Physical and transcriptional mapping on mouse chromosome 17.

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Conserved alternative and antisense transcripts at the programmed cell death 2 locus

<p>Abstract</p> <p>Background</p> <p>The programmed cell death 2 (<it>Pdcd2</it>) gene on mouse chromosome 17 was evaluated as a member of a highly conserved synteny, a candidate for an imprinted locus, and a candidate for the Hybrid sterility 1 (<it>Hst1</it>) gene.</p> <p>Results</p> <p>New mouse transcripts were identified at this locus: an alternative <it>Pdcd2 </it>mRNA skipping the last two coding exons and two classes of antisense RNAs. One class of the antisense RNA overlaps the alternative exon and the other the entire <it>Pdcd2 </it>gene. The antisense RNAs are alternative transcripts of the neighboring TATA-binding protein gene (<it>Tbp</it>) that are located mainly in the cell nucleus. Analogous alternative PDCD2 forms truncating the C-terminal domain were also detected in human and chicken. Alternative transcripts of the chicken <it>PDCD2 </it>and <it>TBP </it>genes also overlap. No correlation in the transcription of the alternative and overlapping mRNAs was detected. Allelic sequencing and transcription studies did not reveal any support for the candidacy of <it>Pdcd2 </it>for <it>Hst1</it>. No correlated expression of <it>Pdcd2 </it>with the other two genes of the highly conserved synteny was observed. <it>Pdcd2</it>, <it>Chd1</it>, and four other genes from this region were not imprinted in the embryo.</p> <p>Conclusion</p> <p>The conservation of alternative transcription of the <it>Pdcd2 </it>gene in mouse, human and chicken suggests the biological importance of such truncated protein. The biological function of the alternative <it>PDCD2 </it>is likely to be opposite to that of the constitutive form. The ratio of the constitutive and alternative <it>Pdcd2 </it>mRNAs differs in the tissues, suggesting a developmental role.</p> <p>The identified <it>Tbp-</it>alternative <it>Pdcd2</it>-antisense transcripts may interfere with the transcription of the <it>Pdcd2 </it>gene, as they are transcribed at a comparable level. The conservation of the <it>Pdcd2</it>/<it>Tbp </it>sense-antisense overlap in the mouse and chicken points out its biological relevance. Our results also suggest that some cDNAs in databases labeled as noncoding are incomplete alternative cDNAs of neighboring protein-coding genes.</p

Fine Haplotype Structure of a Chromosome 17 Region in the Laboratory and Wild Mouse

Extensive linkage disequilibrium among classical laboratory strains represents an obstacle in the high-resolution haplotype mapping of mouse quantitative trait loci (QTL). To determine the potential of wild-derived mouse strains for fine QTL mapping, we constructed a haplotype map of a 250-kb region of the t-complex on chromosome 17 containing the Hybrid sterility 1 (Hst1) gene. We resequenced 33 loci from up to 80 chromosomes of five mouse (sub)species. Trans-species single-nucleotide polymorphisms (SNPs) were rare between Mus m. musculus (Mmmu) and Mus m. domesticus (Mmd). The haplotypes in Mmmu and Mmd differed and therefore strains from these subspecies should not be combined for haplotype-associated mapping. The haplotypes of t-chromosomes differed from all non-t Mmmu and Mmd haplotypes. Half of the SNPs and SN indels but only one of seven longer rearrangements found in classical laboratory strains were useful for haplotype mapping in the wild-derived M. m. domesticus. The largest Mmd haplotype block contained three genes of a highly conserved synteny. The lengths of the haplotype blocks deduced from 36 domesticus chromosomes were in tens of kilobases, suggesting that the wild-derived Mmd strains are suitable for fine interval-specific mapping

<i>Prdm9</i> Incompatibility Controls Oligospermia and Delayed Fertility but No Selfish Transmission in Mouse Intersubspecific Hybrids

<div><p>PR-domain 9 (<i>Prdm9</i>) is the first hybrid sterility gene identified in mammals. The incompatibility between <i>Prdm9</i> from <i>Mus musculus domesticus</i> (Mmd; the B6 strain) and the <i>Hstx2</i> region of chromosome (Chr) X from <i>M. m. musculus</i> (Mmm; the PWD strain) participates in the complete meiotic arrest of mouse intersubspecific (PWD×B6)F1 hybrid males. Other studies suggest that also semisterile intersubspecific hybrids are relevant for mouse speciation, but the genes responsible remain unknown. To investigate the causes of this semisterility, we analyzed the role of <i>Prdm9</i> and Chr X in hybrids resulting from the crosses of PWK, another Mmm-derived inbred strain. We demonstrate that <i>Prdm9</i> and Chr X control the partial meiotic arrest and reduced sperm count in (PWK×B6)F1 males. Asynapsis of heterosubspecific chromosomes and semisterility were partially suppressed by removal of the B6 allele of <i>Prdm9</i>. Polymorphisms between PWK and PWD on Chr X but not in the <i>Prdm9</i> region were responsible for the modification of the outcome of <i>Prdm9</i> - Chr X F1 hybrid incompatibility. Furthermore, (PWK×B6)F1 hybrid males displayed delayed fertility dependent on the <i>Prdm9</i> incompatibility. While the <i>Drosophila</i> hybrid sterility gene <i>Overdrive</i> causes both delayed fertility and increased transmission of its own chromosome to the offspring, the segregation of Chr X and the <i>Prdm9</i> region from the mouse (PWK×B6)F1 males was normal. Our results indicate extended functional consequences of <i>Prdm9</i> - Chr X intersubspecific incompatibility on the fertility of hybrids and should influence the design of fertility analyses in hybrid zones and of laboratory crosses between Mmm and Mmd strains.</p></div

Cellular composition of primary spermatocytes from adult testes of F1 males.

<p>Age, male age (weeks); N, number of cells (a total from three males); Lep, Leptonema; Zyg, Zygonema; EP, Early pachynema; MP, Mid-Pachynema; LPD, Late Pachynema-Diplonema. Analyzed using antibodies against SYCP3, H1t, and γH2AX on chromosomal spreads (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095806#pone-0095806-g002" target="_blank">Figure 2</a> for representative images). The control data on 9-week-old (B6×B6), (PWD×B6)F1, and (B6.PWD-Chr X.1(s) ×PWD)F1 have been published <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095806#pone.0095806-Bhattacharyya2" target="_blank">[10]</a>. See Results for statistical evaluations.</p

Pachytene phenotypes of PWK F1 males.

<p>Age, male age (weeks); N, number of counted pachynemas from a total of two or three males; SB, AB, 0B, % pachytene spermatocytes carrying a normal sex body and all chromosomes synapsed (SB), an abnormal sex body (AB, a sex body containing unsynapsed autosomes), and neither abnormal nor sex body (0B; always carried also unsynapsed chromosomes). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095806#pone-0095806-g002" target="_blank">Figure 2A</a> for representative phenotypes and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095806#pone-0095806-t001" target="_blank">Table 1</a> for other abbreviations. Antibodies against SYCP3, SYCP1, and γH2AX were used to stage the cells on chromosomal spreads. See the text for statistical evaluations.</p

Testicular cross-section from (B6.PWD-Chr X.1s×PWK)F1.

<p>(<b>A</b>), (<b>B</b>) at nine (A, magnification 100x, B, 200x); (<b>C</b>), (<b>D</b>) at 25 weeks of age (C 100x, D 200x). Tubules in both the younger and older adult contained sperm (marked by asterisks in A, C and by “Sp” arrows in B, D). Pa, pachytene spermatocytes; Rs, round spermatids.</p