The Experts below are selected from a list of 33234 Experts worldwide ranked by ideXlab platform
Yoichi Matsuda - One of the best experts on this subject based on the ideXlab platform.
-
Molecular cytogenetic characterization of chromosome site-specific Repetitive Sequences in the Arctic lamprey (Lethenteron camtschaticum, Petromyzontidae).
DNA research : an international journal for rapid publication of reports on genes and genomes, 2017Co-Authors: Junko Ishijima, Chizuko Nishida, Yoshinobu Uno, Mitsuo Nunome, Shigehiro Kuraku, Yoichi MatsudaAbstract:All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S-28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific Repetitive DNA Sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. Three types of Repetitive Sequences were detected; a 200-bp AT-rich Repetitive sequence, LCA-EcoRIa that co-localized with the 18S-28S rRNA gene clusters of 3 chromosomal pairs; a 364-bp AT-rich LCA-EcoRIb sequence that showed homology to the EcoRI sequence family from the sea lamprey (Petromyzon marinus), which contains short repeats as centromeric motifs; and a GC-rich 702-bp LCA-ApaI sequence that was distributed on nearly all chromosomes and showed significant homology with the integrase-coding region of a Ty3/Gypsy family long terminal repeat (LTR) retrotransposon. All three Repetitive Sequences are highly conserved within the Petromyzontidae or within Petromyzontidae and Mordaciidae. Molecular cytogenetic characterization of these site-specific repeats showed that they may be correlated with programed genome rearrangement (LCA-EcoRIa), centromere structure and function (LCA-EcoRIb), and site-specific amplification of LTR retroelements through homogenization between non-homologous chromosomes (LCA-ApaI).
-
highly differentiated zw sex microchromosomes in the australian varanus species evolved through rapid amplification of Repetitive Sequences
PLOS ONE, 2014Co-Authors: Kazumi Matsubara, Stephen D Sarre, Yoichi Matsuda, Arthur Georges, Jennifer Marshall A Graves, Tariq EzazAbstract:Transitions between sex determination systems have occurred in many lineages of squamates and it follows that novel sex chromosomes will also have arisen multiple times. The formation of sex chromosomes may be reinforced by inhibition of recombination and the accumulation of Repetitive DNA Sequences. The karyotypes of monitor lizards are known to be highly conserved yet the sex chromosomes in this family have not been fully investigated. Here, we compare male and female karyotypes of three Australian monitor lizards, Varanus acanthurus, V. gouldii and V. rosenbergi, from two different clades. V. acanthurus belongs to the acanthurus clade and the other two belong to the gouldii clade. We applied C-banding and comparative genomic hybridization to reveal that these species have ZZ/ZW sex micro-chromosomes in which the W chromosome is highly differentiated from the Z chromosome. In combination with previous reports, all six Varanus species in which sex chromosomes have been identified have ZZ/ZW sex chromosomes, spanning several clades on the varanid phylogeny, making it likely that the ZZ/ZW sex chromosome is ancestral for this family. However, Repetitive Sequences of these ZW chromosome pairs differed among species. In particular, an (AAT)n microsatellite repeat motif mapped by fluorescence in situ hybridization on part of W chromosome in V. acanthurus only, whereas a (CGG)n motif mapped onto the W chromosomes of V. gouldii and V. rosenbergi. Furthermore, the W chromosome probe for V. acanthurus produced hybridization signals only on the centromeric regions of W chromosomes of the other two species. These results suggest that the W chromosome Sequences were not conserved between gouldii and acanthurus clades and that these Repetitive Sequences have been amplified rapidly and independently on the W chromosome of the two clades after their divergence.
-
Chromosome size-correlated and chromosome size-uncorrelated homogenization of centromeric Repetitive Sequences in New World quails
Chromosome Research, 2014Co-Authors: Satoshi Ishishita, Yuri Tsuruta, Chizuko Nishida, Darren K Griffin, Masaoki Tsudzuki, Atsushi Nakamura, Yoichi MatsudaAbstract:Many families of centromeric Repetitive DNA Sequences isolated from Struthioniformes, Galliformes, Falconiformes, and Passeriformes are localized primarily to microchromosomes. However, it is unclear whether chromosome size-correlated homogenization is a common characteristic of centromeric Repetitive Sequences in Aves. New World and Old World quails have the typical avian karyotype comprising chromosomes of two distinct sizes, and C-positive heterochromatin is distributed in centromeric regions of most autosomes and the whole W chromosome. We isolated six types of centromeric Repetitive Sequences from three New World quail species ( Colinus virginianus , CVI; Callipepla californica , CCA; and Callipepla squamata , CSQ; Odontophoridae) and one Old World quail species ( Alectoris chukar , ACH; Phasianidae), and characterized the Sequences by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization. The 385-bp CVI- Msp I, 591-bp CCA- BamH I, 582-bp CSQ- BamH I, and 366-bp ACH- Sau 3AI fragments exhibited tandem arrays of the monomer unit, and the 224-bp CVI- Hae III and 135-bp CCA- Hae III fragments were composed of minisatellite-like and microsatellite-like repeats, respectively. ACH- Sau 3AI was a homolog of the chicken nuclear membrane repeat sequence, whose homologs are common in Phasianidae. CVI- Msp I, CCA- BamH I, and CSQ- BamH I showed high homology and were specific to the Odontophoridae. CVI- Msp I was localized to microchromosomes, whereas CVI- Hae III, CCA- BamH I, and CSQ- BamH I were mapped to almost all chromosomes. CCA- Hae III was localized to five pairs of macrochromosomes and most microchromosomes. ACH- Sau 3AI was distributed in three pairs of macrochromosomes and all microchromosomes. Centromeric Repetitive Sequences may be homogenized in chromosome size-correlated and -uncorrelated manners in New World quails, although there may be a mechanism that causes homogenization of centromeric Repetitive Sequences primarily between microchromosomes, which is commonly observed in phasianid birds.
-
molecular cloning and characterization of the Repetitive dna Sequences that comprise the constitutive heterochromatin of the a and b chromosomes of the korean field mouse apodemus peninsulae muridae rodentia
Chromosome Research, 2008Co-Authors: Kazumi Matsubara, Chizuko Nishida, Kazuhiko Yamada, Kimiyuki Tsuchiya, Shu Umemoto, Naoki Ikeda, Takahito Chijiwa, Kazuo Moriwaki, Yoichi MatsudaAbstract:Three novel families of Repetitive DNA Sequences were molecularly cloned from the Korean field mouse (Apodemus peninsulae) and characterized by chromosome in-situ hybridization and filter hybridization. They were all localized to the centromeric regions of all autosomes and categorized into major satellite DNA, type I minor, and type II minor Repetitive Sequences. The type II minor Repetitive sequence also hybridized interspersedly in the non-centromeric regions. The major satellite DNA sequence, which consisted of 30 bp elements, was organized in tandem arrays and constituted the majority of centromeric heterochromatin. Three families of Repetitive Sequences hybridized with B chromosomes in different patterns, suggesting that the B chromosomes of A. peninsulae were derived from A chromosomes and that the three Repetitive Sequences were amplified independently on each B chromosome. The minor Repetitive Sequences are present in the genomes of the other seven Apodemus species. In contrast, the major satellite DNA Sequences that had a low sequence homology are present only in a few species. These results suggest that the major satellite DNA was amplified with base substitution in A. peninsulae after the divergence of the genus Apodemus from the common ancestor and that the B chromosomes of A. peninsulae might have a species-specific origin.
Louise Prakash - One of the best experts on this subject based on the ideXlab platform.
-
yeast dna repair protein rad5 that promotes instability of simple Repetitive Sequences is a dna dependent atpase
Journal of Biological Chemistry, 1994Co-Authors: Robert E Johnson, Satya Prakash, Louise PrakashAbstract:Abstract The RAD5 gene of Saccharomyces cerevisiae functions in postreplication repair of ultraviolet damaged DNA, and interestingly, it also has a role in increasing the instability of simple Repetitive Sequences in the genome. In contrast to DNA mismatch repair genes which function in maintaining constant length of repeat Sequences, RAD5 promotes alterations in the length of repeat Sequences. In this work, we purify the RAD5 protein to near homogeneity from yeast cells and show that it is a single-stranded DNA-dependent ATPase. The possible roles of RAD5 ATPase in postreplication gap filling and in increasing the incidence of length alterations of repeat Sequences are discussed.
-
saccharomyces cerevisiae rad5 encoded dna repair protein contains dna helicase and zinc binding sequence motifs and affects the stability of simple Repetitive Sequences in the genome
Molecular and Cellular Biology, 1992Co-Authors: Robert E Johnson, Satya Prakash, Samuel T Henderson, Thomas D Petes, Michael Bankmann, Louise PrakashAbstract:rad5 (rev2) mutants of Saccharomyces cerevisiae are sensitive to UV light and other DNA-damaging agents, and RAD5 is in the RAD6 epistasis group of DNA repair genes. To unambiguously define the function of RAD5, we have cloned the RAD5 gene, determined the effects of the rad5 deletion mutation on DNA repair, DNA damage-induced mutagenesis, and other cellular processes, and analyzed the sequence of RAD5-encoded protein. Our genetic studies indicate that RAD5 functions primarily with RAD18 in error-free postreplication repair. We also show that RAD5 affects the rate of instability of poly(GT) repeat Sequences. Genomic poly(GT) Sequences normally change length at a rate of about 10(-4); this rate is approximately 10-fold lower in the rad5 deletion mutant than in the corresponding isogenic wild-type strain. RAD5 encodes a protein of 1,169 amino acids of M(r) 134,000, and it contains several interesting sequence motifs. All seven conserved domains found associated with DNA helicases are present in RAD5. RAD5 also contains a cysteine-rich sequence motif that resembles the corresponding Sequences found in 11 other proteins, including those encoded by the DNA repair gene RAD18 and the RAG1 gene required for immunoglobin gene arrangement. A leucine zipper motif preceded by a basic region is also present in RAD5. The cysteine-rich region may coordinate the binding of zinc; this region and the basic segment might constitute distinct DNA-binding domains in RAD5. Possible roles of RAD5 putative ATPase/DNA helicase activity in DNA repair and in the maintenance of wild-type rates of instability of simple Repetitive Sequences are discussed.
Chengzhi Liang - One of the best experts on this subject based on the ideXlab platform.
-
assembly of chromosome scale contigs by efficiently resolving Repetitive Sequences with long reads
Nature Communications, 2019Co-Authors: Chengzhi LiangAbstract:The abundant Repetitive Sequences in complex eukaryotic genomes cause fragmented assemblies, which lose value as reference genomes, often due to incomplete gene Sequences and unanchored or mispositioned contigs on chromosomes. Here we report a genome assembly method HERA, which resolves repeats efficiently by constructing a connection graph from an overlap graph. We test HERA on the genomes of rice, maize, human, and Tartary buckwheat with single-molecule sequencing and mapping data. HERA correctly assembles most of the previously unassembled regions, resulting in dramatically improved, highly contiguous genome assemblies with newly assembled gene Sequences. For example, the maize contig N50 size reaches 61.2 Mb and the Tartary buckwheat genome comprises only 20 contigs. HERA can also be used to fill gaps and fix errors in reference genomes. The application of HERA will greatly improve the quality of new or existing assemblies of complex genomes. Repetitive Sequences in complex eukaryote genomes can cause fragmented assemblies with incomplete gene Sequences and unanchored or mispositioned contigs. Here, the authors report HERA, a method to improve genome assemblies by efficiently resolving repeats using single-molecule sequencing data.
-
assembly of chromosome scale contigs by efficiently resolving Repetitive Sequences with long reads
bioRxiv, 2018Co-Authors: Chengzhi LiangAbstract:Due to the large number of Repetitive Sequences in complex eukaryotic genomes, fragmented and incompletely assembled genomes lose value as reference Sequences, often due to short contigs that cannot be anchored or mispositioned onto chromosomes. Here we report a novel method Highly Efficient Repeat Assembly (HERA), which includes a new concept called a connection graph as well as algorithms for constructing the graph. HERA resolves repeats at high efficiency with single-molecule sequencing data, and enables the assembly of chromosome-scale contigs by further integrating genome maps and Hi-C data. We tested HERA with the genomes of rice R498, maize B73, human HX1 and Tartary buckwheat Pinku1. HERA can correctly assemble most of the tandemly Repetitive Sequences in rice using single-molecule sequencing data only. Using the same maize and human sequencing data published by Jiao et al. (2017) and Shi et al. (2016), respectively, we dramatically improved on the sequence contiguity compared with the published assemblies, increasing the contig N50 from 1.3 Mb to 61.2 Mb in maize B73 assembly and from 8.3 Mb to 54.4 Mb in human HX1 assembly with HERA. We provided a high-quality maize reference genome with 96.9% of the gaps filled (only 76 gaps left) and several incorrectly positioned Sequences fixed compared with the B73 RefGen_v4 assembly. Comparisons between the HERA assembly of HX1 and the human GRCh38 reference genome showed that many gaps in GRCh38 could be filled, and that GRCh38 contained some potential errors that could be fixed. We assembled the Pinku1 genome into 12 scaffolds with a contig N50 size of 27.85 Mb. HERA serves as a new genome assembly/phasing method to generate high quality Sequences for complex genomes and as a curation tool to improve the contiguity and completeness of existing reference genomes, including the correction of assembly errors in Repetitive regions.
Nattiya Hirankarn - One of the best experts on this subject based on the ideXlab platform.
-
dna methylation status of the interspersed Repetitive Sequences for line 1 alu herv e and herv k in trabeculectomy specimens from glaucoma eyes
Journal of Ophthalmology, 2018Co-Authors: Sunee Chansangpetch, Sasiprapa Prombhul, Visanee Tantisevi, Pimpayao Sodsai, Anita Manassakorn, Nattiya Hirankarn, Shan C LinAbstract:Background/Aims. Epigenetic mechanisms via DNA methylation may be related to glaucoma pathogenesis. This study aimed to determine the global DNA methylation level of the trabeculectomy specimens among patients with different types of glaucoma and normal subjects. Methods. Trabeculectomy sections from 16 primary open-angle glaucoma (POAG), 12 primary angle-closure glaucoma (PACG), 16 secondary glaucoma patients, and 10 normal controls were assessed for DNA methylation using combined-bisulfite restriction analysis. The percentage of global methylation level of the interspersed Repetitive Sequences for LINE-1, Alu, HERV-E, and HERV-K were compared between the 4 groups. Results. There were no significant differences in the methylation for LINE-1 and HERV-E between patients and normal controls. For the Alu marker, the methylation was significantly lower in all types of glaucoma patients compared to controls (POAG 52.19% versus control 52.83%, ; PACG 51.50% versus control, ; secondary glaucoma 51.95% versus control, ), whereas the methylation level of HERV-K was statistically higher in POAG patients compared to controls (POAG 49.22% versus control 48.09%, ). Conclusions. The trabeculectomy sections had relative DNA hypomethylation of Alu in all glaucoma subtypes and relative DNA hypermethylation of HERV-K in POAG patients. These methylation changes may lead to the fibrotic phenotype in the trabecular meshwork.
-
types of dna methylation status of the interspersed Repetitive Sequences for line 1 alu herv e and herv k in the neutrophils from systemic lupus erythematosus patients and healthy controls
Journal of Human Genetics, 2014Co-Authors: Patadon Sukapan, Apiwat Mutirangura, Paramate Promnarate, Yingyos Avihingsanon, Nattiya HirankarnAbstract:Changes of the DNA methylation at the interspersed Repetitive Sequences can occur in various conditions including cancer as well as autoimmune diseases. We previously reported the hypomethylation of LINE-1 and HERV-E in the lymphocytes of systemic lupus erythematosus (SLE) patients. As neutrophils are another important cell type contributing to SLE pathogenesis, in this study, we evaluated the methylation levels and patterns for LINE-1, ALU, HERV-E and HERV-K in the neutrophils from SLE patients compared with the healthy controls. We observed that the methylation levels, especially for LINE-1, in the neutrophils from SLE patients were significantly lower than the healthy controls (P-value<0.0001). Interestingly, this hypomethylation was not correlated with the activity of the disease. Furthermore, the methylation levels and patterns for Alu, HERV-E and HERV-K in the neutrophils from the SLE patients were not significantly different from the healthy controls. In addition, we further investigated whether there were any correlations between the intragenic LINE-1 and differential expressions of the neutrophils from the SLE patients using public arrays data. The upregulated genes in the neutrophils from the SLE patients were significantly associated with the genes containing LINE-1s compared with the healthy controls (P-value GSE27427=7.74 × 10−3; odds ratio (OR)=1.28). Interestingly, this association was mainly found among genes with antisense LINE-1s (P-value GSE27427=6.22 × 10−3; OR=1.38). Bioinformatics data suggest that LINE-1 hypomethylation may affect expression of the genes that may contribute to the pathogenesis of SLE. However, additional functional studies of these proposed genes are warranted to prove this hypothesis.
Robert E Johnson - One of the best experts on this subject based on the ideXlab platform.
-
yeast dna repair protein rad5 that promotes instability of simple Repetitive Sequences is a dna dependent atpase
Journal of Biological Chemistry, 1994Co-Authors: Robert E Johnson, Satya Prakash, Louise PrakashAbstract:Abstract The RAD5 gene of Saccharomyces cerevisiae functions in postreplication repair of ultraviolet damaged DNA, and interestingly, it also has a role in increasing the instability of simple Repetitive Sequences in the genome. In contrast to DNA mismatch repair genes which function in maintaining constant length of repeat Sequences, RAD5 promotes alterations in the length of repeat Sequences. In this work, we purify the RAD5 protein to near homogeneity from yeast cells and show that it is a single-stranded DNA-dependent ATPase. The possible roles of RAD5 ATPase in postreplication gap filling and in increasing the incidence of length alterations of repeat Sequences are discussed.
-
saccharomyces cerevisiae rad5 encoded dna repair protein contains dna helicase and zinc binding sequence motifs and affects the stability of simple Repetitive Sequences in the genome
Molecular and Cellular Biology, 1992Co-Authors: Robert E Johnson, Satya Prakash, Samuel T Henderson, Thomas D Petes, Michael Bankmann, Louise PrakashAbstract:rad5 (rev2) mutants of Saccharomyces cerevisiae are sensitive to UV light and other DNA-damaging agents, and RAD5 is in the RAD6 epistasis group of DNA repair genes. To unambiguously define the function of RAD5, we have cloned the RAD5 gene, determined the effects of the rad5 deletion mutation on DNA repair, DNA damage-induced mutagenesis, and other cellular processes, and analyzed the sequence of RAD5-encoded protein. Our genetic studies indicate that RAD5 functions primarily with RAD18 in error-free postreplication repair. We also show that RAD5 affects the rate of instability of poly(GT) repeat Sequences. Genomic poly(GT) Sequences normally change length at a rate of about 10(-4); this rate is approximately 10-fold lower in the rad5 deletion mutant than in the corresponding isogenic wild-type strain. RAD5 encodes a protein of 1,169 amino acids of M(r) 134,000, and it contains several interesting sequence motifs. All seven conserved domains found associated with DNA helicases are present in RAD5. RAD5 also contains a cysteine-rich sequence motif that resembles the corresponding Sequences found in 11 other proteins, including those encoded by the DNA repair gene RAD18 and the RAG1 gene required for immunoglobin gene arrangement. A leucine zipper motif preceded by a basic region is also present in RAD5. The cysteine-rich region may coordinate the binding of zinc; this region and the basic segment might constitute distinct DNA-binding domains in RAD5. Possible roles of RAD5 putative ATPase/DNA helicase activity in DNA repair and in the maintenance of wild-type rates of instability of simple Repetitive Sequences are discussed.
