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Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

ABSTRACT: Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions, including elements that are predominantly found at either developmentally regulated or at housekeeping genes. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters--one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor--and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors--Dref and Trl--that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.

SUBMITTER: Zabidi MA

PROVIDER: S-EPMC6795551 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

Zabidi Muhammad A MA Arnold Cosmas D CD Schernhuber Katharina K Pagani Michaela M Rath Martina M Frank Olga O Stark Alexander A

Nature 20141215 7540

Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specif ...[more]

PMID: 25517091

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Project description:The transcription activity of the tumor-specific promoter may be increased using specific DNA sequences such as simian virus 40 (SV40). Human heparanase (HPSE) gene promoter is also considered a tumor-specific promoter. However, whether or not the SV40 enhancer affects the tumor specificity of HPSE remains to be determined. The SV40 enhancer sequence, 237 bp in length, was amplified and correctly inserted into the assigned multiple clone sites (MCS) of the eukaryotic expression vector pEGFP-Hp, which was constructed in advance. The recombinant plasmid pEGFP-Hp-SV40e was consistent with the anticipated Genbank data and transfected into human umbilical vein endothelial cell (ECV) and tumor cell lines, including hepatoma carcinoma (HepG2), laryngeal carcinoma (Hep2) and chronic myelogenous leukemia cell lines (K562) using lipofectamine, respectively. The expression of the reporter gene, green fluorescent protein (GFP), was detected using fluorescence microscopy and flow cytometry. The length of the amplified SV40 enchancer was 237 bp and the sequence was in accordance with the GenBank data. The recombinant plasmid pEGFP-Hp-SV40 was consistent with the anticipated results. Fluorimetric analysis showed that the fluorescence of pEGFP-Hp-SV40e in ECV cells was as dim as pEGFP-Hp, and obviously weaker than pEGFPN1. In tumor cells including HepG2, Hep2 and K562 cells, the fluorescence of pEGFP-Hp-SV40e was similar to that of pEGFP-N1, which was clearly brighter than pEGFP-Hp. The average transfecion rates in the 4 types of cells were 4.1, 17.2, 8.8 and 6.4% in the pEGFP-Hp; 18.3, 29.3, 17.0 and 13.0% in the pEGFP-Nl and 4.3, 28.8, 16.4 and 11.7% in the pEGFP-Hp-SV40e groups, respectively. The ratio of pEGFP-Hp-SV40e to pEGFP-Hp in all cells was 1.05, 1.67, 1.86 and 1.83, respectively. In conclusion, the inserted SV40 enhancer sequence is able to improve the transcriptional activity of the human HPSE gene promoter, but does not affect its tumor specificity.

Project description:Transcriptional cofactors communicate regulatory cues from enhancers to promoters and are central effectors of transcription activation and gene expression, which is a hallmark of all multicellular organisms. However, the extent to which different cofactors display intrinsic specificity for distinct promoters is unclear. Testing intrinsic COF – CP preferences requires the systematic assessment of transcriptional activation for many CPs in the presence or absence of a given COF in an otherwise constant standardized reporter system. We therefore combined a plasmid-based high-throughput reporter assay, Self-Transcribing Active Core Promoter-sequencing (STAP-seq), with the specific recruitment of individual COFs to create a high-throughput activator bypass-like assay. Using this assay, we tested whether 23 different individually tethered Drosophila melanogaster COFs could activate transcription from any of 72,000 CP candidates in S2 cells. We selected COFs that represent different functional classes and enzymatic activities: histone-acetyl transferases (Nejire - the fly ortholog of CBP/P300, Mof, Gcn5 - ortholog of pCAF, Atac2, Tip60, Br140), three components of the COMPASS-like histone H3K4 methyltransferase complexes (Lpt, Trr and Trx), nucleosome remodeling ATP-ase (Brm), two Chromo or Chromo-shadow domain (Chro and Mof) and three Bromodomain (Brd8, Brd9 and fs(1)h - ortholog of Brd4) -containing COFs, three subunits of the Mediator Complex (MED15, MED24 and MED25), three subunits of the TFIID general transcription factor (Taf4, Tbp and Trf2) and three less well-characterized COFs (EMSY, Gfzf and Pzg). We used the strong transcriptional activator P65 as a positive and GFP as a negative control. In addition, we tested 6 COFs and the 2 controls in two other Drosophila cell lines: ovarian somatic cells (OSC) and Kc167 cells. We uncovered five classes of core promoters, distinguished by their differential response to specific cofactors and by the presence of known sequence elements, such as the TATA-box, Down-stream Promoter Element, or TCT motif. Moreover, the five promoter types show distinct chromatin properties at endogenous loci. The observed compatibilities between cofactors and promoters can explain how different enhancers specifically activate distinct sets of genes, alternative promoters within the same genes, or even distinct transcription starting sites within the same promoters. Thus, cofactor–promoter compatibilities may underlie distinct transcriptional programs.

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Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

Publications

Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.

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