Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question. However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.
Biological Evolution ; Genome* ; Genome, Human ; Humans* ; Neanderthals* ; Pseudogenes ; Retroelements

Since Mycobacterium leprae, the causative organism of Leprosy, proliferate inside macrophages, it has been speculated that catalase encoded by the katG gene may protect acid-fast bacilli from the deleterious effects of peroxide generated from macrophage and may play a crucial role in the survival of M. leprae in vivo. The homology of E. coli katG gene is also identified from M. tuberculosis and M. leprae recently. However, the katG gene of M. leprae is thought to be a pseudogene, unlike that of M. tuberculosis, because it contains multiple deletions, implicating that isoniazid(INH), which is activated to a potent tuberculocidal agent by catalase encoded by the katG gene, is unlikely to be of therapeutic benefit to leprosy patients. We have tested 1) the role of KatG protein in activation of INH by using INH susceptible test of M. smegmatis mc(2)155 and BH1, and 2) the effect of INH on M. leprae growth by radiorespirometric assay to examine the catalase-like activity in M. leprae. It was found that the viability of M. leprae was decreased at 20 microgram/ml of INH and higher concentrations. We confirmed the role of KatG protein in activation of INH and our results suggest that a catalase-like activity other than katG is present in M. leprae.
Catalase ; Humans ; Isoniazid* ; Leprosy ; Macrophages ; Mycobacterium leprae ; Pseudogenes ; Tuberculosis

OBJECTIVETo determine the genome structure of human telomeric repeat binding factor 1 (TERF1) and its pseudogenes.

METHODSSequences were obtained from GenBank and analyzed using the BLAST program and other relevant biology program (Sequencher, DNA Strider and Autoassembler, etc) to determine the genome and pseudogenome structure of TERF1. PCR and sequencing were performed to verify the results.

RESULTTERF1 gene which mapped to 8q13 was divided into 10 exons. It had four processed pseudogenes located on chromosome 13, 18, 21 and X respectively (Psi TERF1-13 Psi TERF1-18 Psi TERF1-21 and Psi TERF1-X ). They were entire intronless TERF1 genes which lacked some exons. Three homologous fragments of at least 60 kb on the flanking region of Psi TERF1-13, Psi TERF1-18 and Psi TERF1-21, respectively were noted.

CONCLUSIONTERF1 gene has 10 exons. It has four processed pseudogenes which are located on chromosome 13, 18, 21, and X, respectively. Large homologous fragments that belong to the recently duplicated segments are transchromosomal duplications.

Chromosome Mapping ; Genetic Structures ; Humans ; Pseudogenes ; Telomeric Repeat Binding Protein 1 ; genetics

Animals ; Codon, Nonsense ; Disease ; genetics ; Drosophila ; genetics ; metabolism ; Drosophila Proteins ; genetics ; Humans ; Pseudogenes ; Receptors, Odorant ; genetics

Even though it represents 6 13% of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over 80 % of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about 10% of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.
3' Untranslated Regions* ; Alu Elements* ; Clinical Coding ; DNA ; Exons ; Genome, Human ; Humans ; Molecular Biology ; Pseudogenes* ; RNA, Messenger*

Pseudogenes, which have long been described as "fossils", play a very important role in eukaryotic genomes. Recently, studies on the so called "junk gene" have attracted more attention. Far from being silent, pseudogenes participate in various biological activities, including being a part in the transcription process, or participating in the formation of small interfering RNA (siRNA) which regulated gene expression by means of the RNA-interference pathway. Recent studies have also shown that pseudogenes regulate tumor suppression through competing for the microRNA (miRNA) with their parent genes. However, a deeper understanding of function analysis of pseudogenes depends on the comprehensive and accurate identification. With the sequencing completion of many genomes and the innovation of bioinformatics tools, efficient and precise identification of pseudogenes have become available in a genome-wide scale. Our review focused particularly on the method of pseudogene identification, the mechanism of its regulatory roles and its potential to be applied in directed evolution. Besides, the promising research direction of pseudogenes was proposed.
Gene Expression Regulation ; Genes, Tumor Suppressor ; physiology ; MicroRNAs ; genetics ; Pseudogenes ; genetics ; physiology ; RNA Interference ; RNA, Small Interfering ; genetics

Congenital adrenal hyperplasia (CAH), an autosomal recessive disorder, is due to deficiency of the enzymes involved in adrenal steroidogenesis. Phenotypic manifestations vary as a result of the degree of glucocorticoid or mineralocorticoid deficiency and androgen excess present. Among Filipinos, the estimated crude incidence of CAH is approximately 1 in 7,000, which is higher than what is reported in most populations. More than 90% of all cases result from a 21-hydroxylase (21-OH) (cytochrome P450c21) enzyme deficiency involving two 21-OH genes, the active gene (CYP21) and a pseudogene (CYP21P). Studies have shown that mutations result from unequal crossover during meiosis which leads to complete deletion of the gene, gene conversion events or to point mutations. To date, there are no published data on the types of mutations present among Filipinos diagnosed with congenital adrenal hyperplasia. The objective of this study is to describe the profile of Filipino patients diagnosed with CAH and to determine the disease-causing alleles in the 21-OH gene of these patients. Using a method of combined differential polymerase chain reaction and amplification created restriction site approach, direct probing for the presence of known mutations in exons 1,3,4,6,7,8 and intron 2 of the CYP21 and CYP21P genes among Filipino patients with CAH was performed. A total of 12 unrelated CAH patients were examined. A majority of these cases had a premature splicing error mutation at nucleotide 656 of intron 2. The determination of the most frequent alleles in our population can facilitate rapid screening for mutations in the 21-OH gene and lead to a definitive diagnosis of CAH.

Human ; Male ; Female ; Steroid 21-hydroxylase ; Adrenal Hyperplasia, Congenital ; Introns ; Glucocorticoids ; Mineralocorticoids ; Alleles ; Pseudogenes ; Rna Splicing ; Nucleotides

Steroid 21 hydroxylase deficiency is a major cause of congenital adrenal hyperplasia(CAH) and is caused by genetic impairment (CYP21B) of this enzyme. In the human genome, CYP21B is located within MHC class III region on the short arm of chromosome 6. Most of the genes in this region are highly polymorphic and crowded. Also the CYP21B gene is accompanied by its pseudogene (CYP21A) and tandemly arranged with two genes of fourth component of complement. This highly complex gene arrangement in this area may predispose genetic unstability of CYP21 genes,i.e. mutations. In the current study, we tried to investigate the frequency of duplication and deletion of CYP21 genes and pattern of the genetic alteration of these genes by RFLPs. We also compared the genetic alteration of CYP21 in normal subjects with those of the CAH patients. According to our study, 15% of the normal Korean population have duplication or deletion of CYP21. There was one normal subject with heterozygous deletion of CYP21B gene. Of the 5 CAH patients examined, we found abnormal patterns in 2 patients. One was a large scale gene conversion and the other was a deletion of CYP21B and C4 locus II genes with gene conversion. These results suggest that high frequency of duplication and deletion of CYP21 and C4 in the general population may provide the genetic pool of instable CYP21 genes and these duplicated or deleted genes may result in gene conversions between CYP21A(pseudogene) and CYP21B(true gene) by preventing the normal recombination event.
Adrenogenital Syndrome* ; Arm ; Chromosomes, Human, Pair 6 ; Complement System Proteins ; Gene Conversion ; Gene Order ; Genome, Human ; Humans ; Polymorphism, Restriction Fragment Length ; Pseudogenes ; Recombination, Genetic ; Steroid 21-Hydroxylase*

CYP21A2 mutation analysis of congenital adrenal hyperplasia (CAH) is challenging because of the genomic presence of a homologous CYP21A2 pseudogene and the significant incidence of pseudogene conversion and large deletions. The objective of this study was to accurately analyze the CYP21A2 genotype in Korean CAH patients using a combination of complementary methods. Long-range PCR and restriction fragment length polymorphism analyses were performed to confirm valid amplification of CYP21A2 and to detect large gene conversions and deletions before direct sequencing. Multiple ligation-dependent probe amplification (MLPA) analysis was conducted concurrently in 14 CAH-suspected patients and six family members of three patients. We identified 27 CYP21A2 mutant alleles in 14 CAH-suspected patients. The c.293-13A>G (or c.293-13C>G) was the most common mutation, and p.Ile173Asn was the second, identified in 25% and 17.9% of alleles, respectively. A novel frame-shift mutation of c.492delA (p.Glu 164Aspfs*24) was detected. Large deletions were detected by MLPA in 10.7% of the alleles. Mutation studies of the six familial members for three of the patients aided in the identification of haplotypes. In summary, we successfully identified CYP21A2 mutations using both long-range PCR and sequencing and dosage analyses. Our data correspond relatively well with the previously reported mutation spectrum analysis.
Adrenal Hyperplasia, Congenital* ; Alleles ; Gene Conversion ; Genotype ; Haplotypes ; Humans ; Incidence ; Korea ; Polymerase Chain Reaction* ; Polymorphism, Restriction Fragment Length* ; Pseudogenes ; Spectrum Analysis

T-cell receptor gamma alternate reading frame protein (TARP) is expressed by human prostate epithelial, prostate cancer, and mammary cancer cells, but is not found in normal mammary tissue. To date, this protein has only been described in humans. Additionally, no animal model has been established to investigate the potential merits of TARP as tumor marker or a target for adoptive tumor immunotherapy. In this study conducted to characterize feline T-cell receptor gamma sequences, constructs very similar to human TARP transcripts were obtained by RACE from the spleen and prostate gland of cats. Transcription of TARP in normal, hyperplastic, and neoplastic feline mammary tissues was evaluated by conventional RT-PCR. In felines similarly to the situation reported in humans, a C-region encoding two open reading frames is spliced to a J-region gene. In contrast to humans, the feline J-region gene was found to be a pseudogene containing a deletion within its recombination signal sequence. Our findings demonstrated that the feline TARP ortholog is transcribed in the prostate gland and mammary tumors but not normal mammary tissues as is the case with human TARP.
Animals ; Cats ; Continental Population Groups ; Humans ; Immunotherapy ; Models, Animal ; Open Reading Frames ; Prostate ; Prostatic Neoplasms ; Protein Sorting Signals ; Pseudogenes ; Reading Frames ; Receptors, Antigen, T-Cell ; Recombination, Genetic ; Spleen