Dataset Information

Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors.

ABSTRACT: Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC) assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes.

SUBMITTER: Hudry B

PROVIDER: S-EPMC3383740 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors.

Hudry Bruno B Remacle Sophie S Delfini Marie-Claire MC Rezsohazy René R Graba Yacine Y Merabet Samir S

PLoS biology 20120626 6

Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence ...[more]

PMID: 22745600

Similar Datasets

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.

Project description:BackgroundRNA-seq studies in metazoa have revealed a distinct, double-peaked (bimodal) distribution of gene expression independent of species and cell type. However, two studies in filamentous fungi yielded conflicting results, with a bimodal distribution in Pyronema confluens and varying distributions in Sordaria macrospora. To obtain a broader overview of global gene expression distributions in fungi, an additional 60 publicly available RNA-seq data sets from six ascomycetes and one basidiomycete were analyzed with respect to gene expression distributions.ResultsClustering of normalized, log2-transformed gene expression levels for each RNA-seq data set yielded distributions with one to five peaks. When only major peaks comprising at least 15% of all analyzed genes were considered, distributions ranged from one to three major peaks, suggesting that fungal gene expression is not generally bimodal. The number of peaks was not correlated with the phylogenetic position of a species; however, higher filamentous asco- and basidiomycetes showed up to three major peaks, whereas gene expression levels in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe had only one to two major peaks, with one predominant peak containing at least 70% of all expressed genes. In several species, the number of peaks varied even within a single species, e.g. depending on the growth conditions as evidenced in the one to three major peaks in different samples from Neurospora crassa. Earlier studies based on microarray and SAGE data revealed distributions of gene expression level that followed Zipf's law, i.e. log-transformed gene expression levels were inversely proportional to the log-transformed expression rank of a gene. However, analyses of the fungal RNA-seq data sets could not identify any that confirmed to Zipf's law.ConclusionsFungal gene expression patterns cannot generally be described by a single type of distribution (bimodal or Zipf's law). One hypothesis to explain this finding might be that gene expression in fungi is highly dynamic, and fine-tuned at the level of transcription not only for individual genes, but also at a global level.

Dataset Information

Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors.

Publications

Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets