BMC Genomics 2009, 10:150 http://www.biomedcentral.com/1471-2164/10/150 Genes were considered as "circadian" on the basis of information from both the KEGG pathway database and additional annotation from the literature. FC: fold change of CX over Sham operated animals; FDR: P-values for the interaction between strain and treatment effects after adjustment for multiple comparisons with an FDR transformation (see methods); FDR values < 0.1 are formatted in bold. Table 3: Summary of results concerning circadian genes Gene Symbol Gene Name Arntl Dbp Tef Per2 Cry2 Clock Nr1d2 Per3 Rora Per1 Csnk1e Csnk1d Nr1d1 Bhlhb2 aryl hydrocarbon receptor nuclear translocator-like D site albumin promoter binding protein thyrotroph embryonic factor period homolog 2 (Drosophila) cryptochrome 2 (photolyase-like) circadian locomoter output cycles kaput nuclear receptor subfamily 1, group D, member 2 period homolog 3 (Drosophila) RAR-related orphan receptor alpha period homolog 1 (Drosophila) casein kinase 1, epsilon casein kinase 1, delta nuclear receptor subfamily 1, group D, member 1 basic helix-loop-helix domain containing, class B2 the long arm (Yq) in multiple copies [32,33]. Out of these 13 genes, we found only 5 of them to be expressed in hearts, i.e. Ddx3y, Uty, Eif2s3y, Jarid1d and Sly (data not shown). These genes appear to be expressed in a ubiqui- tous fashion, as we have detected by RT-PCR correspond- ing amplification products in many other non-cardiac tissues (listed below in the Methods section; data not shown). The first four of these genes were present on the ∀∋∋(%)∗(+,−%∗%.,/∃0 ∀%∗%.1 ∀+,/2/%+∋+(∀(+)(%+( ∃%& !∀ ## %3+ agpFDenoiigndasgeursirosrbaglemen7nirsniurctemehcremeadpcatwriooiizrtnihnsignodtfihfcfeoerKerEenGscpeGosnipnd5ien3xgspiprgrenosastleinoingnspowaftihnthwteatrhyae,catinodn Diagram summarizing differences in expression of interaction genes enriched within the KEGG p53 sig- naling pathway, and possible interactions of corre- sponding proteins with the androgen receptor. Boxes are in red or green when gene expression is increased or decreased in CX male C57BL/6J mice, respectively. Lines ter- minating with an arrowhead indicate positive regulation, those terminating with a bar indicate negative regulation. The values represent the ratio of mRNA abundance in CX male C57BL/6J vs C57.YA hearts. C57BL/6J C57.YA Interaction FC -1.10 -1.05 1.02 1.11 -1.08 -1.10 1.08 1.08 1.02 -1.01 1.02 1.04 -1.36 1.14 FDR 0.531 0.772 0.851 0.531 0.370 0.284 0.561 0.503 0.845 0.923 0.826 0.789 0.017 0.251 FC -5.30 2.94 2.16 2.95 1.42 -1.62 1.84 1.67 1.46 1.92 1.23 1.23 -1.39 1.15 FDR 0.000 0.000 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.004 0.016 0.061 0.006 0.135 FDR 0.006 0.006 0.008 0.009 0.019 0.024 0.033 0.034 0.081 0.087 0.230 0.437 0.920 0.942 Illumina MouseRef-8 v2.0 BeadChip, whose analysis revealed possibly significant differences among experi- mental groups. For Ddx3y, the effect of strain was signifi- cant (P < 0.05), but not that of surgery nor the interaction between the two. For Eif2s3y, the interaction (but not strain or surgery) was significant (P < 0.01). However, quantification of the level of expression of Ddx3y and Eif2s3y in the same samples by quantitative RT-PCR did not reveal any significant effect of strain or surgery in hearts from adult mice (Figure 8). We also measured by quantitative RT-PCR the level of expression of all 5 genes in hearts of C57BL.6J and C57.YA mice at different times during development. At the time of birth (but at no other tested time), both Ddx3y and Eif2s3y showed lower levels of expression in hearts from C57BL/6J male mice com- pared to their C57.YA counterparts (Figure 9). However, no polymorphism was found between the 2 strains for the regions including ~1 kb of upstream promoter and each exon (including 30 bp of intron flanking sequences as well as ~1 kb of the 3'-untranslated region). It therefore remains to be determined whether the perinatal differ- ences in expression of these two chrY genes may relate to differences in the effects of post-pubertal testosterone dur- ing adult life, and if so, by which mechanism. Likewise, which polymorphisms on chrY may be responsible for such differences needs additional sequencing. Conclusion The increased size of cardiomyocytes from adult male C57BL/6J mice compared to C57BL/6J-chrYA resulted from the absence of hypertrophic effects of post-pubertal testosterone on cells from the latter strain. However, gene profiling revealed that the lack or hypertrophic effects Page 7 of 11 (page number not for citation purposes)