Splicing of the triplet periodicity in genes from different species

2011 ◽  
Author(s):  
Yulia M. Suvorova ◽  
Eugene V. Korotkov
Keyword(s):  
Triplet Periodicity

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

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Bo Chen ◽  
Ping Ji
Keyword(s):  
Random Walk ◽  
Complex Plane ◽  
Query Sequence ◽  
Nucleotide Sequences ◽  
Sequence Pattern ◽  
Coding Regions ◽  
Persistent Pattern ◽  
Triplet Periodicity ◽  
Self Adaptive

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.

Structural-Statistical Properties of DNA Coding Regions

2015 ◽  
Vol 10 (2) ◽  
pp. 387-397 ◽  
Author(s):  
В.А. Кутыркин ◽  
V.A. Kutyrkin
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Statistical Approach ◽  
Statistical Properties ◽  
Statistical Characteristics ◽  
Dna Coding ◽  
Coding Regions ◽  
Unknown Type ◽  
Triplet Periodicity ◽  
Special Meaning

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.

scholarly journals An Approach for Searching Insertions in Bacterial Genes Leading to the Phase Shift of Triplet Periodicity

2011 ◽  
Vol 9 (4-5) ◽  
pp. 158-170 ◽  
Author(s):  
Maria A. Korotkova ◽  
Nikolay A. Kudryashov ◽  
Eugene V. Korotkov
Keyword(s):  
Phase Shift ◽  
Bacterial Genes ◽  
Triplet Periodicity

scholarly journals RPS15 mutations Repress mRNA Translation in Chronic Lymphocytic Leukemia Cells

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 1843-1843
Author(s):  
Stavroula Ntoufa ◽  
Stamatia Laidou ◽  
Fotis Psomopoulos ◽  
Marina Gerousi ◽  
Larry Mansouri ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Cell Line ◽  
Cell Lines ◽  
Research Funding ◽  
Mrna Translation ◽  
Ribosome Profiling ◽  
Lymphocytic Leukemia ◽  
Mrna Levels ◽  
Transcription Level ◽  
Triplet Periodicity

Abstract 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.

Further Observations on Periodicities of Nucleotide Occurrences in Natural DNA's

1985 ◽  
Vol 40 (11-12) ◽  
pp. 854-857
Author(s):  
N. Burr Furlong ◽  
Koenraad Marien
Keyword(s):  
Dna Sequences ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Periodic Characteristic ◽  
Entire Sequence ◽  
The Difference ◽  
The Relationship ◽  
Triplet Periodicity ◽  
Information Values ◽  
Specific Nucleotide

Abstract There are non-random features in the occurrences of nucleotides in the DNA’s of certain organisms which are detectable by statistical analyses of the entire sequence. Earlier, using the bacteriophage Phi-X 174 DNA sequence, we had reported that the self-information values for one type of dinucleotide association showed a marked periodicity when their autocorrelation coefficients were graphed. A similar, but computationally simpler, analysis has been developed which gives a comparable indication of periodicity. The difference, in average autocorrelation coefficients obtained with this analysis, between the peak values and all others has been used as an index to compare the extent of periodic non-randomness for a series of natural DNA sequences and for various artificial sequences. Calculations show that triplet periodicity, the relationship between dinucleotides separated by a single nucleotide, is characteristic only of the natural sequences of certain filamentous phages and is not found prominently in any other DNA analyzed (including sequences of similar length from plasmids, yeast, bacteria and higher animals). By shuffling nucleotides in a given sequence or by substituting selected nucleotides to alter various positions in both periodic and aperiodic sequences, we have found that an excess or deficiency of a given nucleotide at one of the three positions in a triplet reading frame can simulate the periodic characteristic. Thus, it appears that this global statistical analysis detects the tendency for single­ strand phages to utilize a specific nucleotide, rather than one randomly selected, to constitute codons.

Detection change points of triplet periodicity of gene

Gene ◽  
2012 ◽  
Vol 491 (1) ◽  
pp. 58-64 ◽  
Author(s):  
Yulia M. Suvorova ◽  
Valentina M. Rudenko ◽  
Eugene V. Korotkov
Keyword(s):  
Change Points ◽  
Triplet Periodicity
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