Sequence Composition and Gene Content of the Short Arm of Rye (Secale cereale) Chromosome 1

BACKGROUND: The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. METHODOLOGY/PRINCIPAL FINDINGS: Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. CONCLUSIONS: The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye

S6K1 Alternative Splicing Modulates Its Oncogenic Activity and Regulates mTORC1

Ribosomal S6 kinase 1 (S6K1) is a major mTOR downstream signaling molecule that regulates cell size and translation efficiency. Here, we report that short isoforms of S6K1 are overproduced in breast cancer cell lines and tumors. Overexpression of S6K1 short isoforms induces transformation of human breast epithelial cells. The long S6K1 variant (Iso-1) induced opposite effects. It inhibits Ras-induced transformation and tumor formation, while its knockdown or knockout induces transformation, suggesting that Iso-1 has a tumor-suppressor activity. Furthermore, we found that S6K1 short isoforms bind and activate mTORC1, elevating 4E-BP1 phosphorylation, cap-dependent translation, and Mcl-1 protein levels. Both a phosphorylation-defective 4E-BP1 mutant and the mTORC1 inhibitor rapamycin partially blocked the oncogenic effects of S6K1 short isoforms, suggesting that these are mediated by mTORC1 and 4E-BP1. Thus, alternative splicing of S6K1 acts as a molecular switch in breast cancer cells, elevating oncogenic isoforms that activate mTORC1

Histogram of relative fluorescence intensity (‘flow karyotype’) obtained after flow cytometric analysis of DAPI-stained chromosome suspension of wheat-rye 1RS telosome addition line.

<p>The karyotype contains four peaks representing the chromosomes of wheat (labelled I, II, III, and 3B) and a peak of the telocentric chromosome 1RS. The peak of chromosome 1RS is clearly discernible and chromosomes can be easily sorted. Insert: Images of the flow-sorted chromosome 1RS after FISH with probes for telomeric sequences (red) and pSc200 (green) subtelomeric DNA sequences. The chromosomes were counterstained with DAPI (blue).</p

Distribution of Highly Homolog Bins (HHB) on the chromosome arms of rice and <i>Brachypodium distachyon.</i>

<p>Distribution of Highly Homolog Bins (HHB) on the chromosome arms of rice and <i>Brachypodium distachyon.</i></p

Representation of diverse repeat elements in1RS.

<p>*Sequence reads with more than 50% SSR sequence = SSR reads.</p

Number of gene loci and gene functions identified in 1RS.

<p>*RAP-DB, Triticum/Hordeum/Oryza Unigene DB, Secale Unigene DB, Wheat 1ABDS DB, Brachypodium distachyon Protein DB and NT Cereal DB.</p><p>**All EST entries with no annotation.</p><p>***Based on the RGA database.</p

Synteny of the 1RS chromosome arm to rice and <i>Brachypodium distachyon</i> genomes.

<p>Synteny of the 1RS chromosome arm to rice and <i>Brachypodium distachyon</i> genomes.</p

Comparison of gene content of 1RS and 1HS based on homology to the rice chromosomes 5 and 10.

<p>Comparison of gene content of 1RS and 1HS based on homology to the rice chromosomes 5 and 10.</p

Synteny of 1RS sequence reads with the non-TE related gene models of <i>Oryza sativa</i> and <i>Brachypodium distachyon</i>.

<p>The frequency of gene hits, in the in silico generated bins of the <i>Oryza sativa</i> and <i>Brachypodium distachyon</i> genomes, were expressed as multiples of standard deviation (SD). <b>A</b>: <i>Oryza sativa</i> chromosomes 1–12. <b>B</b>: <i>Brachypodium distachyon</i> chromosomes 1–5. <b>CEN</b>: Centromere. <b>Colour coding: </b><b>0</b> Bin with no 1RS homology. <b>1</b> Bins with non-significant 1RS homology <b>2</b> Bins with significant 1RS homology at 95% level (1.98 SD) <b>3</b> Bins with significant 1RS homology at 99% level (Highly Homolog Bin, 2.58 SD).</p