Detection of potential positive regulatory motifs of transcription in yeast introns by comparative analysis of oligonucleotide frequencies

The Masculinizing gene is a candidate male pathway developmental factor in the mud crab Scylla paramamosain

The Masculinizer (Masc) gene plays a crucial role in masculinization during insect embryonic gonadal development. Nevertheless, the Masc expression pattern and function in crabs remain largely unknown. In the present study, we screened and validated the Masc gene from transcriptome data of mud crab S. paramamosain. The Masc relative transcript level in the testis was significantly higher than that of ovaries and other tissues, as measured by quantitative real-time PCR. In situ hybridization showed that Masc exhibited a significant signal throughout all stages of testicular development. The phylogenetic analysis revealed conservation in the evolution of crustaceans, potentially indicating its functional importance. Masc RNA interference showed that the expression of testis bias-related genes decreased significantly while the ovary bias-related genes increased significantly. Transcriptome data suggested that Masc regulates several signaling pathways, including the mTOR, Wnt, insulin, and other sex-related pathways. These results indicate that Masc may play a role in mud crab male development with possible application in sex control in aquaculture.

Promoters and introns as key drivers for enhanced gene expression in Saccharomyces cerevisiae

The transcription of genes in the yeast Saccharomyces cerevisiae is governed by multiple layers of regulatory elements and proteins, cooperating to ensure optimum expression of the final protein product based on the cellular requirements. Promoters have always been regarded as the most important determinant of gene transcription, but introns also play a key role in the expression of intron-encoding genes. Some introns can enhance transcription when introduced either promoter-proximal or embedded in the open reading frame of genes. However, the outcome is seldom predictable, with some introns increasing or decreasing transcription depending on the promoter and reporter gene employed. This chapter provides an overview of the general structure and function of promoters and introns and how they may cooperate during transcription to allow intron-mediated enhancement of gene expression. Since S. cerevisiae is a suitable host for recombinant protein production on a commercial level, stronger and more controllable promoters are in high demand. Enhanced gene expression can be achieved via promoter engineering, which may include introns that increase the efficacy of recombinant expression cassettes. Different models for the role of introns in transcription are briefly discussed to show how these intervening sequences can actively interact with the transcription machinery. Furthermore, recent examples of improved protein production via the introduction of promoter-proximal introns are highlighted to showcase the potential value of intron-mediated enhancement of gene expression.

Polymorphisms in the AOX2 gene are associated with the rooting ability of olive cuttings

Different rooting ability candidate genes were tested on an olive cross progeny. Our results demonstrated that only the AOX2 gene was strongly induced. OeAOX2 was fully characterised and correlated to phenotypical traits. The formation of adventitious roots is a key step in the vegetative propagation of trees crop species, and this ability is under strict genetic control. While numerous studies have been carried out to identify genes controlling adventitious root formation, only a few loci have been characterised. In this work, candidate genes that were putatively involved in rooting ability were identified in olive (Olea europaea L.) by similarity with orthologs identified in other plant species. The mRNA levels of these genes were analysed by real-time PCR during root induction in high- (HR) and low-rooting (LR) individuals. Interestingly, alternative oxidase 2 (AOX2), which was previously reported to be a functional marker for rooting in olive cuttings, showed a strong induction in HR individuals. From the OeAOX2 full-length gene, alleles and effective polymorphisms were distinguished and analysed in the cross progeny, which were segregated based on rooting. The results revealed a possible correlation between two single nucleotide polymorphisms of OeAOX2 gene and rooting ability.

[Analysis of transcriptional regulatory sites in introns of human and mouse ribosomal protein genes]

Previous studies from oligonucleotides in the ribosomal protein (RP) genes of the yeast and fruitfly indicated that the potential transcriptional regulatory sites are located in the introns of the genes. The transcriptional regulatory sites in introns are still poorly understood. To explore the functional significance of transcriptional regulation of introns, we extracted over-represented oligonucleotides (also known as motifs) in the first introns of the human and mouse ribosomal protein genes by statistical comparative analysis, and found that over 85% of these oligonucleotides were consistent with the known transcriptional factor binding sites, which might be potential transcriptional regulatory elements. By analyzing the base compositions of these elements, we found that a majority (>95%) of the detected motifs were rich in C and G and only a few of them were rich in A and T. Moreover, the oligonucleotides were close to the 5'-ends of the first introns (the distances between the motifs and the transcriptional start sites or upstream regions of genes are short). We speculated that the properties of over-represented motifs in the first introns might be associated with the transcriptional control.

Analysis of intron sequence features associated with transcriptional regulation in human genes

Although some preliminary work has revealed the potential transcriptional regulatory function of the introns in eukaryotes, additional evidences are needed to support this conjecture. In this study, we perform systemic analyses of the sequence characteristics of human introns. The results show that the first introns are generally longer and C, G and their dinucleotide compositions are over-represented relative to other introns, which are consistent with the previous findings. In addition, some new phenomena concerned with transcriptional regulation are found: i) the first introns are enriched in CpG islands; and ii) the percentages of the first introns containing TATA, CAAT and GC boxes are relatively higher than other position introns. The similar features of introns are observed in tissue-specific genes. The results further support that the first introns of human genes are likely to be involved in transcriptional regulation, and give an insight into the transcriptional regulatory regions of genes.

Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they pertain

This report deals with the study of compositional properties of human gene sequences evaluating similarities and differences among functionally distinct sectors of the gene independently of the reading frame. To retrieve the compositional information of DNA, we present a neighbor base dependent coding system in which the alphabet of 64 letters (DNA triplets) is compressed to an alphabet of 14 letters here termed triplet composons. The triplets containing the same set of distinct bases in whatever order and number form a triplet composon. The reading of the DNA sequence is performed starting at any letter of the initial triplet and then moving, triplet-to-triplet, until the end of the sequence. The readings were made in an overlapping way along the length of the sequences. The analysis of the compositional content in terms of the composon usage frequencies of the gene sequences shows that: (i) the compositional content of the sequences is far from that of random sequences, even in the case of non-protein coding sequences; (ii) coding sequences can be classified as components of compositional clusters; and (iii) intron sequences in a cluster have the same composon usage frequencies, even as their base composition differs notably from that of their home coding sequences. A comparison of the composon usage frequencies between human and mouse homologous genes indicated that two clusters found in humans do not have their counterpart in mouse whereas the others clusters are stable in both species with respect to their composon usage frequencies in both coding and noncoding sequences.

Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast

Transcriptional regulation in eukaryotic genes generally requires combinatorial binding on DNA of multiple transcription factors. Though many analyses have been performed for identification of combinatorial patterns in promoter sequences, there are few studies concerned with introns of genes. Here our study focuses on the transcriptional synergistic (cooperative) regulation between upstream promoters and introns of ribosomal protein (RP) genes in Saccharomyces cerevisiae yeast. We first extract some potential transcriptional regulatory motifs based on a statistical comparative analysis. 98% of these motifs are accordance with experimental analyses. Then by pairing these motifs each other, we identify some potential synergistic motif pairs between upstream regions and introns of yeast RP genes (RPGs). Among 48 detected motif pairs, 44 match the binding sites for interacting transcriptional factors known from experiments or predictions. Checking the positions of these motif pairs in yeast RPGs, it is found that both motifs of the detected motif pairs are enriched in specific regions of upstream regions and introns, respectively. Some motif pairs present distance and orientation preferences, which may be favorable for transcription factors to bind simultaneously to DNA. These results will be helpful to understand the mechanism of synergistic regulation in yeast RPGs.

Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

BACKGROUND

Regulation of gene expression in Plasmodium falciparum (Pf) remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found.

RESULTS

The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs -- the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs -- were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS); this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action.

CONCLUSION

The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast

Background

More than two thirds of the highly expressed ribosomal protein (RP) genes in Saccharomyces cerevisiae contain introns, which is in sharp contrast to the genome-wide five percent intron-containing genes. It is well established that introns carry regulatory sequences and that the transcription of RP genes is extensively and coordinately regulated. Here we test the hypotheses that introns are innately associated with heavily transcribed genes and that introns of RP genes contribute regulatory TF binding sequences. Moreover, we investigate whether promoter features are significantly different between intron-containing and intronless RP genes.

Results

We find that directly measured transcription rates tend to be lower for intron-containing compared to intronless RP genes. We do not observe any specifically enriched sequence motifs in the introns of RP genes other than those of the branch point and the two splice sites. Comparing the promoters of intron-containing and intronless RP genes, we detect differences in number and position of Rap1-binding and IFHL motifs. Moreover, the analysis of the length distribution and the folding free energies suggest that, at least in a sub-population of RP genes, the 5' untranslated sequences are optimized for regulatory function.

Conclusion

Our results argue against the direct involvement of introns in the regulation of transcription of highly expressed genes. Moreover, systematic differences in motif distributions suggest that RP transcription factors may act differently on intron-containing and intronless gene promoters. Thus, our findings contribute to the decoding of the RP promoter architecture and may fuel the discussion on the evolution of introns.