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Background  LTR-retrotransposons became functional neogenes through evolution by acquiring promoter sequences, regulatory elements and sequence modification. Mammalian retrotransposon transcripts ( Mart1-9 ), also called  sushi-ichi- related retrotransposon-homolog ( SIRH ) genes, are a class of Ty3/gypsy LTR-retroelements showing moderate homology to the  sushi-ichi  LTR-retrotransposon in pufferfish.  Rtl1/Mart1  and  Peg10/Mart2  expression in mouse placenta and demonstration of their functional roles during placental development exemplifies their importance in cellular processes. In this study, we analyzed all eleven mouse  Mart  genes from the blastocyst stage and throughout placentogenesis in order to gain information about their expression and regulation.    Results  Quantitative PCR,  in situ  hybridization (ISH) and immunoblotting showed various expression patterns of the 11 mouse  Mart  genes through different placental stages. Zcchc5/ Mart3, Zcchc16/ Mart4 and Rgag1/Mart9  expression was undetectable.  Rtl1/Mart1, Peg10/Mart2, Rgag4/Mart5 – Cxx1a,b,c/Mart8b,c,a  gene expression was very low at the blastocyst stage. Later placental stages showed an increase of expression for  Rtl1/Mart1, Rgag4/Mart5 – Cxx1a,b,c/Mart8b,c,a,  the latter up to 1,489 molecules/ng cDNA at E9.5. From our recently published findings  Peg10/Mart2  was the most highly expressed  Mart  gene. ISH demonstrated sense and antisense transcript co-localization of  Rgag4/Mart5  to  Cxx1a,b,c/Mart8b,c,a  in trophoblast subtypes at the junctional zone, with an accumulation of antisense transcripts in the nuclei. To validate these results, we developed a TAG-aided sense/antisense transcript detection (TASA-TD) method, which verified sense and antisense transcripts for  Rtl1/Mart1, Rgag4/Mart5 – Cxx1a,b,c/Mart8b,c,a . Except for  Rtl1/Mart1  and  Cxx1a,b/Mart8b,c  all other  Mart  genes showed a reduced amount of antisense transcripts. Northern blot and 5′ and 3′ RACE confirmed both sense and antisense transcripts for  Ldoc1/Mart7  and  Cxx1a,b,c/Mart8b,c,a . Immunoblotting demonstrated a single protein throughout all placental stages for Ldoc1/Mart7, but for Cxx1a,b,c/Mart8b,c,a a switch occurred from a 57 kDa protein at E10.5 and E14.5 to a 25 kDa protein at E16.5 and E18.5.    Conclusions  RNA and protein detection of mouse  Mart  genes support neo-functionalization of retrotransposons in mammalian genomes. Undetectable expression of  Zcchc5/Mart3, Zcchc16/Mart4  and  Rgag1/Mart9  indicate no role during mouse placentogenesis.  Rgag4/Mart5  to  Cxx1a,b,c/Mart8b,c,a  gene expression support a role for differentiation from the ectoplacental cone.  Mart  antisense transcripts and protein alterations predict unique and complex molecular regulation in a time directed manner throughout mouse placentogenesis.    Electronic supplementary material  The online version of this article (doi:10.1186/s12977-015-0138-8) contains supplementary material, which is available to authorized users.

Selective expression of sense and antisense transcripts of the sushi-ichi-related retrotransposon – derived family during mouse placentogenesis