期刊名称：International Journal of Hybrid Information Technology
印刷版ISSN：1738-9968
出版年度：2013
卷号：6
期号：2
出版社：SERSC
摘要：Alternative splicing (AS) and Gene duplication are two well known evolutionary and ubiquitous mechanisms. Both have the common gist for conveying the functional diversity by means of escalating gene variegation. The objective of this study is to understand the established hidden relationship between both of these mechanisms to find the answer for the long standing puzzle circumventing the evolution of genome size while utilizing the computational power. We investigated that the alternative splicing can promise to unveil the nature as well as operation of cellular codes meticulously which play inevitable role of combinations of regulatory elements in pre-mRNA. This study also describe in detail of the cellular complements of splicing regulators, which collectively establish regulated splicing pathways. We have proposed a computational framework based on subset theory to address a part of the inexplicable functional diversity paradox which is also known as c-value enigma. The operational detail of this framework has been discussed to give an insight into the possible solution towards the problem of more proteins than their corresponding genetic material.
关键词：Alternative splicing; C-value enigma; Functional diversity paradox; Regulatory ;mechanism; Intron; Exon; Subset theory problem ;1.;Introduction ;Machine C-value may be defined as the amount of DNA in a haploid nucleus or one half ;the amounts in a diploid cell of a eukaryotic organism. Alternatively the concept of C-value ;may be used interchangeably to genome size. C-value is described in weight (picograms) or ;counting of base pairs (bp). A single sperm of Drosophila melanogaster for example contains ;1.64x10;8 ;nucleotide pairs or 0.18 picogram (pg) of DNA where C-value in pg is computed by ;assuming 9.13 X 10;8;nucleotide pairs per picogram [1]. The C-value enigma or C-value ;paradox is a term used to describe the complex puzzle encompassing the widespread ;variation in nuclear genome size among eukaryotic species. The C-value enigma undoubtedly ;goes beyond taxonomic boundaries leading towards a heightened demand to study the ;genome size evolution; whether in animals; plants or other organisms.;The core idea ;underlying the C-value paradox is spurred by the fact that no serious and straight forward ;correlation found between morphological or organismal complexity and genome size. This ;reality can be highlighted by the fact that some single-celled protists have been observed with ;genomes much larger as compared to humans though human's genome is far much complex. ; var currentpos;timer; function initialize() { timer=setInterval("scrollwindow()";10);} function sc(){clearInterval(timer); }function scrollwindow() { currentpos=document.body.scrollTop; window.scroll(0;++currentpos); if (currentpos != document.body.scrollTop) sc();} document.onmousedown=scdocument.ondblclick=initializeInternational Journal of Hybrid Information Technology ;Vol. 6; No. 2; March; 2013 ;108 ;Such observation may negate the popular evolutionary theory. Briefly but important and ;independent component question of the C-value enigma can be summarized as: ;What types of non-coding DNA are found in different eukaryotic genomes; and in what ;proportions. ;Gregory [2] illustrated some interesting statistical values related to C-value enigma for ;haploid nuclear DNA over the data summarized. The graph is plotted between C-value in ;picogram versus various species. Vertical line in each bar is portraying the average of C-value. ;The graph is depicting that most C-value in animals as well as in plants are small with a few ;exceptions of some groups. Gregory [2] showed in this graph that there is no correlation or ;connection ever observed so far between the complexity of different species and their related ;genome size. Gregory in quest of investigation for C-value paradox reported that variation in ;genome size is principally due to direct selection on the amount of bulk DNA through its ;underlying effects on cell volume and organismal cellular characteristics [2; 3; 4]. ;Second part of this puzzle narrates that "From where does this non-coding DNA come; and ;how is it spread and/or lost from genomes over time." ;C-value puzzle has been a renowned problem in the field of molecular biology. It can be ;concluded that species related specific characteristics emerged as a surprise to the early ;researchers where several orders of magnitude of genome materials was revealed among ;various eukaryotes. It was stated that "the lowly liverwort has 18 times as much DNA as we; ;and the slimy; dull salamander known as Amphiuma has 26 times our complement of DNA" ;[5]. ;Third part of the puzzle describes: "What effects; or perhaps even functions; does this non-;coding DNA have for chromosomes; nuclei; cells; and organisms." ;A possible answer to solve this puzzle leads to develop two broad kinds of theories. These ;include mutation pressure and optimal DNA theory. In mutation pressure theory; major ;portion of non-coding DNA in eukaryotic genomes is considered as junk or selfish DNA. The ;role of non coding DNA is limited to only evolution of secondary DNA through ;transcriptional and translational regulation of protein-coding sequences. On the other hand ;optimal DNA theory is focused on highlighting the strong connection between DNA content; ;cell and nuclear volumes. Most of the available evidences go in favor of later theory. Gregory ;(2001) developed a model of nucleotypic influence which falls under the category of optimal ;DNA theory. They by means of the result obtained from this model; concluded that large ;amounts of DNA exhibit large and slowly dividing cells. ;Fourth part of the C-value enigma argues: "Why do some species exhibit remarkably ;streamlined chromosomes; while others possess massive amounts of non-coding DNA." ;Analysis of genome size is directly related to the understanding of the functions of genetic ;material. Such analysis leads to the scrutinization of mRNA diversity which acts as a ;signature of genome functionality. The foundation of novel genes and its associated new ;functionalities is an important step towards evolution of organisms [6]. It was reported that ;more than seventy percent of whole human genetic material can generate multiple transcripts ;via alternative splicing [7; 8]. Exon shuffling; gene duplication; lateral gene transfer; retro ;position; de novo origination and gene fission/fusion are considered essential means in novel ;genes generation [8; 9; 10]. Alternative splicing can be considered as an essential step ;towards proteome diversity and transcriptome. This makes alternative splicing an exciting and ;appealing area of interest during the evolutionary course. Although new genes typically
