Studies on the growth inhibition and differentiation of serum-free mouse embryo (SFME) cells

Serum-free mouse embryo (SFME) cells are derived in medium in which serum is replaced with growth factors and other supplements. They display unusual properties. They do not lose proliferative potential or show gross chromosomal aberration upon extended culture, they depend on epidermal growth factor (EGF) for survival, and are reversibly growth inhibited by plasma and serum. In the presence of transforming growth factor beta (TGF-β) SFME cells express the astrocyte marker, glial fibrillary acidic protein (GFAP). The growth inhibitory activity of human plasma on serum-free mouse embryo cells was investigated. Human plasma did not inhibit SFME cells transformed with the human Ha-ras oncogene. The activity was present in delipidated plasma and was not dialyzable against 1 M acetic acid. The activity could be precipitated by methanol, bound to concanavalin Aagarose and was retarded by Sephadex G-50 in 200 mM acetic acid. A fifty to hundred fold purification was achieved, although the differential inhibition of untransformed versus transformed cells was lost in the course of the purification. Using the technique of differential screening of a cDNA library a calf serum- and TGF -β-regulated mRNA species was identified in SFME cells. This mRNA was approximately 8.5 kilobases in size and brain-specific. Picomolar quantities of TGF-β caused an increase of this message in SFME cells within four hours. This increase was reversed when TGF-β was removed from the culture medium

Does chromatin function as a metabolite reservoir?

Alternative histone acylations integrate gene expression with cellular metabolic states. Recent measurements of cellular acyl-coenzyme A (acyl-CoA) pools highlight the potential that histone post-translational modifications (PTMs) contribute directly to the regulation of metabolite pools. A metabolite-centric view throws new light onto roles and evolution of histone PTMs

The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

Within the genomes of metazoans, nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors. Here we have sought to investigate which chromatin remodelling enzymes are responsible for this. We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding. At many other factor binding sites SNF2H and the related enzyme SNF2L contribute to nucleosome organisation. The action of SNF2H at CTCF sites is functionally important as depletion of CTCF or SNF2H affects transcription of a common group of genes. This suggests that chromatin remodelling ATPase's most closely related to the Drosophila ISWI protein contribute to the function of many human gene regulatory elements

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.

BACKGROUND: Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS: Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. CONCLUSIONS: Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors

Transcription factor-mediated chromatin remodelling: mechanisms and models

AbstractThe association of DNA with nucleosomes in chromatin severely restricts the access of the regulatory factors that bring about transcription. In vivo active promoters are characterised by altered, almost transparent chromatin structures that allow the interaction of the transcriptional machinery. Recently, enzymatic activities have been discovered that facilitate the binding of transcription factors to chromatin by modifying nucleosomal structures in a process that requires energy. The mechanisms by which chromatin is remodelled may involve nucleosome movements, their transient unfolding, their partial or even complete disassembly. The dynamic properties of chromatin that underlie these structural changes are fundamental to the process of regulated gene expression