Genome-wide analysis of histone modifications in human pancreatic islets.

The global diabetes epidemic poses a major challenge. Epigenetic events contribute to the etiology of diabetes; however, the lack of epigenomic analysis has limited the elucidation of the mechanistic basis for this link. To determine the epigenetic architecture of human pancreatic islets we mapped the genome-wide locations of four histone marks: three associated with gene activation-H3K4me1, H3K4me2, and H3K4me3-and one associated with gene repression, H3K27me3. Interestingly, the promoters of the highly transcribed insulin and glucagon genes are occupied only sparsely by H3K4me2 and H3K4me3. Globally, we identified important relationships between promoter structure, histone modification, and gene expression. We demonstrated co-occurrences of histone modifications including bivalent marks in mature islets. Furthermore, we found a set of promoters that is differentially modified between islets and other cell types. We also use our histone marks to determine which of the known diabetes-associated single-nucleotide polymorphisms are likely to be part of regulatory elements. Our global map of histone marks will serve as an important resource for understanding the epigenetic basis of type 2 diabetes.

Glucocorticoid receptor interacting protein-1 restores glucocorticoid responsiveness in steroid-resistant airway structural cells.

Glucocorticoid (GC) insensitivity represents a profound challenge in managing patients with asthma. The mutual inhibition of transcriptional activity between GC receptor (GR) and other regulators is one of the mechanisms contributing to GC resistance in asthma. We recently reported that interferon regulatory factor (IRF)-1 is a novel transcription factor that promotes GC insensitivity in human airway smooth muscle (ASM) cells by interfering with GR signaling (Tliba et al., Am J Respir Cell Mol Biol 2008;38:463-472). Here, we sought to determine whether the inhibition of GR function by IRF-1 involves its interaction with the transcriptional co-regulator GR-interacting protein 1 (GRIP-1), a known GR transcriptional co-activator. We here found that siRNA-mediated GRIP-1 depletion attenuated IRF-1-dependent transcription of the luciferase reporter construct and the mRNA expression of an IRF-1-dependent gene, CD38. In parallel experiments, GRIP-1 silencing significantly reduced GR-mediated transactivation activities. Co-immunoprecipitation and GST pull-down assays showed that GRIP-1, through its repression domain, physically interacts with IRF-1 identifying GRIP-1 as a bona fide transcriptional co-activator for IRF-1. Interestingly, the previously reported inhibition of GR-mediated transactivation activities by either TNF-alpha and IFN-gamma treatment or IRF-1 overexpression was fully reversed by increasing cellular levels of GRIP-1. Together, these data suggest that the cellular accumulation of IRF-1 may represent a potential molecular mechanism mediating altered cellular response to GC through the depletion of GRIP-1 from the GR transcriptional regulatory complexes.

Site-directed mutagenesis of the Thauera aromatica strain T1 tutE tutFDGH gene cluster.

Benzylsuccinate synthase, encoded by the tutF, tutD, and tutG genes of Thauera aromatica strain T1, is responsible for the first step of anaerobic toluene metabolism. Previous work has shown that these genes are part of the tutE tutFDGH gene cluster and strains carrying a mutation in the tutE, tutF, tutD, or tutG genes are unable to metabolize toluene. In this study, we performed site-directed mutagenesis of the tutE, tutF, and tutG genes and determined that the cysteines at position 72 and 79 of TutE are likely to be critical for the radical activation of benzylsuccinate synthase, while the cysteine alanine at positions 9 and 10 of TutF, and the cysteine at position 29 of TutG are also essential for toluene metabolism. Additionally, we report that the tutH gene is necessary for toluene metabolism and the glycine lysine serine (part of the putative ATP/GTP binding domain) at positions 52-54 of the TutH protein is essential for toluene metabolism.