POU domain genes are differentially expressed in the early stages after lineage commitment of the PNS-derived stem cell line, RT4-AC

REST is a key regulator in brain-specific homeobox gene expression during neuronal differentiation

Brain-specific homeobox (Bsx) is specifically expressed at the early embryonic stages during brain development. Several studies show that Bsx plays important roles in brain development; however, the mechanisms of its transcriptional regulation remain to be established. In this study, we show that binding of repressor element silencing transcription factor (REST) to the neuron restrictive silencer element (NRSE) represses Bsx transcription in non-neuronal P19 cells. The Bsx promoter contains several putative binding sites for transcription factors, including NRSE for REST and the GC box for the transcriptional activator, Sp1. Upon neuronal differentiation of P19 cells with retinoic acid, Bsx gene expression increased, whereas that of the REST gene decreased. Electrophoretic mobility shift analyses demonstrated that recombinant REST proteins bound the NRSE region of the Bsx promoter. In neuronal NS20Y cells, transcriptional activity of the Bsx promoter was decreased upon expression of REST. Moreover, dominant-negative REST derepressed Bsx transcription in P19 cells. Sp1-mediated transcriptional activity of the Bsx promoter was attenuated by treatment with mithramycin A, a GC box-binding drug, but was enhanced upon mutation of NRSE. Co-immunoprecipitation and chromatin immunoprecipitation assays showed that the Bsx promoter appeared to be modulated by direct interactions between REST and Sp1. The CpG sites of NRSE and GC box were completely unmethylated, signifying no interference of DNA methylation. Our results suggest that binding of REST to NRSE suppresses the Sp1-mediated activation of Bsx in non-neuronal cells.

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 genes. To gain insight into the structure and function of bivalent domains, we mapped key histone modifications and subunits of Polycomb-repressive complexes 1 and 2 (PRC1 and PRC2) genomewide in human and mouse ES cells by chromatin immunoprecipitation, followed by ultra high-throughput sequencing. We find that bivalent domains can be segregated into two classes—the first occupied by both PRC2 and PRC1 (PRC1-positive) and the second specifically bound by PRC2 (PRC2-only). PRC1-positive bivalent domains appear functionally distinct as they more efficiently retain lysine 27 tri-methylation upon differentiation, show stringent conservation of chromatin state, and associate with an overwhelming number of developmental regulator gene promoters. We also used computational genomics to search for sequence determinants of Polycomb binding. This analysis revealed that the genomewide locations of PRC2 and PRC1 can be largely predicted from the locations, sizes, and underlying motif contents of CpG islands. We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells.

Polycomb-group (PcG) proteins play essential roles in the epigenetic regulation of gene expression during development. PcG proteins are repressors that catalyze lysine 27 tri-methylation on histone H3. They are antagonized by trithorax-group proteins that catalyze lysine 4 tri-methylation. Recent studies of ES cells revealed a novel chromatin pattern consisting of overlapping lysine 27 and lysine 4 tri-methylation. Genomic regions with these opposing modifications were termed “bivalent domains” and proposed to silence developmental regulators while keeping them “poised” for alternate fates. However, our understanding of PcG regulation and bivalent domains remains limited. For instance, bivalent domains affect over 2,000 promoters with diverse functions, which suggests that they may function in diverse cellular processes. Moreover, the mechanisms that underlie the targeting of PcG complexes to specific genomic regions remain completely unknown. To gain insight into these issues, we used ultra high-throughput sequencing to map PcG complexes and related modifications genomewide in human and mouse ES cells. The data identify two classes of bivalent domains with distinct regulatory properties. They also reveal striking relationships between genome sequence and chromatin state that suggest a prominent role for the DNA sequence in dictating the genomewide localization of PcG complexes and, consequently, bivalent domains in ES cells.

Repressor element-1 silencing transcription factor/neuronal restrictive silencer factor (REST/NRSF) can regulate HSV-1 immediate-early transcription via histone modification

Background

During primary infection of its human host, Herpes Simplex Virus Type-1 (HSV-1) establishes latency in neurons where the viral genome is maintained in a circular form associated with nucleosomes in a chromatin configration. During latency, most viral genes are silenced, although the molecular mechanisms responsible for this are unclear. We hypothesized that neuronal factors repress HSV-1 gene expression during latency. A search of the HSV-1 DNA sequence for potential regulatory elements identified a Repressor Element-1/Neuronal Restrictive Silencer Element (RE-1/NRSE) located between HSV-1 genes ICP22 and ICP4. We predicted that the Repressor Element Silencing Transcription Factor/Neuronal Restrictive Silencer Factor (REST/NRSF) regulates expression of ICP22 and ICP4.

Results

Transient cotransfection indicated that REST/NRSF inhibited the activity of both promoters. In contrast, cotransfection of a mutant form of REST/NRSF encoding only the DNA-binding domain of the protein resulted in less inhibition. Stably transformed cell lines containing episomal reporter plasmids with a chromatin structure showed that REST/NRSF specifically inhibited the ICP4 promoter, but not the ICP22 promoter. REST/NRSF inhibition of the ICP4 promoter was reversed by histone deacetylase (HDAC) inhibitor Trichostatin A (TSA). Additionally, chromatin immuno-precipitation (ChIP) assays indicated that the corepressor CoREST was recruited to the proximity of ICP4 promoter and that acetylation of histone H4 was reduced in the presence of REST/NRSF.

Conclusion

Since the ICP4 protein is a key transactivator of HSV-1 lytic cycle genes, these results suggest that REST/NRSF may have an important role in the establishment and/or maintenance of HSV-1 gene silencing during latency by targeting ICP4 expression.

Gene signatures of progression and metastasis in renal cell cancer

PURPOSE

To address the progression, metastasis, and clinical heterogeneity of renal cell cancer (RCC).

EXPERIMENTAL DESIGN

Transcriptional profiling with oligonucleotide microarrays (22,283 genes) was done on 49 RCC tumors, 20 non-RCC renal tumors, and 23 normal kidney samples. Samples were clustered based on gene expression profiles and specific gene sets for each renal tumor type were identified. Gene expression was correlated to disease progression and a metastasis gene signature was derived.

RESULTS

Gene signatures were identified for each tumor type with 100% accuracy. Differentially expressed genes during early tumor formation and tumor progression to metastatic RCC were found. Subsets of these genes code for secreted proteins and membrane receptors and are both potential therapeutic or diagnostic targets. A gene pattern ("metastatic signature") derived from primary tumor was very accurate in classifying tumors with and without metastases at the time of surgery. A previously described "global" metastatic signature derived by another group from various non-RCC tumors was validated in RCC.

CONCLUSION

Unlike previous studies, we describe highly accurate and externally validated gene signatures for RCC subtypes and other renal tumors. Interestingly, the gene expression of primary tumors provides us information about the metastatic status in the respective patients and has the potential, if prospectively validated, to enrich the armamentarium of diagnostic tests in RCC. We validated in RCC, for the first time, a previously described metastatic signature and further showed the feasibility of applying a gene signature across different microarray platforms. Transcriptional profiling allows a better appreciation of the molecular and clinical heterogeneity in RCC.

Cell-type non-selective transcription of mouse and human genes encoding neural-restrictive silencer factor

Neural-restrictive silencer (NRS) has been identified in at least twenty neuron-specific genes, and its nuclear DNA-binding factor, NRSF (also known as RE1-silencing transcription factor (REST)), has been cloned from human and rat, and was shown to repress transcription by recruiting corepressors mSin3 and/or CoREST via its N- and C-terminal domains, leading to chromatin reorganization by mSin3-associated histone deacetylase, HDAC. However, it is largely unknown how NRSF gene expression is regulated. To elucidate the mechanisms for gene expression of NRSF, we isolated the transcriptional unit of the NRSF gene from mouse and human, identified three 5'-non-coding exons in addition to three coding exons, determined transcription start sites, and identified two basal promoter activities in the upstream of the first two non-coding exons. Both promoters functioned equally in neuronal and non-neuronal cells, suggesting that levels of initial transcripts of NRSF gene are similar in neuronal and non-neuronal cells. These results suggest that the level of NRSF gene expression is not determined by transcription per se, and rather is modulated at the post-transcriptional level, e.g. splicing, mRNA stability, and/or post-translational modifications, in a cell-specific manner. Consistent with this idea, NRSF protein was apparently present even in neuronal cells and tissues, but was unable to bind to the NRS element, suggesting that NRSF is regulated at least in part post-translationally.