Allele-specific expression variation at different ploidy levels in Squalius alburnoides

Decoding allelic diversity, transcript variants and transcriptional complexity of CENH3 gene in Brassica oleracea var. botrytis

Histone proteins play a critical role in the primary organization of nucleosomes, which is the fundamental unit of chromatin. Among the five types of the histones, histone H3 has multiple variants, and the number differs among the species. Amongst histone H3 variants, centromeric histone H3 (CENH3) is crucial for centromere identification and proper chromosomal segregation during cell division. In the present study, we have identified 17 putative histone H3 genes of Brassica oleracea. Furthermore, we have done a detailed characterization of the CENH3 gene of B. oleracea. We showed that a single CENH3 gene exhibits allelic diversity with at least two alleles and alternative splicing pattern. Also, we have identified a CENH3 gene-specific co-dominant cleaved amplified polymorphic sequence marker SNP34(A/C) to distinguish CENH3 alleles and follow their expression in leaf and flower tissues. The gene structure analysis of the CENH3 gene revealed the conserved 5'-CAGCAG-3' sequence at the intron 3-exon 4 junction in B. oleracea, which serves as an alternative splicing site with one-codon (alanine) addition/deletion. However, this one-codon alternative splicing feature is not conserved in the CENH3 genes of wild allied Brassica species. Our finding suggests that transcriptional complexity and alternative splicing might play a key role in the transcriptional regulation and function of the CENH3 gene in B. oleracea. Altogether, data generated from the present study can serve as a primary information resource and can be used to engineer CENH3 gene towards developing haploid inducer lines in B. oleracea.

A prototype of the mammalian sulfotransferase 1 (SULT1) family in Xenopus laevis: Characterization of a biased usage of SULT1 genes located in the S-subgenome

BLAST searches previously carried out against Xenopus genome databases, using the cloned X. laevis cytosolic sulfotransferase 1 (SULT1) cDNA sequence, revealed the presence of more than a dozen members of this gene family. Among them, 11 genes composed of five sets, four pairs and a triplet, were homeologous genes in the X. laevis allotetraploid genome consisting of S- and L-subgenomes (≥83% identity within a set). Phylogenetic and synteny analyses of tetrapod SULT1 genes demonstrated that X. laevis possessed six subfamilies, four of which were related to mammalian SULT1 gene subfamilies, while two were ectothermic vertebrate-specific and amphibian-specific SULT1 gene subfamilies. Five sets of homeologous SULT1 genes were located as a gene cluster, and showed S-subgenome-biased gene expression patterns. Acetylation levels of histone H3 at lysine 9 and H4 were also higher in the homeologous SULT1 genes on the S-subgenome than those on the L-subgenome, however, methylation levels of histone H3 at lysine 9 and DNA methylation levels showed no correlation with their transcript levels. In conclusion, histone modifications such as acetylation may be a key factor that controls the S-subgenome-biased expression of the homeologous SULT1 genes.