Modular transposition and the dynamical structure of eukaryote regulatory evolution

Cc, King

doi:10.1007/bf00133716

Cited by 11 publications

(9 citation statements)

References 83 publications

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“…The small degree of divergence of this particular Ala sequence from the modem consensus suggests that insertion was probably relatively recent (in the last 10-40 million years), and the selected changes at the binding sites probably occurred later. The putative role of Alu sequences is consistent with the proposal that repeated sequences could be a source of variation by moving into positions of significance to gene regulation (35)(36)(37)(38)(39)(40), and there have been recent theoretical discussions of the possible role of Alu sequences (41)(42)(43)(44)(45)(46)(47)(48)(49)(50) …”

Section: Lack Of Lineages Of Au Insertssupporting

confidence: 76%

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes.

Britten

1994

Proc. Natl. Acad. Sci. U.S.A.

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Mutations have been examined in the 1500 interspersed Alk repeats of human DNA that have been sequenced and are nearly full length. There is a set of particular changes at certain pt that rarely occur (termed suppressd changes) compared to the average of (2) that give rise to the sequences and mutation of the inserts in situ after insertion. The special features of the source genes that cause insertion of hundreds of thousands of copies are not known, but the source genes must be transcribed, and the mechanism of insertion is probably retroposition (3). The evolutionary changes in the source genes can be identified because large families of Alu repeats share diagnostic nucleotides at certain positions (2, 4). The relationships of the families of Alu sequences have been reexamined (5), including those judged to be recently inserted (6-9). It appears that several source genes are active at present or have been in the recent past, giving rise to several types of inserted Alu repeats matching each of the sources in sequence (7,9,10).A central aspect of the Alu sequences is that almost all of the source gene sequence has been conserved through the history of the Alu sequences. The diagnostic positions are exceptions, since the nucleotides at these positions changed at some time in the past, giving rise to variant source genes. Some of the variants became predominant new sources of inserted copies, the changed nucleotides were maintained for extended periods of time, and the many copies formed recognizable families of Alu sequences. It is significant that the fully conserved positions of the source genes include most of the CpGs, even though these have changed rapidly after the copies were inserted. As a result of the conservation, there is a large group of positions for which we almost certainly know what the nucleotide was at the time of insertion. The existence of such positions has been previously shown (2), and the principal set of them (not including the CpGs, the diagnostic positions, and a few other positions) is examined in this work. Evidence is presented for their conservation. The 195 chosen positions are termed the CONSBI (conserved before insertion) positions and are shown as uppercase letters in Fig. 1. Systematic and S aic Chang Identfed by C ring Two Randoml Chosen Sets of Ala SequencesIt is possible to recognize systematic processes as opposed to stochastic events that affect the nucleotides at specific positions by examining the relationship of mutations between subsets of the known sequences. A set of nearly full-length Ala sequences was divided into two equal randomly chosen sets (789 each), and all of the members of each set were compared with the consensus of recently inserted copies (Fig. 1). The divergences at each position were summed, and Fig. 2 is a graph of the fractional divergence of each position in one set plotted against the fractional divergence of the same position in the other set. The correlation of the points along the diagonal is expected, as many of these are diagnos...

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Section: Lack Of Lineages Of Au Insertssupporting

confidence: 76%

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes.

Britten

1994

Proc. Natl. Acad. Sci. U.S.A.

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“…(Haynes et al 1981;Kido et al 1991;Nisson et al 1988;Xiong and Eickbush 1988), suggesting that these elements may represent the progeny of an evolutionarily conserved process with important-yet-unknown functions. The impact of retroposition on the evolution and speciation of various eucaryotes has been lately the subject of much speculation (Kido et al 1991;Brosius 1991;Fontdevila 1992;King 1992;Shapiro 1992;Strenberg et al 1992). One emerging conclusion from these analyses is that an important proportion of the genetic changes could be viewed as the rearrangement of basic genetic motifs and that these rearrangements could precipitate species discontinuities.…”

Section: Introductionmentioning

confidence: 99%

An analysis of retroposition in plants based on a family of SINEs from Brassica napus

et al. 1994

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The identification of a family of SINE retroposons dispersed in the genome of oilseed rape Brassica napus has provided the basis for an evolutionary analysis of retroposition in plants. The repetitive elements (called S1Bn) are 170 bp long and occupy roughly 500 loci by haploid genome. They present characteristic features of SINE retroposons such as a 3' terminal A-rich region, two conserved polymerase III motifs (box A and B), flanking direct repeats of variable sizes, and a primary and secondary sequence homology to several tRNA species. A consensus sequence was made from the alignment of 34 members of the family. The retroposon population was divided into five subfamilies based on several correlated sets of mutations from the consensus. These precise separations in subfamilies based on "diagnostic" mutations and the random distribution of mutations observed inside each subfamily are consistent with the master sequence model proposed for the dispersion of mammalian retroposons. An independent analysis of each subfamily provides strong evidence for the coexpression of at least three subfamily master sequences (SMS). In contrast to mammalian retroposition, diagnostic positions are not shared between SMS. We therefore propose that SMS were all derived from a general master sequence (GMS) and independently activated for retroposition after a variable period of random drift. Possible models for plant retroposition are discussed.

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“…Many biologists speculate that processes in the world of transposons, existing on a substratum of genomes of the greater biological community, are the main source of evolutionary creativity [10, 26, 56, 57]. …”

Section: Introductionmentioning

confidence: 99%

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem

Zamdborg

Holloway

Merelo

et al. 2015

Information Sciences

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Modern evolutionary computation utilizes heuristic optimizations based upon concepts borrowed from the Darwinian theory of natural selection. Their demonstrated efficacy has reawakened an interest in other aspects of contemporary biology as an inspiration for new algorithms. However, amongst the many excellent candidates for study, contemporary models of biological macroevolution attract special attention. We believe that a vital direction in this field must be algorithms that model the activity of “genomic parasites”, such as transposons, in biological evolution. Many evolutionary biologists posit that it is the co-evolution of populations with their genomic parasites that permits the high efficiency of evolutionary searches found in the living world. This publication is our first step in the direction of developing a minimal assortment of algorithms that simulate the role of genomic parasites. Specifically, we started in the domain of genetic algorithms (GA) and selected the Artificial Ant Problem as a test case. This navigation problem is widely known as a classical benchmark test and possesses a large body of literature. We add new objects to the standard toolkit of GA - artificial transposons and a collection of operators that operate on them. We define these artificial transposons as a fragment of an ant's code with properties that cause it to stand apart from the rest. The minimal set of operators for transposons is a transposon mutation operator, and a transposon reproduction operator that causes a transposon to multiply within the population of hosts. An analysis of the population dynamics of transposons within the course of ant evolution showed that transposons are involved in the processes of propagation and selection of blocks of ant navigation programs. During this time, the speed of evolutionary search increases significantly. We concluded that artificial transposons, analogous to real transposons, are truly capable of acting as intelligent mutators that adapt in response to an evolutionary problem in the course of co-evolution with their hosts.

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Modular transposition and the dynamical structure of eukaryote regulatory evolution

Cited by 11 publications

References 83 publications

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes.

Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes.

An analysis of retroposition in plants based on a family of SINEs from Brassica napus

Forced evolution in silico by artificial transposons and their genetic operators: The ant navigation problem

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