Start/stop Codon-like Trinucleotides (CLTs) and Extended Clusters as New Language of DNA

Abstract

Abstract. DNA nucleotide sequences carry genetic information of different kinds, not just coding instructions for protein synthesis. They can play a role, for example, in alternative conformations and gene regulators. The present paper introduces the extended start/stop codon-like trinucleotides (CLTs) for noncoding DNA sequences, based on trinucleotide cluster extension generated by specific single-nucleotide multiplications. Extended cluster analysis gives rise to rich information potential as a "new language" of DNA ("CLT-language"). The analysis of start/stop-CLTs extended clusters provides qualitative and quantitative differentiation and characterization of alpha satellites, as well as of other repetitive and non-repetitive noncoding sequences. As a measure of CLT extension of DNA sequences the extension factor r is introduced. Start/stop CLTs enable a distinction of three segments within alpha satellite, the first and the second as wrapping sequences and the third as a linker. Within a linker there are no start/stop CLTs. On the basis of start/stop-CLTs, it is hypothesized that these noncoding sequences may be involved in the networks of gene regulators. (doi: 10.5562/cca1948)

Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification

“…If these trinucleotides have a signaling role in coding sequences, could they have a role of some regulators in noncoding regions? To our knowledge, not much attention was given to this question (Rosandić et al, 2011(Rosandić et al, , 2013.…”

Global Repeat Map Method for Higher Order Repeat Alpha Satellites in Human and Chimpanzee Genomes (Build 37.2 Assembly)

“…If the consensus HOR contains alpha monomers which are reverse complement to the convention of 61 (referred to as revers-complement (RC) monomers), then the array m01, m02, ... is reverse complement to consensus HOR; this is the case for 11mer in chromosome 1, 13mer in chromosome 4, 13mer in chromosome 5, 7mer in chromosome 9, 18mer in chromosome 10, 12mer in chromosome 11, 13mer in chromosome 19, 12mer in chromosome X and 45mer in chromosome Y. HOR consensus sequences are presented in Table 3 (chromosomes 2/10mer, 4/13mer, 9/11mer, and 9/7mer) and in Ref. 55 Only two chromosome (8 and Y) assemblies have arrays of highly homogenous higher-order alpha satellite DNA both on p and q arms (Figure 4). Because all chromosomes are known to contain higher-order alpha satellites at centromeres, 7,8 the fact that only the chromosomes 8 and Y have this level of success indicates that most current assemblies probably terminate at some distance from functional centromere.…”

“…As a measure of CLT-clustering of genomic sequences the corresponding extension factor r was introduced. 55 Recently, we have identified HORs in chromosome 5 of chimpanzee (5mer), orangutan (14mer), and macaque (two 3mers). N -unsequenced segment inside contig NW_003456961.1 * 171 bp segment with divergence of 53.5 % with respect to mc18 consensus sequence…”

“…In the next step, a new method of codon-like trinucleotides (CLTs) extensions 55 is applied to analyze the differences in structure of human and chimpanzee alpha satellite monomers in HORs in chromosome 4. Inspired by much interest in gene regulators, we analyzed trinucleotides corresponding to the start (ATG) and stop (TGA, TAA, TAG) CLTs in monomer sequences.…”

“…If we compare these results with base to base divergences, we can conclude that the main difference between human and chimpanzee alpha satellites lies in extensions of codonlike trinucleotides. Having in mind that small and seemingly insignificant differences in a nonlinear network of genes and regulators could produce significant functional differences, 55 we hypothesize that these start/stopCLTs differences could have been important factor in human evolution and separation of human from other primates.…”