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Host Defense and Parasite Evasion
Published in Eric S. Loker, Bruce V. Hofkin, Parasitology, 2023
Eric S. Loker, Bruce V. Hofkin
Two additional mechanisms of allelic variation involve expression of VSG genes that are not initially adjacent to promoters. Some of these genes remain unexpressed until a crossover event places one of them in an expression site. As the crossover occurs, the new VSG gene replaces the previously expressed VSG gene, which is then moved away from the promoter site. Finally, many VSG genes are pseuodogenes, arranged in long subtelomeric arrays (Figure 4.29). Because they are not adjacent to promoters, these genes cannot be directly expressed. Rather, they are first replicated and then the duplicate copy of the gene replaces the currently active VSG gene at the expression site. The pseudogene serving as a template remains in place. Thus, the pseudogenes are like a stored collection of genes that might be copied and subsequently expressed at any time. Both of these mechanisms occur following the transition to the blood-form trypomastigote, with the use of pseudogenes more likely to occur later, following the establishment of the chronic infection. This recombination appears to involve double-stranded breaks in the 70-base pair repeats, but the manner in which these breaks occur remains under investigation.
Phylogeny of the mucosal immune system
Published in Phillip D. Smith, Richard S. Blumberg, Thomas T. MacDonald, Principles of Mucosal Immunology, 2020
Robert D. Miller, Irene Salinas
In birds, B cells that have undergone V(D)J recombination in the bone marrow must migrate to the bursa to complete their development. In the bursa of Fabricius, avian B cells complete their development by introducing mutations into their recombined V genes using AID-mediated gene conversion. This is an essential step because of the lack of repertoire diversity generated by V(D)J recombination alone. The chicken IgH locus contains only a single functional V gene and a large array of nonfunctional V pseudogenes. Although the pseudogenes cannot be recombined and expressed, they can be used as a source of donor sequences for gene conversion (Figure 2.4).
Transcriptionally Regulatory Sequences of Phylogenetic Significance
Published in S. K. Dutta, DNA Systematics, 2019
Pseudogenes, processed genes, and orphons are all inactive DNA sequences which may well be the relics of evolving functional genes, resulting from nonimpeded mutations. While several mechanisms can explain their inactivity, the ones relevant to transcription may include the abolishing of signals for initiation, altered splice junctions, and improper processing of primary transcripts.
Long noncoding RNA/circular RNA regulates competitive endogenous RNA networks in rheumatoid arthritis: molecular mechanisms and traditional Chinese medicine therapeutic significances
Published in Annals of Medicine, 2023
Jianting Wen, Jian Liu, Lei Wan, Fanfan Wang
Noncoding RNAs (ncRNAs) account for more than 98% of the human genome and play an important role in gene expression and regulation, including Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), transcribed pseudogenes [21]. miRNAs (20–200 nucleotides) function by binding to complementary sequences in the 3′-untranslated region (UTR) of their target mRNAs, thereby triggering translational repression of transcripts or mRNA degradation [22]. lncRNAs (more than 200 nucleotides) usually do not encode proteins and act as transcriptional regulators [21]. circRNAs are endogenous ncRNAs lacking the 5′ and 3′ ends, and their loop-like structure gives them a higher stability [23]. The sequence of a pseudogene is usually similar to the corresponding gene, but is at least partially lost, such as not encoding a protein or encoding a protein without function [24]. Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), as well as transcribed pseudogenes, correlate with many diseases, including RA belonging to autoimmune diseases [25–27]. Although many studies have provided evidence that both lncRNAs and circRNAs become a research hotspot in RA through their functions in many life activities [28,29]. However, at the sequence level, lncRNAs and circRNAs are poorly conserved across species.
Reviewing the occurrence of large genomic rearrangements in patients with inherited cancer predisposing syndromes: importance of a comprehensive molecular diagnosis
Published in Expert Review of Molecular Diagnostics, 2022
Débora Leite Rocha, Patricia Ashton-Prolla, Clévia Rosset
There are genomic regions that are more prone to LGR occurrence. Genomic regions rich in interspersed Alu sequences (repeated sequences with significant homology) and tandemly arranged short sequence repeats (highly repetitive noncoding human DNA) are hotspots for homologous recombination events, resulting in large duplications or deletions [61–63]. The presence of pseudogenes with high sequence homology to the functional gene is another cause of unequal recombination and consequently the occurrence of large rearrangements. For example, the BRCA1 gene has an extremely high density of intronic Alu repeats and the NF1 gene has flanking regions with short tandem repeat sequences, which predispose to the whole NF1 deletion, causing a more severe NF1 phenotype [63,64].
Detection of an α-Globin Fusion Gene Using Real-Time Polymerase Chain Reaction-Based Multicolor Melting Curve
Published in Hemoglobin, 2020
Ai-Ping Ju, Fan Jiang, Jian Li, Xue-Wei Tang, Dong-Zhi Li
Pseudogenes, the nonfunctional homologs of functional genes, arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript [11]. Recombination events between functional genes and their highly homologous pseudogenes were responsible for most gene mutations [12,13]. The ψα1 and α2 genes have high sequence similarity, more than 80.0%, at the nucleotide level [14]. It has been speculated that the fusion gene arose from a recombination between the ψα1 gene exon 3 of the Chinese –α4.2 deletion allele and the α2 gene exon 3 of the wild-type allele. The real prevalence of this fusion gene in the Chinese population is unknown. Indeed, we had never encountered it before until we used MMCA as the routine molecular screening method for common Chinese thalassemia alleles. We first reported the melt curve of the fusion gene that might be helpful for those investigators who use MMCA in their thalassemia prevention program.