Increased complexity of gene structure and base composition in vertebrates

Wu, Ying; Yuan, Huizhong; Tan, Shan; Chen, Jian-Qun; Tian, Dacheng; Yang, Haiwang

doi:10.1016/j.jgg.2011.06.004

Cited by 4 publications

(2 citation statements)

References 46 publications

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“…The median fractions of SBSs that occurred at G•C bp were 0.78 (mean ± SD, 0.75±0.11) for the EWS datasets and 0.56 (mean ± SD, 0.60±0.13) for the GWS datasets (Fig. 1A), significantly higher than the average GC-content exome-wide (0.55) [38] and genome-wide (0.41), respectively [39] (both P values were ∼2.2×10 −16 , the smallest computable number by implementation of the binomial exact test in R). Thus, SBSs occurred more frequently at G•C bp, as compared to A•T bp, than expected by chance alone, both in cancer genomes and in the germline as a cause of inherited disease.…”

Section: Resultsmentioning

confidence: 90%

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

Bacolla

Temiz

et al. 2013

PLoS Genet

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Single base substitutions constitute the most frequent type of human gene mutation and are a leading cause of cancer and inherited disease. These alterations occur non-randomly in DNA, being strongly influenced by the local nucleotide sequence context. However, the molecular mechanisms underlying such sequence context-dependent mutagenesis are not fully understood. Using bioinformatics, computational and molecular modeling analyses, we have determined the frequencies of mutation at G•C bp in the context of all 64 5′-NGNN-3′ motifs that contain the mutation at the second position. Twenty-four datasets were employed, comprising >530,000 somatic single base substitutions from 21 cancer genomes, >77,000 germline single-base substitutions causing or associated with human inherited disease and 16.7 million benign germline single-nucleotide variants. In several cancer types, the number of mutated motifs correlated both with the free energies of base stacking and the energies required for abstracting an electron from the target guanines (ionization potentials). Similar correlations were also evident for the pathological missense and nonsense germline mutations, but only when the target guanines were located on the non-transcribed DNA strand. Likewise, pathogenic splicing mutations predominantly affected positions in which a purine was located on the non-transcribed DNA strand. Novel candidate driver mutations and tissue-specific mutational patterns were also identified in the cancer datasets. We conclude that electron transfer reactions within the DNA molecule contribute to sequence context-dependent mutagenesis, involving both somatic driver and passenger mutations in cancer, as well as germline alterations causing or associated with inherited disease.

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Section: Resultsmentioning

confidence: 90%

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

Bacolla

Temiz

et al. 2013

PLoS Genet

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“…We hypothesize an increase in exon number so the intron leads to the complexity of lncRNA genes, which could be a potential factor for structural and functional variations and an impetus factor in the evolution of structural complexity in lncRNA genes. This hypothesis is supported by a study in animals from different lineages, which showed that the number of exons per gene, including intron and 3'UTR region, progressively expanded from invertebrate ancestors to vertebrates during evolution 34 . Localization analysis revealed that lncRNAs are more abundant in the nucleus of A. thaliana and O. sativa, which is analogous to their abundance reported in Drosophila and humans 35,36 .…”

Section: Discussionmentioning

confidence: 81%

Deciphering shared attributes of plant long non-coding RNAs through a comparative computational approach

Yadav,

Jalmi,

Tiwari

et al. 2023

Sci Rep

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Over the past decade, long non-coding RNA (lncRNA), which lacks protein-coding potential, has emerged as an essential regulator of the genome. The present study examined 13,599 lncRNAs in Arabidopsis thaliana, 11,565 in Oryza sativa, and 32,397 in Zea mays for their characteristic features and explored the associated genomic and epigenomic features. We found lncRNAs were distributed throughout the chromosomes and the Helitron family of transposable elements (TEs) enriched, while the terminal inverted repeat depleted in lncRNA transcribing regions. Our analyses determined that lncRNA transcribing regions show rare or weak signals for most epigenetic marks except for H3K9me2 and cytosine methylation in all three plant species. LncRNAs showed preferential localization in the nucleus and cytoplasm; however, the distribution ratio in the cytoplasm and nucleus varies among the studied plant species. We identified several conserved endogenous target mimic sites in the lncRNAs among the studied plants. We found 233, 301, and 273 unique miRNAs, potentially targeting the lncRNAs of A. thaliana, O. sativa, and Z. mays, respectively. Our study has revealed that miRNAs, which interact with lncRNAs, target genes that are involved in a diverse array of biological and molecular processes. The miRNA-targeted lncRNAs displayed a strong affinity for several transcription factors, including ERF and BBR-BPC, mutually present in all three plants, advocating their conserved functions. Overall, the present study showed that plant lncRNAs exhibit conserved genomic and epigenomic characteristics and potentially govern the growth and development of plants.

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