A Spectral Rotation Method with Triplet Periodicity Property for Planted Motif Finding Problems

Background: Genes are known as functional patterns in the genome and are presumed to have biological significance. They can indicate binding sites for transcription factors and they encode certain proteins. Finding genes from biological sequences is a major task in computational biology for unraveling the mechanisms of gene expression. Objective: Planted motif finding problems are a class of mathematical models abstracted from the process of detecting genes from genome, in which a specific gene with a number of mutations is planted into a randomly generated background sequence, and then gene finding algorithms can be tested to check if the planted gene can be found in feasible time. Method: In this work, a spectral rotation method based on triplet periodicity property is proposed to solve planted motif finding problems. Results: The proposed method gives significant tolerance of base mutations in genes. Specifically, genes having a number of substitutions can be detected from randomly generated background sequences. Experimental results on genomic data set from Saccharomyces cerevisiae reveal that genes can be visually distinguished. It is proposed that genes with about 50% mutations can be detected from randomly generated background sequences. Conclusion: It is found that with about 5 insertions or deletions, this method fails in finding the planted genes. For a particular case, if the deletion of bases is located at the beginning of the gene, that is, bases are not randomly deleted, then the tolerance of the method for base deletion is increased.

RPS15 mutations Repress mRNA Translation in Chronic Lymphocytic Leukemia Cells

We and others recently reported mutations within the RPS15 gene, encoding a component of the 40S ribosomal subunit, in clinically aggressive chronic lymphocytic leukemia (CLL). RPS15 mutations resided within an evolutionary conserved region, alluding to an oncogenic rather than a tumor-suppressor role. Our pilot functional analysis revealed that, similar to other ribosomal proteins (RPs), RPS15 also binds MDM2 and may impact on the p53 response. Here, we performed ribosome profiling in order to gain global insight into changes in translation induced by RPS15 mutations in CLL cells. This technique involves measuring translational efficiency (TE), by comparing the levels of ribosome-associated mRNA footprints against the total mRNA for each gene. For 6 CLL cases bearing mutant (mut, n=3) or wildtype (wt, n=3) RPS15, we obtained both ribosome-protected footprints (RPFs) and matching mRNA sequencing data. In parallel, we created stable MEC1 CLL cell lines expressing an additional copy of wt or mut RPS15 (131S) by lentiviral transduction; validation of the transgene expression was performed by Sanger sequencing of amplified cDNAs. Ribosome footprinting and subsequent library preparation of RPFs and total mRNA for all samples was performed with the Illumina Truseq Ribo Profile Kit and all libraries were sequenced on a NextSeq500 instrument. Reads were aligned to the human hg19 genome using Bowtie2. SystemPipeR was used to determine the percentage of reads mapping to 5' UTRs, CDS, and 3' UTRs and triplet periodicity was assessed using RibORF. The RPFs were of high quality, as assessed by expected RPF size (28-30nt), CDS enrichment, and triplet periodicity. To determine differentially expressed genes between RPS15-mut vs RPS15-wt cases we used DESeq2 while, for differentially translated genes we used Xtail. Changes in transcription and translation between PRS15-wt vs RPS15-mut cases showed limited overlap in both primary CLL cells and cell lines (12.8% and 12.9%, respectively), indicating the potential of ribosome profiling to reveal additional information compared to RNA sequencing alone. In primary CLL cells, 474 genes showed differences only at the transcription level (log2FC mRNA>I1I, p<0.05), while 742 genes were modulated only at the translation level (log2FC RPF>I1I, p<0.05). We identified 322 genes with differential TE (log2FC TE<I1I, p<0.05) between PRS15-wt vs RPS15-mut CLL cases; 262/322 (81%) showed reduced TE in RPS15-mut versus RPS15-wt cases. Similar analysis for the stable MEC1 cell lines revealed 749 genes displaying differences only at the transcription level (log2FC mRNA>I1I), while 1859 genes were regulated only at the translation level (log2FC RPF>I1I). Overall, 771 genes displayed differential TE (log2FC TE<I1I, adjusted p<0.1) between PRS15-wt vs RPS15-mut MEC1 cell lines; 48% of the genes showed reduced TE in mut vs wt cell lines and the remaining 52% augmented TE. The slightly different results compared to those obtained from primary CLL cells, may be attributed to the following reasons: (i) MEC1 cells are TP53-aberrant; (ii) the PRS15-wt cell line overexpresses the RPS15 gene compared to primary CLL cells; and,( iii) the RPS15-mut cell line expresses both the wt and mut RPS15 mRNAs (22% of the mapped reads correspond to the mut RPS15 and 78% to the wt gene, respectively). Gene ontology analysis (Enrichr) of the genes showing differential TE, revealed that in both primary CLL cells and MEC1 cell lines a large fraction of the deregulated transcripts is implicated in RNA binding processes (adj-p=0.0001; adj-p=1.98X10^-13, respectively) which are known to induce translational repression. Interestingly, in primary CLL cells, amongst genes with reduced TE we identified genes implicated in tRNA biosynthesis, protein processing in the endoplasmatic reticulum and the Hippo signaling pathway (p<0.01). Additionally, enrichment analysis revealed that a proportion of genes with reduced TE were targets of the MYC transcription factor (adj-p=0.0005). RP genes, despite unchanged mRNA levels, showed changes in RPF levels and differential TE, suggesting that RPs are also deregulated at the translational level. In conclusion, we show that RPS15 mutations rewire the translation program of CLL cells by reducing the TE of critical molecules, including translation initiation factors and other regulatory elements. Disclosures Hadzidimitriou: Abbvie: Research Funding; Gilead: Research Funding; Janssen: Honoraria, Research Funding. Stamatopoulos:Janssen: Honoraria, Research Funding; Abbvie: Honoraria, Research Funding; Gilead: Honoraria, Research Funding.

Structural-Statistical Properties of DNA Coding Regions

Structural-statistical characteristics of the coding DNA sequences (CDSs) from human genome are investigated in the frame of spectral-statistical approach (the 2S-approach). Properties of 3-regularity and latent profile periodicity are among of such the characteristics. Special meaning and intrinsic existence of these properties are confirmed by researching the binary recoded CDSs. The only one kind of singular recoding, that identifies complementary nucleotides, serves to persistence of the original CDSs characteristics. Usage of nonsingular binary recoding proves a statement that latent triplet periodicity in the CDSs of human genome belongs to earlier unknown type called as profile periodicity.

Study of triplet periodicity differences inside and between genomes

Triplet periodicity (TP) is a distinctive feature of the protein coding sequences of both prokaryotic and eukaryotic genomes. In this work, we explored the TP difference inside and between 45 prokaryotic genomes. We constructed two hypotheses of TP distribution on a set of coding sequences and generated artificial datasets that correspond to the hypotheses. We found that TP is more similar inside a genome than between genomes and that TP distribution inside a real genome dataset corresponds to the hypothesis which implies that a common TP pattern exists for the majority of sequences inside a genome. Additionally, we performed gene classification based on TP matrixes. This classification showed that TP allows identification of the genome to which a given gene belongs with more than 85% accuracy.

An Exploration of the Triplet Periodicity in Nucleotide Sequences with a Mature Self-Adaptive Spectral Rotation Approach

Previously, for predicting coding regions in nucleotide sequences, a self-adaptive spectral rotation (SASR) method has been developed, based on a universal statistical feature of the coding regions, named triplet periodicity (TP). It outputs a random walk, that is, TP walk, in the complex plane for the query sequence. Each step in the walk is corresponding to a position in the sequence and generated from a long-term statistic of the TP in the sequence. The coding regions (TP intensive) are then visually discriminated from the noncoding ones (without TP), in the TP walk. In this paper, the behaviors of the walks for random nucleotide sequences are further investigated qualitatively. A slightly leftward trend (a negative noise) in such walks is observed, which is not reported in the previous SASR literatures. An improved SASR, named the mature SASR, is proposed, in order to eliminate the noise and correct the TP walks. Furthermore, a potential sequence pattern opposite to the TP persistent pattern, that is, the TP antipersistent pattern, is explored. The applications of the algorithms on simulated datasets show their capabilities in detecting such a potential sequence pattern.

Study of the triplet periodicity phase shifts in genes

The definition of a phase shift of triplet periodicity (TP) is introduced. The mathematical algorithm for detection of TP phase shift of nucleotide sequences has been developed. Gene sequences from Kegg-46 data bank were analyzed with a purpose of searching genes with a phase shift of TP. The presence of a phase shift of triplet periodicity has been shown for 318329 genes (~10% from the number of genes in Kegg-46). We suppose that shifts of the TP phase may indicate the shifts of reading frame (RF) in genes. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.