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Figure 1 | BMC Molecular Biology

Figure 1

From: Histone gene expression and histone mRNA 3' end structure in Caenorhabditis elegans

Figure 1

Conserved sequence elements in the 3'UTR of C. elegans histone genes. 3' UTR regions of histone H2A, H2B, H3 and H4 genes were downloaded from Wormbase, aligned using ClustalW and the conserved sequence elements were identified (the alignment of histone gene 3'UTRs is shown in additional file 1). The consensus sequences for the 3'UTR elements of histones H2A, H2B, H3 and H4 are shown separately. The hairpin element, the core of the binding site for CDL-1, is boxed in black. A conserved element with the core sequence AATCC located at the position of a putative U7 snRNP binding site (HDE?), and a polyadenylation signal sequence are indicated. The 32–36 nucleotide region encompassing the hairpin structure is absolutely conserved at nearly all positions. The only significant deviation from the consensus is found in the hairpin loop of four histone H2B genes where the sequence is CTTA instead of CTTT. The core AATCC element is absolutely conserved in most histone genes except for H3 genes, where the first nucleotide is a G instead of an A in 5 out of 13 sequences. Other deviations from the consensus are minor and normally involve only one nucleotide. The core sequence is embedded in longer conserved elements that differ between the different histone gene types. The AATAAA polyadenylation signal is absolutely conserved in H2A genes, 11 out of 14 H2B genes, 12 out of 13 H3 genes and 11 out of 14 H4 genes. The other H2B, H3 and H4 genes have previously described variants of this sequence [39]. Further elements involved in polyadenylation are a CA dinucleotide at the cleavage site and a G/GU rich downstream element. Such elements can be found downstream of the polyadenylation signal, but their position and, in case of the G/GU rich element, their sequence are less well conserved (see also additional file 1).

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