Alzheimer's disease (AD), a neurodegenerative disorder with complex etiologies, manifests through a cascade of pathological changes before clinical symptoms become apparent. Among these early changes, alterations in the expression of non-coding RNAs (ncRNAs) have emerged as pivotal events. In this study, we focused on the aberrant expression of ncRNAs and revealed that Lamr1-ps1, a pseudogene of the laminin receptor, significantly exacerbates early spatial learning and memory deficits in APP/PS1 mice. Through a combination of bioinformatics prediction and experimental validation, we identified the miR-29c/Bace1 pathway as a potential regulatory mechanism by which Lamr1-ps1 influences AD pathology. Importantly, augmenting the miR-29c-3p levels in mice ameliorated memory deficits, underscoring the therapeutic potential of targeting miR-29c-3p in early AD intervention. This study not only provides new insights into the role of pseudogenes in AD but also consolidates a foundational basis for considering miR-29c as a viable therapeutic target, offering a novel avenue for AD research and treatment strategies.
Animals ; Alzheimer Disease/pathology* ; Pseudogenes/genetics* ; Mice ; Memory Disorders/metabolism* ; MicroRNAs/genetics* ; Disease Models, Animal ; Spatial Learning/physiology* ; Mice, Transgenic ; Presenilin-1/genetics* ; Male ; Amyloid Precursor Protein Secretases/metabolism* ; Mice, Inbred C57BL ; Aspartic Acid Endopeptidases/metabolism*

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

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

OBJECTIVETo investigate the expression of PTEN (phosphatase and tension homology deletion on chromosome 10, PTEN) and its pseudogene PTENP1 in acute leukemia (AL) and correlation between them, and to explore the role of PTENP1 on the PTEN expression in AL cells.

METHODSPTEN and PTENP1 mRNA expression were evaluated in bone marrow (BM) samples from 138 newly diagnosed AL patients and 15 healthy controls by quantitative real-time RT-PCR (qRT-PCR). pCDH1-PTENP1 3'UTR-GFP lentivirus vectors were constructed. 293T cells were transfected by calcium phosphate precipitation to produce retrovirus. HL-60 cell line was infected with the retroviral vectors expressing pCDH1-GFP and pCDH1-PTENP1 3'UTR-GFP respectively. The flow cell sorter was used to sort the HL-60 with GFP positively expressed. The mRNA expression of PTEN and PTENP1 was detected by qRT-PCR, the expression of PTEN protein by western blot, and the impact of PTENP13'UTR on the proliferation of HL-60 cells by MTT assay.

RESULTSAML patients showed significantly lower PTEN and PTENP1 mRNA expression in BM compared to healthy controls. Correlation analysis showed that the expression of PTEN and PTENP1 mRNA were positively correlated (P < 0.05). The 108 cases of PTENP1(+) AML were classified according to the prognostic classification of 2011 NCCN Clinical Practice Guidelines in AML, there was no difference among different subgroups. HL-60 cell line was infected with the retroviral vectors expressing pCDH1-GFP (control group) and pCDH1-PTENP1 3'UTR-GFP respectively. Compared with the control group, PTENP1 mRNA level of HL-60 infected with the retroviral vectors expressing pCDH1-PTENP1 3'UTR-GFP increased significantly, and PTEN mRNA level also increased. While the PTEN protein level and the cell growth rate of the PTENP1 3'UTR group didn't change significantly.

CONCLUSIONPTEN and PTENP1 mRNA expression level of BM cells from AL patients is significantly lower. There is a positive correlation between expression of PTEN and PTENP1 mRNA. PTENP1 may regulate the expression of PTEN in mRNA level.

Adolescent ; Adult ; Aged ; Case-Control Studies ; Child ; Female ; Gene Expression ; HL-60 Cells ; Humans ; Leukemia ; genetics ; Male ; Middle Aged ; PTEN Phosphohydrolase ; genetics ; Pseudogenes ; genetics ; RNA, Messenger ; genetics ; Transfection ; Young Adult

OBJECTIVETo detect the genomic deletion mutation in the NEMO gene of a family with incontinentia pigmenti (IP; MIM 308310).

METHODSA pedigree of IP was investigated. By using long PCR, the Delta4-10 deletion in NEMO gene was tested with specific primers In2/JF3R, and Delta4-10 deletion in pseudogene DeltaNEMO was investigated with primers Rev-2/JF3R. NEMO gene of 80 normal controls was also tested.

RESULTSThe deletion of exons 4-10 in both NEMO gene and the pseudogene DeltaNEMO was detected in all the patients in the family, but was not found in the normal individuals in this IP family and 80 unrelated controls.

CONCLUSIONThe study showed that the family with IP, which showed anticipation, was caused by NEMODelta4-10 deletion in the NEMO gene. Long PCR analysis is proven to be an efficient tool for identification of NEMO rearrangements. It could provide useful information for the genetic counseling of the family involved.

Adolescent ; Child ; Electrophoresis ; Exons ; genetics ; Family ; Female ; Humans ; I-kappa B Kinase ; genetics ; Incontinentia Pigmenti ; genetics ; Infant ; Male ; Pseudogenes ; genetics ; Sequence Deletion

In our previous studies, DAZAP2 gene expression was down-regulated in untreated patients of multiple myeloma (MM). For better studying the structure and function of DAZAP2, a full-length cDNA was isolated from mononuclear cells of a normal human bone marrow, sequenced and deposited to Genbank (AY430097). This sequence has an identical ORF (open reading frame) as the NM_014764 from human testis and the D31767 from human cell line KG-1. Phylogenetic analysis and structure prediction reveal that DAZAP2 homologues are highly conserved throughout evolution and share a polyproline region and several potential SH2/SH3 binding sites. DAZAP2 occurs as a single-copy gene with a four-exon organization. We further noticed that the functional DAZAP2 gene is located on Chromosome 12 and its pseudogene gene is on Chromosome 2 with electronic location of human chromosome in Genbank, though no genetic abnormalities of MM have been reported on Chromosome 12. The ORF of human DAZAP2 encodes a 17-kDa protein, which is highly similar to mouse Prtb. The DAZAP2 protein is mainly localized in cytoplasm with a discrete pattern of punctuated distribution. DAZAP2 may associate with carcinogenesis of MM and participate in yet-to-be identified signaling pathways to regulate proliferation and differentiation of plasma cells.
Amino Acid Sequence ; Base Sequence ; Chromosomes, Human, Pair 12 ; genetics ; Chromosomes, Human, Pair 2 ; genetics ; Cytoplasm ; metabolism ; DNA Primers ; DNA, Complementary ; genetics ; Down-Regulation ; Gene Components ; Humans ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Multiple Myeloma ; genetics ; metabolism ; Phylogeny ; Pseudogenes ; genetics ; RNA-Binding Proteins ; genetics ; metabolism ; Sequence Alignment ; Sequence Analysis, DNA

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

OBJECTIVETo study the distribution of poly(ADP-ribose) polymerase(PARP) pseudogene polymorphism and the association with susceptibility to lung cancer in Chinese people.

METHODSThe subjects of this study included 63 patients with lung cancer and 82 healthy controls matched in gender and age. Genome DNA was extracted from white blood cells. Products from PCR with a pair of specific primer were electrophoresized in agarose including EB. Under ultraviolet, observation and imaging were performed.

RESULTSThere was no significant difference in genotype between the cases and controls. The frequencies of B allele in cases and controls were 0.095 and 0.116 respectively. Whether there was B allele or not, smoking was a risk factor of lung cancer (P<0.05). As the genotype was AA and AB or BB, smoking OR was 2.28 and 4.83 respectively. Among non-smokers, the risk at lung cancer did not increase in AB or BB genotypes(P=0.202).

CONCLUSIONFrequency of B allele is relatively lower in Chinese people than in other races. In smokers, B allele may be a susceptible marker of lung cancer, and there is synergistic function between B allele and smoking.

Adult ; Aged ; Alleles ; China ; DNA, Neoplasm ; genetics ; Female ; Gene Frequency ; Genetic Predisposition to Disease ; Genotype ; Humans ; Lung Neoplasms ; enzymology ; genetics ; Male ; Middle Aged ; Poly(ADP-ribose) Polymerases ; genetics ; Polymorphism, Genetic ; Pseudogenes ; genetics

OBJECTIVETo search for genomic DNA sequence of the augmenter of liver regeneration (ALR) of rat.

METHODSPolymerase chain reaction (PCR) with specific primers was used to amplify the sequence from the rat genome.

RESULTSA piece of genomic DNA sequence and a piece of pseudogene of rat ALR were identified. The lengths of the gene and pseudogene are 1508 bp and 442 bp, respectively. The ALR gene of rat includes 3 exons and 2 introns. The 442 bp DNA sequence may represent a pseudogene or a ALR-related peptide. Predicted amino acid sequence analysis showed that there were 14 different amino acid residues between the gene and pseudogene. ALR-related peptide is 84 amino acid residues in length and relates closely to ALR protein.

CONCLUSIONThere might be a multigene family of ALR in rat.

Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA ; genetics ; Female ; Humans ; Liver Regeneration ; genetics ; Male ; Mice ; Molecular Sequence Data ; Polymerase Chain Reaction ; Proteins ; genetics ; Pseudogenes ; genetics ; Rats