Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Albrecht‐Buehler, Guenter

doi:10.1073/pnas.0605553103

Cited by 101 publications

(108 citation statements)

References 27 publications

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“…According to Chargaff's second parity rule (PR2), the frequency of a mononucleotide or oligonucleotide should be (statistically) equal to that of its reverse complement on the same strand of a long genomic DNA (15,16). PR2 has been validated in many organisms, from bacteria to mammals, and presumably ref lects symmetric DNA mutations and repair (16).…”

mentioning

confidence: 99%

RNA landscape of evolution for optimal exon and intron discrimination

Zhang

Li²,

Krainer³

et al. 2008

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

104

109

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Accurate pre-mRNA splicing requires primary splicing signals, including the splice sites, a polypyrimidine tract, and a branch site, other splicing-regulatory elements (SREs). The SREs include exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs), which are typically located near the splice sites. However, it is unclear to what extent splicing-driven selective pressure constrains exonic and intronic sequences, especially those distant from the splice sites. Here, we studied the distribution of SREs in human genes in terms of DNA strand-asymmetry patterns. Under a neutral evolution model, each mononucleotide or oligonucleotide should have a symmetric (Chargaff's second parity rule), or weakly asymmetric yet uniform, distribution throughout a pre-mRNA transcript. However, we found that large sets of unbiased, experimentally determined SREs show a distinct strand-asymmetry pattern that is inconsistent with the neutral evolution model, and reflects their functional roles in splicing. ESEs are selected in exons and depleted in introns and vice versa for ESSs. Surprisingly, this trend extends into deep intronic sequences, accounting for one third of the genome. Selection is detectable even at the mononucleotide level, so that the asymmetric base compositions of exons and introns are predictive of ESEs and ESSs. We developed a method that effectively predicts SREs based on strand asymmetry, expanding the current catalog of SREs. Our results suggest that human genes have been optimized for exon and intron discrimination through an RNA landscape shaped during evolution.DNA strand asymmetry ͉ exon and intron recognition ͉ exon identity elements ͉ intron identity elements ͉ splicing-regulatory elements M ost mammalian genes are split, with exons (Ϸ150 nt) separated by much longer introns (Ϸ3,000 nt). To produce a mature transcript from a prem-RNA, introns are spliced out, and exons are ligated by a large protein/snRNA complex, the spliceosome. Extensive efforts have been made to elucidate the splicing code, i.e., the combinations of cis-regulatory elements and trans-acting factors responsible for splicing efficiency and fidelity. Besides the degenerate splice-site motifs, which are necessary but not sufficient for specific exon and intron recognition, other sequence elements are required for both constitutive and alternative splicing (1, 2). Many splicing-regulatory elements (SREs) have been identified by experimental or computational approaches (3-10). Among them, two classes of well studied SREs are exonic splicing enhancers (ESEs) recognized by SR proteins, and exonic splicing silencers (ESSs) recognized by certain hnRNP proteins (1, 2). Adding further complexity, the effect of an SRE on splicing is often context-dependent. For example, an SR-protein-dependent ESE element, when present in an intron, can act as an intronic splicing silencer (ISS) to repress splicing (11), whereas a number of ESSs, such as the GGG motif, are also pote...

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mentioning

confidence: 99%

RNA landscape of evolution for optimal exon and intron discrimination

Zhang

Li²,

Krainer³

et al. 2008

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

104

109

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“…An interesting feature of the ND distance approach is the strong similarity found for the A/T and C/G nucleotides. This may be explained by the existence of inverted repeats and by the second Chargaff parity rule and its extensions (Qi and Cuticchia, 2001;Albrecht-Buehler, 2006, 2007.…”

Section: Resultsmentioning

confidence: 99%

Genome analysis with distance to the nearest dissimilar nucleotide

Afreixo

Bastos

Pinho

et al. 2011

Journal of Theoretical Biology

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DNA may be represented by sequences of four symbols, but it is often useful to convert those symbols into real or complex numbers for further analysis.Several mapping schemes have been used in the past, but most of them seem to be unrelated to any intrinsic characteristic of DNA. The objective of this work was to study a mapping scheme that is directly related to DNA characteristics, and that could be useful in discriminating between different species.Recently, we have proposed a methodology based on the inter-nucleotide distance, which proved to contribute to the discrimination among species. In this paper, we introduce a new distance, the distance to the nearest dissimilar nucleotide, which is the distance of a nucleotide to first occurrence of a different nucleotide. This distance is related to the repetition structure of single nucleotides. Using the information resulting from the concatenation of the distance to the nearest dissimilar and the inter-nucleotide distance, we found that this new distance brings additional discriminative capabilities. Preprint submitted to Journal of Theoretical BiologyJanuary 31, 2011 This suggests that the distance to the nearest dissimilar nucleotide might contribute with useful information about the evolution of the species.

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“…4). It has been proposed that inversions are a major factor that makes the whole strand of chromosome symmetric (Albrecht-Buehler, 2006;Okamura et al, 2007). Nevertheless, biological significance of the natural inversions in bacterial chromosomes is not clear.…”

Section: The Chromosomal Sequence Changes and Negative Consequencesmentioning

confidence: 99%

The Bacterial Chromosomal Sequence and Related Issues

Phan

Nguyễn

2013

American Journal of Virology

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There has been a rapid increasing in the number of bacterial genomes that are completely sequenced recently. However, nucleotide arrangement in bacterial chromosome is still not clear, though it is known that the chromosomal strand is symmetric as a whole but asymmetric locally. The unequal distribution of adenine and thymine as well as cytosine and guanine in the local genomic sequences has been suggested to be associated with transcription and replication. In the bacterial chromosome, distribution of nucleotides in the leading and lagging strands, which interact with the structurally asymmetric DNA polymerase during replication process, has also been reported to be biased. Recent studies on changing the nucleotide sequence of bacterial chromosomes have revealed the importance of nucleotide arrangement in chromosome, which exerts influences on success of the chromosome engineering experiments. This review highlights common properties of bacterial chromosomal sequences with related issues involved in the nucleotide arrangement in chromosome, emphasizing that arrangement of nucleotides in chromosome regarding local strand asymmetry and chromosomal strand symmetry needs to be made clear so as to help in experimental design for effectiveness in changing chromosomal sequences or creating artificial chromosomes.

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Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Cited by 101 publications

References 27 publications

RNA landscape of evolution for optimal exon and intron discrimination

RNA landscape of evolution for optimal exon and intron discrimination

Genome analysis with distance to the nearest dissimilar nucleotide

The Bacterial Chromosomal Sequence and Related Issues

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