In polymorphic genomic regions indels cluster with nucleotide polymorphism: Quantum Genomics

Longman-Jacobsen, Natalie; Williamson, J.; Dawkins, Roger L.; Gaudieri, Silvana

doi:10.1016/s0378-1119(03)00621-8

Cited by 31 publications

(31 citation statements)

References 18 publications

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“…Variability is observed in terms of the alleles and single nucleotide polymorphisms (SNPs), insertions and deletions (indels) and other duplications, such as copy number variations (CNVs) they contain [5,24,25]. These PFB sequences also reveal an apparent paradox.…”

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

“…There is also an apparent contradiction because the "SNP profile in MHC reveals extreme and interrupted levels of nucleotide diversity..between haplotypes" ( [24,25]. How could this arise if SNPs are suppressed?…”

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

“…How could this arise if SNPs are suppressed? A simple interpretation would consist of step-wise natural selection of point mutations in individual genes over aeons of evolutionary time versus some type of "big bang" mutational event, over the marked haplotypic region followed by bottle-neck selection, as discussed earlier [5,25]. The former would seem too slow given the known slow rate of mutational change estimated using "molecular clock" techniques.…”

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

“…To be consistent in terminology we call this the 'mutational spray' model* followed by population reduction, and thus bottle-neck selection, as the most likely genesis of a new PFB [5,25]. We do not restrict this explanation to blocks within the MHC but assume that may apply in other non-MHC regions of the genome (apart from some highly conserved polymorphic stretches spanning centromeres, which appear to be under a different form of structure-based selection pressure).…”

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

“…Can a plausible molecular mechanism based on supporting evidence from a number of fields of molecular and cell biology be advanced to explain the emergence of PFBs and thus AHs both within and beyond the MHC? (*Note on terminology : Terms such as "mutational/SNP cluster", "mutational/SNP burst" , "big bang burst model" , " quantal burst model", and "mutational/SNP shower" have all been used in the recent literature to describe these clustered mutation phenomena [5,24,25,[30][31][32][33][34]. To simplify the terminology we use the terms "mutational spray " or "SNP spray" to describe the same apparent phenomena.…”

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

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Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

et al. 2011

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how mutations in newly synthesized RNA might be copied back to DNA thus accounting for some of the genome-wide strand biases (e.g. the A-to-G vs T-to-C component of the strand biased spectrum). We hypothesize that the genesis of PFBs and extended AHs occurs during mutagenic episodes in evolution (e.g. retroviral infections) and that many of the critical DNA sequence diversifying events occur first at the RNA level e.g. recombination between RNA strings resulting in tandem and dispersed RNA duplications (retroduplications), RNA mutations via adenosine-to-inosine pre-mRNA editing events as well as error prone RNA synthesis. These are then copied back into DNA by a cellular reverse transcription (RT) process (also likely to be error-prone) we have called "RTmediated long DNA conversion" (RT-LDC). Finally we suggest that all these activities and others can be envisaged as being brought physically under the umbrella of special sites in the nucleus involved in transcription known as "Transcription Factories" (TF).

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Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

Section: Paradox Of the Genesis Of Pfbs And Ahsmentioning

confidence: 99%

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Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

et al. 2011

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On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

et al. 2011

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Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher-order features of the genomic architecture. The human genome is now recognized to contain ‘pervasive architectural flaws’ in that certain DNA sequences are inherently mutation-prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of non-canonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair, and may serve to increase mutation frequencies in generalized fashion (i.e. both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.

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Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species

Glémin

François

Galtier

2019

Methods in Molecular Biology

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A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.

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In polymorphic genomic regions indels cluster with nucleotide polymorphism: Quantum Genomics

Cited by 31 publications

References 18 publications

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

Genesis of ancestral haplotypes: RNA modifications and reverse transcription–mediated polymorphisms

On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species

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