Several “head-to-head” (or “bidirectional”) gene pairs have been studied in individual experiments, but genome-wide analysis of this gene organization, especially in terms of transcriptional correlation and functional association, is still insufficient. We conducted a systematic investigation of head-to-head gene organization focusing on structural features, evolutionary conservation, expression correlation and functional association. Of the present 1,262, 1,071, and 491 head-to-head pairs identified in human, mouse, and rat genomes, respectively, pairs with 1– to 400–base pair distance between transcription start sites form the majority (62.36%, 64.15%, and 55.19% for human, mouse, and rat, respectively) of each dataset, and the largest group is always the one with a transcription start site distance of 101 to 200 base pairs. The phylogenetic analysis among Fugu, chicken, and human indicates a negative selection on the separation of head-to-head genes across vertebrate evolution, and thus the ancestral existence of this gene organization. The expression analysis shows that most of the human head-to-head genes are significantly correlated, and the correlation could be positive, negative, or alternative depending on the experimental conditions. Finally, head-to-head genes statistically tend to perform similar functions, and gene pairs associated with the significant cofunctions seem to have stronger expression correlations. The findings indicate that the head-to-head gene organization is ancient and conserved, which subjects functionally related genes to correlated transcriptional regulation and thus provides an exquisite mechanism of transcriptional regulation based on gene organization. These results have significantly expanded the knowledge about head-to-head gene organization. Supplementary materials for this study are available at http://www.scbit.org/h2h.

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We have reported that several silkworm strains are permissive to intrahemocoelical infection of Autographa californica nucleopolyhedrovirus (AcNPV), contrary to the general belief that AcNPV cannot infect silkworm. In the present study, we address whether the intrahemocoelical infection of AcNPV to the silkworm was an exceptional phenomenon, and the possible genetic basis underlying it. Wilder range test of 31 strains of silkworm Bombyx mori for intrahemocoelical AcNPV infection led to the identification of 14 permissive strains and 17 nonpermissive strains, indicating that the intrahemocoelical infection of AcNPV to the silkworm was not a rare and isolated phenomenon. Productive infection was shown in permissive silkworms, by EGFP fluorescence in various tissues when expression of reporter gene controlled by a very late viral promoter polh. The viral titer in larval hemolymph of permissive silkworms increased and maintained at a higher level hundredfold more than the initial amount of virus, indicating viral replication. A series of genetic cross experiments suggested the existence of only one dominant host anti-AcNPV gene or a set of genetically linked genes, which prevent AcNPV infection in nonpermissive silkworm strain Qingsong and are absent in permissive silkworm strain Haoyue.