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Pseudogene

About: Pseudogene is a research topic. Over the lifetime, 5528 publications have been published within this topic receiving 336634 citations. The topic is also known as: Ψ & pseudogenes.


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Journal ArticleDOI
TL;DR: The results suggest an underlying mechanism for higher mutation rate in GC-rich genomic regions, predict nonlinear accumulation of mutations in pseudogenes over time, and provide a possible explanation for the observed higher diversity of single nucleotide polymorphisms in the synonymous sites of exons compared to the noncoding regions.
Abstract: Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%-60% higher mutation rate in exons than in noncoding DNA. We propose a differential CpG content hypothesis to explain this fundamental, and seemingly unintuitive, pattern. We find that the increased exonic rate is the result of the relative overabundance of synonymous sites involved in CpG dinucleotides, as the evolutionary divergence in non-CpG sites is similar in noncoding DNA and synonymous sites of exons. Expectations and predictions of our hypothesis are confirmed in comparisons involving more distantly related species, including human-orangutan, human-baboon, and human-macaque. Our results suggest an underlying mechanism for higher mutation rate in GC-rich genomic regions, predict nonlinear accumulation of mutations in pseudogenes over time, and provide a possible explanation for the observed higher diversity of single nucleotide polymorphisms (SNPs) in the synonymous sites of exons compared to the noncoding regions.

122 citations

Journal Article
TL;DR: The characterization of eight HLA class I homologous sequences isolated from cosmid and lambda libraries made from lymphoblastiod cell line 721 DNA showed that some of these sequences are linked to one another and to other class I pseudogenes and genes within 50-kb regions, and Hypothetical events in the evolution of the class I region are discussed.
Abstract: We report the characterization of eight HLA class I homologous sequences isolated from cosmid and lambda libraries made from lymphoblastiod cell line 721 DNA. Four of these sequences, each contained within HindIII fragments of 1.7, 2.1, 3.0, and 8.0 kb, have class I homology extending over short intronexon regions. The remaining four are found within 7.5-, 8.0-, 9.0-, and 16.0-kb HindIII fragments, the first having homology to the 5' half of a class I gene whereas the latter three are homologous to the 3' portion of a class I gene. When combined with the characterization of other class I clones, this work brings the total number of HLA class I homologous sequences cloned and characterized to 18. Restriction mapping of cosmid clones showed that some of these sequences are linked to one another and to other class I pseudogenes and genes within 50-kb regions. Reconstruction experiments using the 18 class I genes and pseudogenes were performed that indicated that we had cloned all of the members of the HLA class I gene family detectable using HLA-A2 genomic DNA as probe. An additional 19th member of the class I gene family was identified using an HLA-E cDNA probe. Further Southern analysis with other class I probes indicated the 19 sequences comprise the entire class I gene family in LCL 721. Locus-specific probes were isolated from five of the eight clones and were used in Southern analysis of diverse genomic DNA to examine the polymorphism of the pseudogene sequences, demonstrating that some of them were highly polymorphic and some were missing entirely in certain haplotypes. An additional class I sequence, not contained within the 721 genome, was identified and may be found in association with the HLA-A11-Bw60 haplotype. Sequence comparisons were carried out to examine the evolutionary relationships among the pseudogenes. Hypothetical events in the evolution of the class I region are discussed.

122 citations

Journal ArticleDOI
TL;DR: This analysis sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence and revealed the architectural complexities and dynamic evolution of this region over the past ∼15 million years.
Abstract: Oryza (23 species; 10 genome types) contains the world's most important food crop - rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past ∼15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.

122 citations

Journal ArticleDOI
TL;DR: The authors' pairwise comparisons between numts suggest that most human numts arose from different mitochondrial insertion events and not by DNA duplication within the nuclear genome, which is close to the rate reported for functional genes in other species.
Abstract: The hundreds of mitochondrial pseudogenes in the human nuclear genome sequence (numts) constitute an excellent system for studying and dating DNA duplications and insertions. These pseudogenes are associated with many complete mitochondrial genome sequences and through those with a good fossil record. By comparing individual numts with primate and other mammalian mitochondrial genome sequences, we estimate that these numts arose continuously over the last 58 million years. Our pairwise comparisons between numts suggest that most human numts arose from different mitochondrial insertion events and not by DNA duplication within the nuclear genome. The nuclear genome appears to accumulate mtDNA insertions at a rate high enough to predict within-population polymorphism for the presence/absence of many recent mtDNA insertions. Pairwise analysis of numts and their flanking DNA produces an estimate for the DNA duplication rate in humans of 2.2 × 10−9 per numt per year. Thus, a nucleotide site is about as likely to be involved in a duplication event as it is to change by point substitution. This estimate of the rate of DNA duplication of noncoding DNA is based on sequences that are not in duplication hotspots, and is close to the rate reported for functional genes in other species.

121 citations

Journal ArticleDOI
TL;DR: This mutation was carried by 3 of 20 unrelated patients with 21-hydroxylase deficiency alleles as determined by hybridization with a specific oligonucleotide probe, so that its presence in the abnormal CYP21B gene may be the result of a gene conversion event.
Abstract: We determined the sequence of a mutant CYP21B gene isolated from a patient with the severe, "salt-wasting" form of congenital adrenal hyperplasia due to steroid 21-hydroxylase deficiency. Codon 318 in this gene is changed from CAG, encoding glutamine, to TAG, a nonsense codon. This is predicted to result in a completely nonfunctional enzyme due to premature termination of translation. In addition, when the cloned mutant gene was transfected into mouse Y1 adrenal cells, the resulting mRNA levels were decreased compared with transfected normal CYP21B genes. This mutation was carried by 3 of 20 unrelated patients with 21-hydroxylase deficiency alleles as determined by hybridization with a specific oligonucleotide probe. This mutation is also seen in the normal CYP21A pseudogene, so that its presence in the abnormal CYP21B gene may be the result of a gene conversion event.

121 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023120
2022250
2021123
2020160
2019119
2018127