Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements

We have determined the nucleotide sequence of core histone genes and flanking regions from two of approximately 11 different genomic histone clusters of the nematode Caenorhabditis elegans. Four histone genes from one cluster (H3, H4, H2B, H2A) and two histone genes from another (H4 and H2A) were analyzed. The predicted amino acid sequences of the two H4 and H2A proteins from the two clusters are identical, whereas the nucleotide sequences of the genes have diverged 9% (H2A) and 12% (H4). Flanking sequences, which are mostly not similar, were compared to identify putative regulatory elements. A conserved sequence of 34 base-pairs is present 19 to 42 nucleotides 3′ of the termination codon of all the genes. Within the conserved sequence is a 16-base dyad sequence homologous to the one typically found at the 3′ end of histone genes from higher eukaryotes. The C. elegans core histone genes are organized as divergently transcribed pairs of H3-H4 and H2A-H2B and contain 5′ conserved sequence elements in the shared spacer regions. One of the sequence elements, 5′ CTCCNCCTNCCCACCNCANA 3′, is located immediately upstream from the canonical TATA homology of each gene. Another sequence element, 5′ CTGCGGGGACACATNT 3′, is present in the spacer of each heterotypic pair. These two 5′ conserved sequences are not present in the promoter region of histone genes from other organisms, where 5′ conserved sequences are usually different for each histone class. They are also not found in non-histone genes of C. elegans. These putative regulatory sequences of C. elegans core histone genes are similar to the regulatory elements of both higher and lower eukaryotes. The coding regions of the genes and the 3′ regulatory sequences are similar to those of higher eukaryotes, whereas the presence of common 5′ sequence elements upstream from genes of different histone classes is similar to histone promoter elements in yeast.