVs). Here, we systematically dissected the cellular factors involved in provirus repression in embryonic carcinomas (ECs) and ESCs by a genome-wide siRNA screen. Histone chaperones (Chaf1a/b), sumoylation factors (Sumo2/Ube2i/Sae1/Uba2/Senp6), and chromatin modifiers (Trim28/Eset/Atf7ip) are key determinants that establish provirus silencing. RNA-seq analysis uncovered the roles of Chaf1a/b and sumoylation modifiers in the repression of ERVs. ChIP-seq analysis demonstrates direct recruitment of Chaf1a and Sumo2 to ERVs. Chaf1a reinforces transcriptional repression via its interaction with members of the NuRD complex (Kdm1a, Hdac1/2) and Eset, while Sumo2 orchestrates the provirus repressive function of the canonical Zfp809/Trim28/Eset machinery by sumoylation of Trim28. Our study reports a genome-wide atlas of functional nodes that mediate proviral silencing in ESCs and illuminates the comprehensive, interconnected, and multi-layered genetic and epigenetic mechanisms by which ESCs repress retroviruses within the genome

Trim24 and Trim33 Play a Role in Epigenetic Silencing of Retroviruses in Embryonic Stem Cells

Embryonic stem cells (ESC) have the ability to epigenetically silence endogenous and exogenous retroviral sequences. Trim28 plays an important role in establishing this silencing, but less is known about the role other Trim proteins play. The Tif1 family is a sub-group of the Trim family, which possess histone binding ability in addition to the distinctive RING domain. Here, we have examined the interaction between three Tif1 family members, namely Trim24, Trim28 and Trim33, and their function in retroviral silencing. We identify a complex formed in ESC, comprised of these three proteins. We further show that when Trim33 is depleted, the complex collapses and silencing efficiency of both endogenous and exogenous sequences is reduced. Similar transcriptional activation takes place when Trim24 is depleted. Analysis of the H3K9me3 chromatin modification showed a decrease in this repressive mark, following both Trim24 and Trim33 depletion. As Trim28 is an identified binding partner of the H3K9 methyltransferase ESET, this further supports the involvement of Trim28 in the complex. The results presented here suggest that a complex of Tif1 family members, each of which possesses different specificity and efficiency, contributes to the silencing of retroviral sequences in ESC

The role of Smarcad1 in retroviral repression in mouse embryonic stem cells

Abstract Background Moloney murine leukemia virus (MLV) replication is suppressed in mouse embryonic stem cells (ESCs) by the Trim28-SETDB1 complex. The chromatin remodeler Smarcad1 interacts with Trim28 and was suggested to allow the deposition of the histone variant H3.3. However, the role of Trim28, H3.3, and Smarcad1 in MLV repression in ESCs still needs to be fully understood. Results In this study, we used MLV to explore the role of Smarcad1 in retroviral silencing in ESCs. We show that Smarcad1 is immediately recruited to the MLV provirus. Based on the repression dynamics of a GFP-reporter MLV, our findings suggest that Smarcad1 plays a critical role in the establishment and maintenance of MLV repression, as well as other Trim28-targeted genomic loci. Furthermore, Smarcad1 is important for stabilizing and strengthening Trim28 binding to the provirus over time, and its presence around the provirus is needed for proper deposition of H3.3 on the provirus. Surprisingly, the combined depletion of Smarcad1 and Trim28 results in enhanced MLV derepression, suggesting that these two proteins may also function independently to maintain repressive chromatin states. Conclusions Overall, the results of this study provide evidence for the crucial role of Smarcad1 in the silencing of retroviral elements in embryonic stem cells. Further research is needed to fully understand how Smarcad1 and Trim28 cooperate and their implications for gene expression and genomic stability

Delirium: a symptom of how hospital care is failing older persons and a window to improve quality of hospital care

Delirium, or acute confusional state, which often results from hospital-related complications or inadequate hospital care for older patients, can serve as a marker of the quality of hospital care. By reviewing five pathways that can lead to a greater incidence of delirium—iatrogenesis, failure to recognize delirium in its early stages, attitudes toward the care of the elderly, the rapid pace and technological focus of health care, and the reduction in skilled nursing staff—we identify how future trends and cost-containment practices may exacerbate the problem. Examining delirium also provides an opportunity to improve the quality of hospital care for older persons. Interventions to reduce delirium would need to occur at the local and national levels. Local strategies would include routine cognitive assessment and the creation of systems to enhance geriatric care, such as incentives to change practice patterns, geriatric expertise, case management, and clinical pathways. National strategies might include providing education for physicians and nurses to improve the recognition of delirium and the awareness of its clinical implications, improving quality monitoring systems for delirium, and creating environments to facilitate the provision of high-quality geriatric care

Allelic inactivation of rDNA loci

Human cells contain several hundred ribosomal genes (rDNA) that are clustered into nucleolar organizer regions (NORs) on the short arms of five different acrocentric chromosomes. Only ∼50% of the gene copies are actually expressed in somatic cells. Here, we used a new cytological technique to demonstrate that rDNA is regulated allelically in a regional manner, with one parental copy of each NOR being repressed in any individual cell. This process is similar to that of X-chromosome inactivation in females. Early in development, one copy of each NOR becomes late-replicating, thus probably marking it for inactivation and subsequent targeted de novo methylation at rDNA promoter regions. Once established, this multichromosomal allelic pattern is then maintained clonally in somatic cells. This pathway may serve as an epigenetic mechanism for controlling the number of available rDNA copies during development