Triplet Frequencies Implementation in Total Transcriptome Analysis

We studied the structuredness in total transcriptome of Siberian larch. To do that, the contigs from total transcriptome has been labeled with the reads comprising the tissue specific transcriptomes, and the distribution of the contigs from the total transcriptome has been developed with respect to the mutual entropy of the frequencies of occurrence of reads from tissue specific transcriptomes. It was found that a number of contigs contain comparable amounts of reads from different tissues, so the chimeric transcripts to be extremely abundant. On the contrary, the transcripts with high tissue specificity do not yield a reliable clustering revealing the tissue specificity. This fact makes usage of total transcriptome for the purposes of differential expression arguable

PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE

Function vs. Taxonomy: The Case of Fungi Mitochondria ATP Synthase Genes

We studied the relations between triplet composition of the family of mitochondrial atp6, atp8 and atp9 genes, their function, and taxonomy of the bearers. The points in 64-dimensional metric space corresponding to genes have been clustered. It was found the points are separated into three clusters corresponding to those genes. 223 mitochondrial genomes have been enrolled into the database

The Evolution and Mechanics of Translational Control in Plants

The expression of numerous plant mRNAs is attenuated by RNA sequence elements located in the 5\u27 and 3\u27 untranslated regions (UTRs). For example, in plants and many higher eukaryotes, roughly 35% of genes encode mRNAs that contain one or more upstream open reading frames (uORFs) in the 5\u27 UTR. For this dissertation I have analyzed the pattern of conservation of such mRNA sequence elements. In the first set of studies, I have taken a comparative transcriptomics approach to address which RNA sequence elements are conserved between various families of angiosperm plants. Such conservation indicates an element\u27s fundamental importance to plant biology, points to pathways for which it is most vital, and suggests the mechanism by which it acts. Conserved motifs were detected in 3% of genes. These include di-purine repeat motifs, uORF-associated motifs, putative binding sites for PUMILIO-like RNA binding proteins, small RNA targets, and a wide range of other sequence motifs. Due to the scanning process that precedes translation initiation, uORFs are often translated, thereby repressing initiation at the an mRNA\u27s main ORF. As one might predict, I found a clear bias against the AUG start codon within the 5\u27 untranslated region (5\u27 UTR) among all plants examined. Further supporting this finding, comparative analysis indicates that, for ~42% of genes, AUGs and their resultant uORFs reduce carrier fitness. Interestingly, for at least 5% of genes, uORFs are not only tolerated, but enriched. The remaining uORFs appear to be neutral. Because of their tangible impact on plant biology, it is critical to differentiate how uORFs affect translation and how, in many cases, their inhibitory effects are neutralized. In pursuit of this aim, I developed a computational model of the initiation process that uses five parameters to account for uORF presence. In vivo translation efficiency data from uORF-containing reporter constructs were used to estimate the model\u27s parameters in wild type Arabidopsis. In addition, the model was applied to identify salient defects associated with a mutation in the subunit h of eukaryotic initiation factor 3 (eIF3h). The model indicates that eIF3h, by supporting re-initation during uORF elongation, facilitates uORF tolerance

Non-Coding Regions of Chloroplast Genomes Exhibit a Structuredness of Five Types

We studied the statistical properties of non-coding regions of chloroplast genomes of 391 plants. To do that, each non-coding region has been tiled with a set of overlapping fragments of the same length, and those fragments were transformed into triplet frequency dictionaries. The dictionaries were clustered in 64-dimensional Euclidean space. Five types of the distributions were identified: ball, ball with tail, ball with two tails, lens with tail, and lens with two tails. Besides, the multigenome distribution has been studied: there are ten species performing an isolated and distant cluster; surprisingly, there is no immediate and simple relation in taxonomy composition of these clusters

Discovery of EST-SSRs in Lung Cancer: Tagged ESTs with SSRs Lead to Differential Amino Acid and Protein Expression Patterns in Cancerous Tissues

Tandem repeats are found in both coding and non-coding sequences of higher organisms. These sequences can be used in cancer genetics and diagnosis to unravel the genetic basis of tumor formation and progression. In this study, a possible relationship between SSR distributions and lung cancer was studied by comparative analysis of EST-SSRs in normal and lung cancerous tissues. While the EST-SSR distribution was similar between tumorous tissues, this distribution was different between normal and tumorous tissues. Trinucleotides tandem repeats were highly different; the number of trinucleotides in ESTs of lung cancer was 3 times higher than normal tissue. Significant negative correlation between normal and cancerous tissue showed that cancerous tissue generates different types of trinucleotides. GGC and CGC were the more frequent expressed trinucleotides in cancerous tissue, but these SSRs were not expressed in normal tissue. Similar to the EST level, the expression pattern of EST-SSRs-derived amino acids was significantly different between normal and cancerous tissues. Arg, Pro, Ser, Gly, and Lys were the most abundant amino acids in cancerous tissues, and Leu, Cys, Phe, and His were significantly more abundant in normal tissues than in cancerous tissues. Next, the putative functions of triplet SSR-containing genes were analyzed. In cancerous tissue, EST-SSRs produce different types of proteins. Chromodomain helicase DNA binding proteins were one of the major protein products of EST-SSRs in the cancerous library, while these proteins were not produced from EST-SSRs in normal tissue. For the first time, the findings of this study confirmed that EST-SSRs in normal lung tissues are different than in unhealthy tissues, and tagged ESTs with SSRs cause remarkable differences in amino acid and protein expression patterns in cancerous tissue. We suggest that EST-SSRs and EST-SSRs differentially expressed in cancerous tissue may be suitable candidate markers for lung cancer diagnosis and prediction