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

Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation

Movement of chromosome sites within interphase cells is critical for numerous pathways including RNA transcription and genome organization. Yet, a mechanism for reorganizing chromatin in response to these events had not been reported. Here, we delineate a molecular chaperone-dependent pathway for relocating activated gene loci in yeast. Our presented data support a model in which a two-authentication system mobilizes a gene promoter through a dynamic network of polymeric nuclear actin. Transcription factor-dependent nucleation of a myosin motor propels the gene locus through the actin matrix, and fidelity of the actin association was ensured by ARP-containing chromatin remodelers. Motor activity of nuclear myosin was dependent on the Hsp90 chaperone. Hsp90 further contributed by biasing the remodeler-actin interaction toward nucleosomes with the non-canonical histone H2A.Z, thereby focusing the pathway on select sites such as transcriptionally active genes. Together, the system provides a rapid and effective means to broadly yet selectively mobilize chromatin sites.

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.