The Homeoproteins MAB-18 and CEH-14 Insulate the Dauer Collagen Gene col-43 from Activation by the Adjacent Promoter of the Spermatheca Gene sth-1 in Caenorhabditis elegans

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Genome searches in this study indicate that the nematode Caenorhabditis elegans genome has 2582 bidirectionally oriented genes that account for more than 25% of the total genes. We analyze the transcriptional repression system for one of these predicted bidirectional promoters, which controls the expression of the spermathecal gene sth-1 and collagen gene col-43. These two genes are separated by 1.3 kb and are transcribed bidirectionally. sth-1 is expressed in spermatheca after the L4 stage and col-43 is expressed in the hypodermal cells of the L2d dauer stage. The upstream regions required for the expression of sth-1 and col-43 shared an overlapped control sequence. Two homeoproteins, MAB-18 and CEH-14, were isolated by yeast one-hybrid screening as binding proteins of the overlapped region. MAB-18 bound to two homeodomain-binding sites and interacted with CEH-14 to repress col-43 expression in spermatheca. These results indicate that the two homeoproteins interact with each other to repress col-43 expression in sth-1-expressing tissues. This is the first report of bidirectional gene regulation analysis in the C. elegans genome.

Introduction

A bidirectional promoter is a regulatory mechanism for differential or simultaneous expression of two genes that are organized in head-to-head configurations. Bidirectional promoters exist in organisms ranging from bacteriophages to mammals, e.g. the cro/cI gene pair of bacteriophage lambda and basement membrane collagen gene pair of human.1, 2 Their existence raises questions about how genes that share a promoter region may be differentially regulated.

During the development and differentiation of living organisms, transcriptional regulation is critical in tissue-specific and stage-specific gene expression. Many of these regulatory events are likely to be controlled by bidirectional promoters. For example, bidirectional genes such as colicin E1/RNA-C genes in Escherichia coli,3 ras2/rop genes in Drosophila,4 bombyxin genes of Bombyx mori,5 haspin/αM290 gene in mice,6 and histone genes in human7 have been reported. Recently, following the completion of the human genome sequencing project, more than 50 bidirectional genes related to DNA repair or DNA replication have been identified.8 Here, we focus on a bidirectional promoter in the Caenorhabditis elegans genome in order to study regulatory mechanisms between genes that are transcribed in opposite directions.

In this study, we identified 2582 bidirectional promoters in the C. elegans genome. We analyzed the manner in which one of these bidirectional genes, sth-1 or col-43, is expressed in different phases of the life-cycle. Two homeoproteins, MAB-18 and CEH-14, were isolated as binding proteins of the intergenic region between both the genes. We concluded that both the homeoproteins repressed col-43 expression in sth-1-expressing tissues. We believe that the control mechanism of bidirectional gene expression presented here will be useful in understanding the life-cycle-dependent morphological changes and in analyzing the interactions of transcriptional complexes in different tissues.

Section snippets

The C. elegans genome has 2582 gene pairs that may be under bidirectional control

We investigated bidirectional promoter candidates in the predicted open reading frames (ORFs) in the C. elegans database WormBase.9 We chose intergenic regions of size less than 2.0 kb because most cis-regulatory regions of C. elegans are located within a 1.0 kb region 5′ upstream of the transcriptional start site.10 These bidirectional genes were commonly found at 2582 positions in all the chromosomes (Table 1; Figure 1(a)). The rates of occurrence of the bidirectional genes were 28.9% and 15.4%

Discussion

We found 2582 bidirectional gene pairs in the C. elegans genome. We focused on the analysis of a bidirectional promoter that is differentially regulated during development, leading to repression of one gene while another gene is expressed. This promoter expresses the sth-1 and col-43 genes in temporally and spatially distinct locations during development. We used reporter genes to analyze expression patterns and yeast one-hybrid screening to isolate homeoproteins that bind to specific sites in

C. elegans strains and culture

All C. elegans strains were derived from the wild-type Bristol strain N2 and were grown under standard conditions.30 daf-11(ks67) mutant was grown at 25 °C for dauer-constitutive phenotype analyses.31

Plasmid construction and sequencing

Promoter∷reporter fusion genes analyzed in this study were constructed using pPD series of vectors.15 pS3434Z, pS3434G and pS672Z were generated by inserting 3434 bp, 3434 bp and 672 bp upstream regions, respectively and some coding regions of sth-1 into pPD95.10, pPD95.81 and pPD22.04, respectively.

Acknowledgements

We thank Peter Okkema for providing the one-hybrid screening vector pRS414/HIS, Robert Barstead for the C. elegans cDNA library, and Andrew Fire for the lacZ and gfp fusion vectors. C. elegans strains were provided by the Caenorhabditis Genetic Center, which is funded by the NIH National Center for Research Resources (NCRR) and by Makoto Koga and Yasumi Oshima. We thank Jonathan Hodgkin, James Kramer and Steve L'Hernault for naming suggestions of sth-1 and col-43. Genome mapping of sth-1 and

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