54 research outputs found
Chromatin dynamics and histone modifications in the intestinal microbiota-host crosstalk
Background The microbiota in our gut is an important component of normal physiology that has co-evolved with us from the earliest multicellular organisms. It is, therefore, not surprising that there is an intimate crosstalk between the microbial world in the gut and the host. Genome regulation through microbiota-host interactions not only affect the host’s immunity, but also metabolic health and resilience against cancer. Chromatin dynamics of the host epithelium involving histone modifications and other facets of the epigenetic machinery play an important role in this process.
Scope of Review In this review we will discuss recent findings relevant to how chromatin dynamics shape the crosstalk between the microbiota and its host, with special focus on the role of histone modifications.
Major Conclusions Host-microbiome interactions are important evolutionary drivers and are, thus, expected to be hardwired into and mould the epigenetic machinery in multicellular organisms. Microbial derived short chain fatty acids (SCFA) emerge as a dominant determinant in microbiome-host interaction and the inhibition of histone deacetylases (HDACs) by SCFA is a key mechanism in this process. The discovery of alternative histone acylations, such as crotonylation, in addition to the canonical histone acetylation reveals a new layer of complexity in this crosstalk
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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
In vitro Enzymatic Assays of Histone Decrotonylation on Recombinant Histones
Class I histone deacetylases (HDACs) are efficient histone decrotonylases, broadening the enzymatic spectrum of these important (epi-)genome regulators and drug targets. Here, we describe an in vitro approach to assaying class I HDACs with different acyl-histone substrates, including crotonylated histones and expand this to examine the effect of inhibitors and estimate kinetic constants
Transcriptome analysis identifies a robust gene expression program in the mouse intestinal epithelium on aging
The intestinal epithelium undergoes constant regeneration driven by intestinal stem cells. How old age affects the transcriptome in this highly dynamic tissue is an important, but poorly explored question. Using transcriptomics on sorted intestinal stem cells and adult enterocytes, we identified candidate genes, which change expression on aging. Further validation of these on intestinal epithelium of multiple middle-aged versus old-aged mice highlighted the consistent up-regulation of the expression of the gene encoding chemokine receptor Ccr2, a mediator of inflammation and several disease processes. We observed also increased expression of Strc, coding for stereocilin, and dramatically decreased expression of Rps4l, coding for a ribosome subunit. Ccr2 and Rps4l are located close to the telomeric regions of chromosome 9 and 6, respectively. As only few genes were differentially expressed and we did not observe significant protein level changes of identified ageing markers, our analysis highlights the overall robustness of murine intestinal epithelium gene expression to old age
The SNF2-Family Member Fun30 Promotes Gene Silencing in Heterochromatic Loci
Chromatin regulates many key processes in the nucleus by controlling access to the underlying DNA. SNF2-like factors are ATP-driven enzymes that play key roles in the dynamics of chromatin by remodelling nucleosomes and other nucleoprotein complexes. Even simple eukaryotes such as yeast contain members of several subfamilies of SNF2-like factors. The FUN30/ETL1 subfamily of SNF2 remodellers is conserved from yeasts to humans, but is poorly characterized. We show that the deletion of FUN30 leads to sensitivity to the topoisomerase I poison camptothecin and to severe cell cycle progression defects when the Orc5 subunit is mutated. We demonstrate a role of FUN30 in promoting silencing in the heterochromatin-like mating type locus HMR, telomeres and the rDNA repeats. Chromatin immunoprecipitation experiments demonstrate that Fun30 binds at the boundary element of the silent HMR and within the silent HMR. Mapping of nucleosomes in vivo using micrococcal nuclease demonstrates that deletion of FUN30 leads to changes of the chromatin structure at the boundary element. A point mutation in the ATP-binding site abrogates the silencing function of Fun30 as well as its toxicity upon overexpression, indicating that the ATPase activity is essential for these roles of Fun30. We identify by amino acid sequence analysis a putative CUE motif as a feature of FUN30/ETL1 factors and show that this motif assists Fun30 activity. Our work suggests that Fun30 is directly involved in silencing by regulating the chromatin structure within or around silent loci
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
SWI/SNF-like chromatin remodeling factor Fun30 supports point centromere function in S. cerevisiae
Budding yeast centromeres are sequence-defined point centromeres and are, unlike in many other organisms, not
embedded in heterochromatin. Here we show that Fun30, a poorly understood SWI/SNF-like chromatin remodeling factor
conserved in humans, promotes point centromere function through the formation of correct chromatin architecture at
centromeres. Our determination of the genome-wide binding and nucleosome positioning properties of Fun30 shows that
this enzyme is consistently enriched over centromeres and that a majority of CENs show Fun30-dependent changes in
flanking nucleosome position and/or CEN core micrococcal nuclease accessibility. Fun30 deletion leads to defects in histone
variant Htz1 occupancy genome-wide, including at and around most centromeres. FUN30 genetically interacts with CSE4,
coding for the centromere-specific variant of histone H3, and counteracts the detrimental effect of transcription through centromeres on chromosome segregation and suppresses transcriptional noise over centromere CEN3. Previous work has shown a requirement for fission yeast and mammalian homologs of Fun30 in heterochromatin assembly. As centromeres in budding yeast are not embedded in heterochromatin, our findings indicate a direct role of Fun30 in centromere chromatin by promoting correct chromatin architecture
Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium
Background How intestinal epithelial cells interact with the microbiota and how this is regulated at the gene expression level are critical questions. Smarcad1 is a conserved chromatin remodeling factor with a poorly understood tissue function. As this factor is highly expressed in the stem and proliferative zones of the intestinal epithelium, we explore its role in this tissue.
Results Specific deletion of Smarcad1 in the mouse intestinal epithelium leads to colitis resistance and substantial changes in gene expression, including a striking increase of expression of several genes linked to innate immunity. Absence of Smarcad1 leads to changes in chromatin accessibility and significant changes in histone H3K9me3 over many sites, including genes that are differentially regulated upon Smarcad1 deletion. We identify candidate members of the gut microbiome that elicit a Smarcad1-dependent colitis response, including members of the poorly understood TM7 phylum.
Conclusions Our study sheds light onto the role of the chromatin remodeling machinery in intestinal epithelial cells in the colitis response and shows how a highly conserved chromatin remodeling factor has a distinct role in anti-microbial defense. This work highlights the importance of the intestinal epithelium in the colitis response and the potential of microbial species as pharmacological and probiotic targets in the context of inflammatory diseases
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
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