Sense and antisense OsDof12 transcripts in rice

<p>Abstract</p> <p>Background</p> <p>Antisense transcription is a widespread phenomenon in plants and mammals. Our previous data on rice gene expression analysis by microarray indicated that the sense and antisense transcripts at the <it>OsDof12 </it>locus were co-expressed in leaves. In current study, we analyzed the expression patterns in detail and looked for the possible mechanism related to their expression patterns.</p> <p>Results</p> <p><it>OsDof12</it>, being a single copy gene located on rice chromosome 3, encodes a predicted Dof protein of 440 amino acids with one intron of 945 bp. The antisense transcript, <it>OsDofl2os</it>, overlaps with both the exonic and intronic regions of <it>OsDof12 </it>and encodes a functionally unknown protein of 104 amino acids with no intron. The sense-antisense <it>OsDof12 </it>transcripts were co-expressed within the same tissues, and their expressions were not tissue-specific in general. At different developmental stages in rice, the <it>OsDof12 </it>and <it>OsDof12os </it>transcripts exhibited reciprocal expression patterns. Interestingly, the expression of both genes was significantly induced under drought treatment, and inhibited by dark treatment. In the <it>Pro</it>_{<it>OsDof</it>12}<it>-GUS </it>and <it>Pro</it>_{<it>OsDof</it>12<it>os</it>}-<it>GUS </it>transgenic rice plants, the expression profiles of GUS were consistent with those of the <it>OsDof12 </it>and <it>OsDof12os </it>transcripts, respectively. In addition, the analysis of cis-regulatory elements indicated that either of the two promoters contained 74 classes of cis-regulatory elements predicted, of which the two promoter regions shared 53 classes.</p> <p>Conclusion</p> <p>Based on the expression profiles of <it>OsDof12 </it>and <it>OsDof12os</it>, the expression patterns of GUS in the <it>Pro</it>_{<it>OsDof</it>12}<it>-GUS </it>and <it>Pro</it>_{<it>OsDof</it>12<it>os</it>}-<it>GUS </it>transgenic rice plants and the predicted common cis-regulatory elements shared by the two promoters, we suggest that the co-expression patterns of <it>OsDof12 </it>and <it>OsDof12os </it>might be attributed to the basically common nature of the two promoters.</p

Searching for bidirectional promoters in Arabidopsis thaliana

<p>Abstract</p> <p>Background</p> <p>A "bidirectional gene pair" is defined as two adjacent genes which are located on opposite strands of DNA with transcription start sites (TSSs) not more than 1000 base pairs apart and the intergenic region between two TSSs is commonly designated as a putative "bidirectional promoter". Individual examples of bidirectional gene pairs have been reported for years, as well as a few genome-wide analyses have been studied in mammalian and human genomes. However, no genome-wide analysis of bidirectional genes for plants has been done. Furthermore, the exact mechanism of this gene organization is still less understood.</p> <p>Results</p> <p>We conducted comprehensive analysis of bidirectional gene pairs through the whole <it>Arabidopsis thaliana </it>genome and identified 2471 bidirectional gene pairs. The analysis shows that bidirectional genes are often coexpressed and tend to be involved in the same biological function. Furthermore, bidirectional gene pairs associated with similar functions seem to have stronger expression correlation. We pay more attention to the regulatory analysis on the intergenic regions between bidirectional genes. Using a hierarchical stochastic language model (HSL) (which is developed by ourselves), we can identify intergenic regions enriched of regulatory elements which are essential for the initiation of transcription. Finally, we picked 27 functionally associated bidirectional gene pairs with their intergenic regions enriched of regulatory elements and hypothesized them to be regulated by bidirectional promoters, some of which have the same orthologs in ancient organisms. More than half of these bidirectional gene pairs are further supported by sharing similar functional categories as these of handful experimental verified bidirectional genes.</p> <p>Conclusion</p> <p>Bidirectional gene pairs are concluded also prevalent in plant genome. Promoter analyses of the intergenic regions between bidirectional genes could be a new way to study the bidirectional gene structure, which may provide a important clue for further analysis. Such a method could be applied to other genomes.</p

Conservation and implications of eukaryote transcriptional regulatory regions across multiple species

<p>Abstract</p> <p>Background</p> <p>Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs). Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts.</p> <p>Results</p> <p>We constructed a hierarchical stochastic language (HSL) model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or <it>OsALYL1</it>, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes.</p> <p>Conclusion</p> <p>Our findings indicate that 1) the HSL model can be used to accurately predict core TRRs of transcripts across species and 2) identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.</p

An AT-hook gene is required for palea formation and floral organ number control in rice

AbstractGrasses have highly specialized flowers and their outer floral organ identity remains unclear. In this study, we identified and characterized rice mutants that specifically disrupted the development of palea, one of the outer whorl floral organs. The depressed palea1 (dp1) mutants show a primary defect in the main structure of palea, implying that palea is a fusion between the main structure and marginal tissues on both sides. The sterile lemma at the palea side is occasionally elongated in dp1 mutants. In addition, we found a floral organ number increase in dp1 mutants at low penetration. Both the sterile lemma elongation and the floral organ number increase phenotype are enhanced by the mutation of an independent gene SMALL DEGENERATIVE PALEA1 (SDP1), whose single mutation causes reduced palea size. E function and presumable A function floral homeotic genes were found suppressed in the dp1–2 mutant. We identified the DP1 gene by map-based cloning and found it encodes a nuclear-localized AT-hook DNA binding protein, suggesting a grass-specific role of chromatin architecture modification in flower development. The DP1 enhancer SDP1 was also positional cloned, and was found identical to the recently reported RETARDED PALEA1 (REP1) gene encoding a TCP family transcription factor. We further found that SDP1/REP1 is downstreamly regulated by DP1

In Memory of the Father of Hybrid Rice

Prof. Yuan devoted his whole life to the research of hybrid rice. On the first anniversary of Prof. Yuan Yuan&rsquo;s death, our research team wrote a paper to commemorate him. In this paper, we recalled his life, his research progress and achievements of hybrid rice. He led and guided his research team to overcome difficulties in hybrid rice research. Hybrid rice has made important contributions to China and world&rsquo;s food security. He is a great researcher worthy of our memory forever in the world

In Memory of the Father of Hybrid Rice

Prof. Yuan devoted his whole life to the research of hybrid rice. On the first anniversary of Prof. Yuan Yuan’s death, our research team wrote a paper to commemorate him. In this paper, we recalled his life, his research progress and achievements of hybrid rice. He led and guided his research team to overcome difficulties in hybrid rice research. Hybrid rice has made important contributions to China and world’s food security. He is a great researcher worthy of our memory forever in the world