A Dual Origin of the Xist Gene Table 4. P-value for similarities found between Xist elements in different species (estimated by program PRSS from FASTA package ). First sequence G.gallus Lnx3 exon3 G.gallus Lnx3 exon5 G.gallus Lnx3 exon5 G.gallus Lnx3 exons 1, 2 G.gallus Rasl11C ex3 G.gallus Wasf3 ex1 G.gallus Wasf3 ex2 G.gallus Uspl exon 1 G.gallus Uspl exon 2 Consensus Xist exon 2 Consensus Xist exon 4 Consensus Xist exon 9 Consensus Xist exon 10 Consensus Xist exon 10 G.gallus Uspl mRNA (ACC NM_001031123.1) Monomer of consensus tandem repeat A Monomer of consensus tandem repeat B 3-mer of consensus tandem repeat F Monomermer of consensus tandem repeat H Monomer of consensus tandem repeat C doi:10.1371/journal.pone.0002521.t004 Second sequence H.sapiens Xist intron 3 H.sapiens Xist intron 3 M.musculus Xist gene exon 5 H.sapiense Xist gene (ACC U80460) promoter H.sapiens Xic locus H.sapiens Xic locus (FTX) H.sapiens Xic locus (FTX) H.sapiens Xic locus (ENOX) H.sapiens Xic locus (ENOX) human ENOX EST BC071776 L3 CR1 L1 LINE ERV2 DNA transposons hAT-10_XT ZOMBI DNA Endogenous Retrovirus ERVB5 versus Endogenous Retrovirus ERV18_MD_I ERV1 DNA transposones HAT2_MD hAT L1 LINE Endogenous Retrovirus ERVB4_3-I_MM PRSS P-value 261025 0.01 0.004 0.007 1029 1025 361026 0.006 761025 0.0007 0.0001 361025 461025 0.13 261025 261025 0.0006 261027 0.001 261025 weak similarity to the endogenous retroviruses is found between blocks of tandem repeats. The comparative analyses allow us to conclude that tandem repeats, which are the main part of exon 1, could indeed have originated from fragments of endogenous retroviruses and other mobile elements (Table 4, Fig. S4). The ancestral Xist gene and its evolution By compiling the Xist sequences representing four eutherian orders, we generated the Xist gene consensus and recognized a number of ancient elements which diverged considerably in the contemporary eutherian species (Fig.S1). We suggest that the consensus in some extent reflects the Xist structure that existed approximately 100 Mya in a common ancestor of Eutheria. We propose that the ancestral Xist gene contained ten exons (Table 1, Fig. 1). Part of exon 1, intron 3 and exons 5 to 7 are all remnants of Lnx3, whereas exons 2 to 4 and 8 to 10 originated from mobile elements of various classes (Fig. 3, Table 2). The promoter region of the ancestral gene evolved from exons 1 and 2 of the Lnx3 gene, flanked by an ancient L3 element at the 59 region (Fig. 3). It is likely that basic arrays of tandem repeats A, B, D, F, and H, which originated from endogenous retroviruses, were already present within exon 1 of the ancestral Xist gene as well as MIR3. It seems Figure 3. The Xist gene evolved from a protein-coding gene and a set of transposable elements. Blue box – exons originating from Lnx3; red box - exons originating from transposable elements; dashed box – pseudoexons. doi:10.1371/journal.pone.0002521.g003 PLoS ONE | www.plosone.org 5 June 2008 | Volume 3 | Issue 6 | e2521