Epigenetic Regulation Of Gene Expression Domains In Pluripotent Stem Cells

Transcriptional and histone modification profiles were analysed in detail across several regions of the mouse genome in order to examine how tissue-specificity is determined at early stages of development and how it is maintained during cell commitment. The analysis was mainly focused on a 2 Mb gene-dense region containing 68 known closely situated genes, having very diverse expression patterns. Transcriptional profiling of this region showed that clustered tissue-restricted and housekeeping genes are associated with clearly defined monovalent or bivalent epigenetic domains. In ES cells, the actively transcribed housekeeping genes were enriched for histone H3K4me1, H3K4me2, H3K4me3, H3K9ac and binding of Pol II. Most of the silent tissue-restricted genes were marked by bivalent domains and had background levels of Pol II. In few cases, substantial levels of Pol II were found at inactive genes situated close to housekeeping genes, suggesting that transcriptional read-through could be occurring at these genes in ES cells. Epigenetic profiling of the gene-dense region in LPS-activated B cells showed that B cells have a very similar histone modification profile to ES cells. Specifically, the analysis showed that bivalent domains which were thought to be a defining characteristic of pluripotent stem cells are equally prevalent in B cells, suggesting that the epigenetic marking of silent genes is quite similar in these two very different cell types. Analysis of a large gene-poor region containing four genes encoding GABAA neurotransmitter receptor subunits showed that the this locus acquires a large bivalent domain of approximately 1.3 Mb following differentiation of ES cells into NS cells and astrocytes. The results obtained in this study demonstrate the complex and diverse nature of histone modifications at tissue-restricted genes and suggest that trans-acting factors are responsible for generating highly specific combinations of histone modifications at each individual gene at different stages of cell differentiation

Ready to Engage? Urban Middle School Teachers’ Responsiveness to Targeted Engagement Interventions on Their Virtual Instructional Practices: An Action Research Study

Teachers’ effectiveness is associated with their instructional practices and is ultimately linked to students’ learning outcomes. In order to impact teachers’ effectiveness, schools focus substantial effort and resources on professional development led by an assumption that teachers’ classroom practices can be improved through targeted interventions. Even if this premise is correct, little information is available about how much a teacher’s practice may change through interventions, or which aspects of instructional practice are more receptive to improving teacher effectiveness (Garret et al., 2019). This study took place at an urban middle school and examined teachers’ responsiveness to targeted engagement intervention in their instructional practices during six weeks of virtual learning. These interventions were addressed through action research and consisted of professional development, coaching, and instructional feedback. There were six teacher participants in this study, three math, and three science. Data collected in this study contains observational field notes, coaching plans, coaching cycles, engagement frequency charts, professional development constructs, surveys, artifacts, and interviews. Findings from this study show: (a) positive responsiveness to teachers’ engagement interventions evidenced by increase in engagement practices during the length of the study; (b) increase in teachers’ perceptions about instructional feedback and professional development; (c) coaching with feedback grounded in data surfaced as most impactful intervention in this study; and; (d) engagement practices relevant to the socio-emotional and behavioral domain were least responsive to change; and (e) teachers’ beliefs and growth mindset drove the need in practice change. There was no evidence of practices in the behavioral engagement domain. Future recommendations of this are geared towards exploration into virtual environments that address: a) socio-emotional and behavioral engagement domains; b) student-teacher relatedness as referenced by Marzano and Pickering (2011), and c) deep understanding and high participation as referenced by Himmele’s (2011) Cognitive Engagement Model

Epigenetic regulation of gene expression domains in pluripotent stem cells

Transcriptional and histone modification profiles were analysed in detail across several regions of the mouse genome in order to examine how tissue-specificity is determined at early stages of development and how it is maintained during cell commitment. The analysis was mainly focused on a 2 Mb gene-dense region containing 68 known closely situated genes, having very diverse expression patterns. Transcriptional profiling of this region showed that clustered tissue-restricted and housekeeping genes are associated with clearly defined monovalent or bivalent epigenetic domains. In ES cells, the actively transcribed housekeeping genes were enriched for histone H3K4me1, H3K4me2, H3K4me3, H3K9ac and binding of Pol II. Most of the silent tissue-restricted genes were marked by bivalent domains and had background levels of Pol II. In few cases, substantial levels of Pol II were found at inactive genes situated close to housekeeping genes, suggesting that transcriptional read-through could be occurring at these genes in ES cells. Epigenetic profiling of the gene-dense region in LPS-activated B cells showed that B cells have a very similar histone modification profile to ES cells. Specifically, the analysis showed that bivalent domains which were thought to be a defining characteristic of pluripotent stem cells are equally prevalent in B cells, suggesting that the epigenetic marking of silent genes is quite similar in these two very different cell types. Analysis of a large gene-poor region containing four genes encoding GABAA neurotransmitter receptor subunits showed that the this locus acquires a large bivalent domain of approximately 1.3 Mb following differentiation of ES cells into NS cells and astrocytes. The results obtained in this study demonstrate the complex and diverse nature of histone modifications at tissue-restricted genes and suggest that trans-acting factors are responsible for generating highly specific combinations of histone modifications at each individual gene at different stages of cell differentiation.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

A H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation

Methylated histone H3K9 and H3K27 are canonical epigenetic silencing modifications in metazoan organisms, but the relationship between the two modifications has not been well characterised. We show that H3K9me3 coexists with H3K27me3 in pluripotent and differentiated cells. However, we find that the functioning of H3K9me3 is altered by H3S10 phosphorylation in differentiated postmitotic osteoblasts and in cycling B cells. Deposition of H3K9me3/S10ph at silent genes is partially mediated by the mitogen and stress activated kinases (MSK1/2) and the Aurora B kinase. Acquisition of H3K9me3/S10ph during differentiation correlates with loss of paused S5 phosphorylated RNA polymerase II, which is present on Polycomb-regulated genes in ES cells. Reduction of the levels of H3K9me3/S10ph by kinase inhibition results in increased binding of RNAPIIS5ph and of the H3K27 methyltransferase Ezh1 at silent promoters. Our results provide evidence of a novel developmentally regulated methyl-phospho switch that modulates Polycomb regulation in differentiated cells and stabilises repressed states

Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care

PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking. METHODS: Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation. RESULTS: We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test. CONCLUSION: WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer

Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care

PURPOSE: The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking. METHODS: Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation. RESULTS: We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test. CONCLUSION: WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer