Cereal genes similar to Snf2 define a new subfamily that includes human and mouse genes

Genes from the SNF2 family play important roles in transcriptional regulation, maintenance of chromosome integrity and DNA repair. This study describes the molecular cloning and characterization of cereal genes from this family. The predicted proteins exhibit a novel C-terminal domain that defines a new subfamily designated SNF2P that includes human and mouse proteins. Comparison between genomic and cDNA sequences showed that cereal Snf2P genes consisted of 17 exons, including one only 8 bp long. Two barley alleles differed by the presence of a 7.7-kb non-LTR retrotransposon in intron 6. An alternative annotation of the orthologous Arabidopsis gene would improve its similarity with the other members of the subfamily. Intron 2 was not spliced out in approximately half of the rice Snf2P mRNAs present in leaves, resulting in a premature stop codon. Transcripts from the barley and wheat Snf2P genes were found in apexes, leaves, sheaths, roots and spikes. The Snf2P genes exist as single copies on wheat chromosome arm 5A(m)L and in the colinear regions on barley chromosome arm 4HL and rice chromosome 3. High-density genetic mapping and RT-PCR suggest that Snf2P is not a candidate gene for the tightly linked vernalization gene Vrn2.