Biomedical subjects

Sam John

Publications and source records attributed to Sam John.

8 recordsLinked to original sources

PubMed2006

Single-cell analysis of glucocorticoid receptor action reveals that stochastic post-chromatin association mechanisms regulate ligand-specific transcription.

The glucocorticoid receptor (GR) dynamically interacts with response elements in the mouse mammary tumor virus (MMTV) promoter to regulate steroid-dependent transcription. In a clonal mammary carcinoma cell line containing a tandem array of MMTV promoter-reporter gene cassettes integrated at a single genomic locus, direct binding of a green fluorescent protein (GFP)-GR fusion protein to the MMTV regulatory elements can be observed in living cells. After ligand treatment, MMTV-dependent transcription in individual cells was detected by RNA fluorescence in situ hybridization (FISH). High-resolution fluorescence images were acquired from large numbers of randomly selected cells. Images were analyzed with a novel automated computer algorithm, measuring the RNA FISH signal and the relative GFP-GR fluorescence intensity at the MMTV array for each cell. Although dexamethasone increased the mean RNA FISH signal approximately 10-fold, RU486 produced only about a 2-fold induction, as expected for this mixed antagonist. For all treatment conditions, the relative GFP-GR fluorescence at the array for the averaged cells paralleled the RNA FISH measurements, suggesting that image analysis accurately detected an increase in steady-state GR association with the MMTV array that was responsible for the increase in transcriptional activity. The antagonist-dependent decreases in GR association with the MMTV promoter were confirmed by chromatin immunoprecipitation experiments, supporting the image analysis results. A pronounced cell-to-cell variability was observed in RNA FISH signal and GR-MMTV association within treatment groups. We observed a nonlinear relationship between GR-MMTV association and RNA FISH in individual cells, indicating that differences in GR-MMTV interaction account for some, but not all, of the transcriptional heterogeneity between individual cells. In selected cell subpopulations with equal levels of GR-MMTV association, there was a decrease in RNA FISH signal with RU486 treatment compared with dexamethasone treatment. These results indicate that stochastic events occurring after GR-promoter association, such as the actions of chromatin remodeling complexes or other cofactors, change in a ligand-dependent manner and regulate heterogeneous transcription in individual cells.

Animals↗

PubMed2006

HDAC1 acetylation is linked to progressive modulation of steroid receptor-induced gene transcription.

Although histone deacetylases (HDACs) are generally viewed as corepressors, we show that HDAC1 serves as a coactivator for the glucocorticoid receptor (GR). Furthermore, a subfraction of cellular HDAC1 is acetylated after association with the GR, and this acetylation event correlates with a decrease in promoter activity. HDAC1 in repressed chromatin is highly acetylated, while the deacetylase found on transcriptionally active chromatin manifests a low level of acetylation. Acetylation of purified HDAC1 inactivates its deacetylase activity, and mutation of the critical acetylation sites abrogates HDAC1 function in vivo. We propose that hormone activation of the receptor leads to progressive acetylation of HDAC1 in vivo, which in turn inhibits the deacetylase activity of the enzyme and prevents a deacetylation event that is required for promoter activation. These findings indicate that HDAC1 is required for the induction of some genes by the GR, and this activator function is dynamically modulated by acetylation.

Acetylation↗

PubMed2006

Chromatin dynamics and the evolution of alternate promoter states.

Eucaryotic gene transcriptional switches utilize changes both in the activity and composition of soluble transcription factor complexes, and epigenetic modifications to the chromatin template. Until recently, alternate states of promoter activity have been associated with the assembly of relatively stable multiprotein complexes on target genes, with transitions in the composition of these complexes occurring on the time scale of minutes or hours. The development of living cell techniques to characterize transcription factor function in real time has led to an alternate view of highly dynamic protein/template interactions. In addition, emerging evidence suggests that energy-dependent processes contribute significantly to the rapid movement of proteins in living cells, and to the exchange of sequence-specific DNA-binding proteins with regulatory elements. Potential mechanisms involved in the unexpectedly rapid flux of factor/template interactions are discussed in the context of a "return-to-template" model for transcription factor function.

Animals↗

PubMed2004

Dynamics of nuclear receptor movement and transcription.

Following a hormone signal, steroid/nuclear receptors bind regulatory elements in chromatin and initiate the recruitment of a variety of multi-protein complexes to promoter sequences. These complexes ultimately lead to the recruitment of general transcription factors and the initiation of transcription. Traditional models suggest that these factors remain statically bound to each other and to chromatin until other signals are received to reduce transcription. Recent findings demonstrate that the processes and actions involved are much more complex than traditional models convey, and that the movement of receptors and coactivators is remarkably dynamic. Transcription factors are highly mobile in the nuclear environment, and interact only briefly with target sites in the nucleus. As a result of these transient interactions, promoters move through many states during activation and repression. Two general concepts emerge from current data: (1) Various transcription factors appear to follow "ordered recruitment" to promoters on a time scale of minutes to hours in response to a stimulus. During this response, the proteins that interact with chromatin may cycle on and off the promoter multiple times. (2) During these ordered recruitment cycles, the individual molecules that form functional complexes often exchange rapidly on a time scale of seconds. This rapid exchange of molecules within a formed complex occurs independently of long-term cycling on chromatin. Several processes are implicated in rapid nuclear dynamics, including potential roles for molecular chaperones, the proteasome degradation machinery and chromatin remodeling complexes.

Animals↗

PubMed2004

Subnuclear trafficking and gene targeting by steroid receptors.

Through the use of novel imaging techniques, we have observed direct steroid receptor binding to a tandem array of a hormone-responsive promoter in living cells. We found that the glucocorticoid receptor (GR) exchanges rapidly with regulatory elements in the continued presence of ligand. We have also reconstituted a GR-dependent nucleoprotein transition with chromatin assembled on promoter DNA, and we discovered that GR is actively displaced from the chromatin template during the chromatin remodeling process. Using high-intensity UV laser crosslinking, we have observed highly periodic interactions of GR with promoter chromatin. These periodic binding events are dependent on GR-directed hSWI/SNF remodeling of the template and require the presence of ATP. Both the in vitro and in vivo results are consistent with a dynamic model ("hit-and-run") in which GR first binds to chromatin after ligand activation, recruits a remodeling activity, and is simultaneously lost from the template. We also find that receptor mobility in the nucleoplasm is strongly enhanced by molecular chaperones. These observations indicate that multiple mechanisms are involved in transient receptor interactions with nucleoplasmic targets.

Animals↗

PubMed2003

Inhibition of human papilloma virus E2 DNA binding protein by covalently linked polyamides.

Polyamides are a class of heterocyclic small molecules with the potential of controlling gene expression by binding to the minor groove of DNA in a sequence-specific manner. To evaluate the feasibility of this class of compounds as antiviral therapeutics, molecules were designed to essential sequence elements occurring numerous times in the HPV genome. This sequence element is bound by a virus-encoded transcription and replication factor E2, which binds to a 12 bp recognition site as a homodimeric protein. Here, we take advantage of polyamide:DNA and E2:DNA co-crystal structural information and advances in polyamide synthetic chemistry to design tandem hairpin polyamides that are capable of displacing the major groove-binding E2 homodimer from its DNA binding site. The binding of tandem hairpin polyamides and the E2 DNA binding protein to the DNA site is mutually exclusive even though the two ligands occupy opposite faces of the DNA double helix. We show with circular permutation studies that the tandem hairpin polyamide prevents the intrinsic bending of the E2 DNA site important for binding of the protein. Taken together, these results illustrate the feasibility of inhibiting the binding of homodimeric, major groove-binding transcription factors by altering the local DNA geometry using minor groove-binding tandem hairpin polyamides.

Binding Sites↗

PubMed2002

Dynamic behavior of transcription factors on a natural promoter in living cells.

Through the use of photobleaching techniques, we examined the dynamic interaction of three members of the transcription apparatus with a target promoter in living cells. The glucocorticoid receptor (GR) interacting protein 1 (GRIP-1) exhibits a half maximal time for fluorescent recovery (tau(R)) of 5 s, reflecting the same rapid exchange as observed for GR. In contrast, the large subunit (RPB1) of RNA polymerase II (pol II) required 13 min for complete fluorescence recovery, consistent with its function as a processive enzyme. We also observe a complex induction profile for the kinetics of GR-stimulated transcription. Our results indicate that GR and GRIP-1 as components of the activating complex are in a dynamic equilibrium with the promoter, and must return to the template many times during the course of transcriptional activation.

Animals↗

PubMed2002

Gal80 confers specificity on HAT complex interactions with activators.

Several yeast transcription activators have been shown to interact with and recruit histone acetyltransferase complexes to promoters in chromatin. The promiscuity of activator/HAT interactions suggests that additional factors temporally regulate these interactions in response to signaling pathways. In this study, we demonstrate that the negative regulator, Gal80, blocks interactions between the SAGA and NuA4 HAT complexes and the Gal4 activator. By contrast, Gal80 did not inhibit SAGA and NuA4 interaction with another activator Gcn4. The function of Gal80 prevented Gal4 targeting of SAGA and displaced SAGA targeted by Gal4 to a promoter within a nucleosome array. In the same set of experiments, targeting of SAGA by Gcn4 was unaffected by Gal80. These studies demonstrate that the specificity of HAT/activator interactions can be dictated by cofactors that modulate activation domain function in response to cellular signals.

Acetyltransferases↗