Functional genomics has provided evidence that the human genome transcribes a large number of non-coding genes in addition to protein-coding genes, including microRNAs and long non-coding RNAs (lncRNAs). Among the group of lncRNAs are pseudogenes tha...
An original bioinformatics technique is developed to identify the protein-coding genes in rodents, lagomorphs and nonhuman primates that are pseudogenized in humans. The method is based on per-gene verification of local synteny, similarity of exon-in...
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pse...
Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also d...
Ferritin, the principal intracellular iron-storage protein localized in the cytoplasm, nucleus, and mitochondria, plays a major role in iron metabolism. The encoding ferritin genes are members of a multigene family that includes some pseudogenes. Eve...
There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they...
Pseudogenes are duplicates of protein-coding genes that have accumulated multiple detrimental alterations, rendering them unable to produce the protein they encode. Initially disregarded as “junk DNA” due to their perceived lack of functi...
Once considered nonfunctional, pseudogene transcripts are now known to provide valuable information for cancer susceptibility, including head and neck cancer (HNC), a serious health problem worldwide, with about 50% unimproved overall survival over t...
Pseudogenes are dead copies of genes. Owing to the absence of functional constraint, all nucleotide substitutions that occur in these sequences are selectively neutral, and thus represent the spontaneous pattern of substitution within a genome. Here,...
Most pseudogenes are generated when an RNA transcript is reverse-transcribed and integrated into the genome at a new location. Pseudogenes are often considered as an imperfect and silent copy of a functional gene because of the accumulation of numero...
A pseudogene is a non-functional copy of a protein-coding gene. Processed pseudogenes, which are created by the reverse transcription of mRNA and subsequent integration of the resulting cDNA into the genome, being a major pseudogene class, represent...
Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regi...
Hepatocellular Carcinoma (HCC), a formidable global health challenge, continues to claim numerous lives due to its asymptomatic nature in the early stages and limited treatment options. In this ever-evolving landscape of cancer research, pseudogenes,...
The chloroplast trnL-F region has been extensively utilized for evolutionary analysis in plants. In the Brassicaceae this fragment contains 1–12 tandemly repeated trnF pseudogene copies in addition to the functional trnF gene. Here we assessed the po...
Background: The cytochrome P450 family 21 subfamily A member 2 gene (CYP21A2) encodes 21-hydroxylase, a key enzyme in adrenal steroid biosynthesis. Despite its physiological importance, the diversity of CYP21A2 transcript variants and their tissue-sp...
Osteosarcoma is a common malignancy with high mortality and poor prognosis due to lack of predictive markers. Increasing evidence has demonstrated that pseudogenes, a type of non-coding gene, play an important role in tumorigenesis. The aim of this s...
Formerly considered nonfunctional “junk DNA,” pseudogenes have been re-evaluated in light of technological advances in bioinformatics and high-throughput sequencing. The limited research to date on pseudogenes in hexaploid common wheat (T...
Inherited copy number variations (CNVs) can provide valuable information for cancer susceptibility and prognosis. However, their association with oropharynx squamous cell carcinoma (OPSCC) is still poorly studied. Using microarrays analysis, we ident...
Several studies have established that pseudogene mRNAs can work as competing endogenous RNAs and, when deregulated, play a key role in the onset of human neoplasias. Recently, we have isolated two HMGA1 pseudogenes, HMGA1P6 and HMGA1P7. These pseudog...
The PMS2 gene is involved in DNA repair by the mismatch repair pathway. Deficiencies in this mechanism have been associated with Lynch Syndrome (LS), which is characterized by a high risk for colorectal, endometrial, ovarian, breast, and other cancer...
Background: Head and neck squamous cell carcinoma remains a highly aggressive malignancy with limited predictive biomarkers for prognosis and radiotherapy response. Increasing evidence indicates that pseudogenes are functionally active regulators of...
The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudog...
Background: Head and neck squamous cell carcinomas are a group of heterogeneous diseases that occur in the mouth, pharynx and larynx and are characterized by poor prognosis. A low overall survival rate leads to a need to develop biomarkers for early...
Various attempts to amplify an AQP11 cDNA from tissues of the spiny dogfish (Squalus acanthias) were made. Two pairs of deoxy-inosine-containing degenerate primers were designed based on conserved amino acid sequences from an AQP11 alignment. These p...
SNORKEL1 (SK1) and SNORKEL2 (SK2) are ethylene responsive factors that regulate the internode elongation of deepwater rice in response to submergence. We previously reported that normal cultivated rice lacks SK genes because the Chromosome 12 region...
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that interact with PIWI proteins and play essential roles in genome stability, gonadal development, and gametogenesis in animals. The Japanese flounder (Paralichthys olivaceus) is an important...
The plastid genomes (plastomes) of angiosperms are typically highly conserved, with extreme reconfiguration being uncommon, although reports of such events have emerged in some lineages. In this study, we conducted a comprehensive comparison of the c...
Hepatocellular carcinoma (HCC) records the second-lowest 5-year survival rate despite the avalanche of research into diagnosis and therapy. One of the major obstacles in treatment is chemoresistance to drugs such as 5-fluorouracil (5-FU), making iden...
Pseudogenes are barely transcribed normally, but some of them are transcribed as long non-coding RNAs during tumorigenesis. The pathological features of pseudogenes in hepatocellular carcinoma (HCC) have not been illustrated clearly. Here, we engaged...
Locus-specific Illumina NGS was used to analyze the polymorphism of the partial 18S rDNA, spacer ITS1, and partial 5.8S rDNA sequences across 25 cactus species (53 accessions) of the subtribes Hylocereinae and Echinocereinae. To ensure data reliabili...
Multidrug resistance (MDR) is one of the main limitations of cancer treatment. The overexpression of drug-efflux pumps, such as P-glycoprotein (P-gp), is a major cause of MDR. Importantly, different studies have shown that extracellular vesicles (EVs...
This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species contai...
Terpenes are the largest and most diverse class of secondary metabolites in plants and play a very important role in plant adaptation to environment. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a rate-limiting enzyme in the process of t...
The complete chloroplast genomes of red currant cultivar ‘Belaya Potapenko’ and gooseberry cultivar ‘Nekrasovskij’ were sequenced and assembled for the first time. The plastomes are 157,802 bp and 157,559 bp in length for Ribe...
Fully mycoheterotrophic orchids provide a powerful system for examining plastome degradation following the loss of dependence on photosynthesis. Here, we assembled and characterized the complete plastome of Neottia kiusiana and compared its structure...
YRNAs are a type of short, noncoding RNAs. A total of four different transcripts can be distinguished, which are YRNA1, YRNA3, YRNA4 and YRNA5. All YRNAs are relatively small, made up of about 100 nucleotides each. YRNAs are characterized by a stem-l...
The transforming growth factor-β (TGF-β) family of cytokines performs a multifunctional signaling, which is integrated and coordinated in a signaling network that involves other pathways, such as Wintless, Forkhead box-O (FOXO) and Hedgehog and regul...
Background/Objectives. Living odontocetes are the only extant mammals that lack anatomical features associated with olfaction. A leading hypothesis for the presumed complete loss of smell (i.e., anosmia) in odontocetes is that olfaction was lost in t...
A study was conducted to investigate the evolutionary relationships of Macrotermes subhyalinus from Oman, in the southeastern part of the Arabian Peninsula. Sequences of the mitochondrial COI and the nuclear large-subunit ribosomal RNA (LSU rRNA, 28S...
Bitter taste receptors (T2Rs) contribute to innate immune responses and taste preferences. Variants in T2R genes (TAS2Rs) may increase the risk of adverse oral health. This study investigated the association of single nucleotide polymorphisms (SNPs)...
AQP8-type water channels are expressed superficially in the plasma membrane or intracellularly in the inner mitochondrial membrane, where they respectively function in osmohomeostasis or as peroxiporins to alleviate oxidative stress. To date only sin...
Background: Many pseudogenes possess biological activities and play important roles in the pathogenesis of various types of cancer including bladder cancer (BlCa), which still lacks suitable molecular biomarkers. Recently, pseudogenes were found to b...
Although bacterial genomes have been traditionally viewed as being very compact, with relatively low amounts of repetitive and non-coding DNA, this view has dramatically changed in recent years. The increase of available complete bacterial genomes ha...
Brucella organisms are responsible for one of the most widespread bacterial zoonoses, named brucellosis. The disease affects several species of animals, including humans. One of the most intriguing aspects of the brucellae is that the various species...
A small phylogenetically conserved sequence of 11,231 bp, termed FAM247, is repeated in human chromosome 22 by segmental duplications. This sequence forms part of diverse genes that span evolutionary time, the protein genes being the earliest as they...
Boxwood blight, a fungal disease of ornamental plants (Buxus spp.), is caused by two sister species, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Compared to Cps, Che is documented to display reduced sensitivity to fungicides, includi...
Mammalian oocytes are surrounded by an extracellular coat called the zona pellucida (ZP), which, from an evolutionary point of view, is the most ancient of the coats that envelope vertebrate oocytes and conceptuses. This matrix separates the oocyte f...
Background/Objectives: Autophagy is an evolutionarily conserved intracellular degradation mechanism that is regulated by a set of autophagy-related (ATG) proteins. The only transmembrane protein among ATGs is the lipid scramblase ATG9, which exists i...
The nuclear ITS1–5.8S rDNA–ITS2 region is among the most widely used markers for phylogenetic studies in plants. We sequenced the ITS1–5.8S rDNA–ITS2 region in several species of Selenicereus, two species of Deamia and Epiphyl...
Noncoding RNAs (ncRNAs) constitute the majority of the human transcribed genome. This largest class of RNA transcripts plays diverse roles in a multitude of cellular processes, and has been implicated in many pathological conditions, especially cance...
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