Transcription of histone gene cluster by differential core-promoter factors

Abstract

The 100 copies of tandemly arrayed Drosophila linker (H1) and core (H2A/B and H3/H4) histone gene cluster are coordinately regulated during the cell cycle. However, the molecular mechanisms that must allow differential transcription of linker versus core histones prevalent during development remain elusive. Here, we used fluorescence imaging, biochemistry, and genetics to show that TBP (TATA-box-binding protein)-related factor 2 (TRF2) selectively regulates the TATA-less Histone H1 gene promoter, while TBP/TFIID targets core histone transcription. Importantly, TRF2-depleted polytene chromosomes display severe chromosomal structural defects. This selective usage of TRF2 and TBP provides a novel mechanism to differentially direct transcription within the histone cluster. Moreover, genome-wide chromatin immunoprecipitation (ChIP)-on-chip analyses coupled with RNA interference (RNAi)-mediated functional studies revealed that TRF2 targets several classes of TATA-less promoters of >1000 genes including those driving transcription of essential chromatin organization and protein synthesis genes. Our studies establish that TRF2 promoter recognition complexes play a significantly more central role in governing metazoan transcription than previously appreciated.[Keywords: TATA-box-binding protein (TBP); TBP-related factor 2 (TRF2); core-promoter recognition; histone gene cluster; ChIP-on-chip; chromatin organization] Supplemental material is available at http://www.genesdev.org.

TRF2: TRansForming the view of general transcription factors

“…64,71 Specifically, TRF2 has been shown to regulate the TATA-less Histone H1 gene, whereas TBP regulates the core histone genes. 71 Recent single cell imaging analysis of the endogenous histone gene cluster in Drosophila cells, showed differential transcription kinetics of TRF2-directed histone H1 gene expression (transcribed throughout S phase) vs. TBP-directed core histones gene expression (only transcribed in a short pulse during early S phase). 72 Furthermore, ChIP-chip analysis revealed that Drosophila TRF2, but not TBP, is associated with a large group of TATAless core promoters, including core promoters of ribosomal protein genes.…”

“…72 Furthermore, ChIP-chip analysis revealed that Drosophila TRF2, but not TBP, is associated with a large group of TATAless core promoters, including core promoters of ribosomal protein genes. 71 The core promoters of most ribosomal protein genes in Drosophila and humans contain a functional TCT motif, which is not recognized by the TBP/TFIID complex. 21 Remarkably, TRF2, but not TBP, has recently been shown to mediate the transcription of ribosomal protein genes that lack a TATA box and have functional TCT motifs.…”

“…84 Additional support for the involvement of TRF2 in Drosophila metamorphosis comes from RNAi depletion of TRF2 in larval salivary glands that results in a significant reduction in the sizes of the cells and the glands. 71 Although these mutant embryos develop to the third instar larval stage, a majority of them fail to pupate or die during pupal stages. Hence, even though a detailed mechanism has not been demonstrated, TRF2 is involved in the regulation of Drosophila metamorphosis.…”

Differential Utilization of TATA Box-binding Protein (TBP) and TBP-related Factor 1 (TRF1) at Different Classes of RNA Polymerase III Promoters

“…3B) provides strong evidence that TBP is utilized for the vast majority of U6 transcription in fruit flies. A number of studies have revealed that transcription by Pol II of different populations of mRNA promoters differentially depends upon TBP or a TBP-related factor (35)(36)(37)(38)(39)(40). To our knowledge, the finding that different classes of Pol III promoters can likewise differentially utilize TBP or a TBP-related factor has not previously been encountered.…”

Drosophila Octamer Elements and Pdm-1 Dictate the Coordinated Transcription of Core Histone Genes

“…A recent study (15) suggests that the TATA-less Drosophila melanogaster histone H1 (dmH1) gene promoter is selectively regulated by TATA box-binding protein-related factor 2 (TRF2) and that this selective usage versus that of TATA-boxbinding protein (TBP) for TATA-containing core histone genes provides a novel mechanism that differentially directs histone gene transcription within the histone gene cluster; however, a detailed molecular description of the mechanism(s) that governs coordinated expression of Drosophila core histone genes is not yet established and requires investigation as one of the critical steps toward understanding Drosophila histone gene regulation pathways.…”