Sequence-Based Estimation of Minisatellite and Microsatellite Repeat Variability
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Retrotransposon- and Microsatellite Sequence-Associated Genomic Changes in Early Generations of a Newly Synthesized Allotetraploid Cucumis 3 Hytivus Chen & Kirkbride
Plant Mol Biol DOI 10.1007/s11103-011-9804-y Retrotransposon- and microsatellite sequence-associated genomic changes in early generations of a newly synthesized allotetraploid Cucumis 3 hytivus Chen & Kirkbride Biao Jiang • Qunfeng Lou • Zhiming Wu • Wanping Zhang • Dong Wang • Kere George Mbira • Yiqun Weng • Jinfeng Chen Received: 27 May 2011 / Accepted: 27 June 2011 Ó Springer Science+Business Media B.V. 2011 Abstract Allopolyploidization is considered an essential generations of a newly synthesized allotetraploid Cucum- evolutionary process in plants that could trigger genomic is 9 hytivus Chen & Kirkbride (2n = 4x = 38) which was shock in allopolyploid genome through activation of tran- derived from crossing between cultivated cucumber scription of retrotransposons, which may be important in C. sativus L. (2n = 2x = 14) and its wild relative C. hystrix plant evolution. Two retrotransposon-based markers, inter- Chakr. (2n = 2x = 24). Extensive genomic changes were retrotransposon amplified polymorphism and retro- observed, most of which involved the loss of parental DNA transposon-microsatellite amplified polymorphism and a fragments and gain of novel fragments in the allotetraploid. microsatellite-based marker, inter simple sequence repeat Among the 28 fragments examined, 24 were lost while four were employed to investigate genomic changes in early were novel, suggesting that DNA sequence elimination is a relatively frequent event during polyploidization in Cucumis. Interestingly, of the 24 lost fragments, 18 were of C. hystrix origin, four were C. sativus-specific, and the Electronic supplementary material The online version of this remaining two were shared by both species, implying that article (doi:10.1007/s11103-011-9804-y) contains supplementary material, which is available to authorized users. -
Frequent Homozygous Deletions in the FRA3B Region in Tumor Cell Lines Still Leave the FHIT Exons Intact
Oncogene (1998) 16, 635 ± 642 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 Frequent homozygous deletions in the FRA3B region in tumor cell lines still leave the FHIT exons intact Liang Wang1, John Darling1, Jin-San Zhang1, Chi-Ping Qian1, Lynn Hartmann2, Cheryl Conover2, Robert Jenkins1 and David I Smith1 1Division of Experimental Pathology, Department of Laboratory Medicine and Pathology; and 2Department of Medical Oncology, Mayo Clinic/Foundation, 200 First Street, SW, Rochester, Maine 55902, USA FRA3B at human chromosomal band 3p14.2 is the most Soreng, 1984). However, whether or not fragile sites active common fragile site in the human genome. The play a causative role in these structural chromosome molecular mechanism of fragility at this region remains alterations has yet to be determined. unknown but does not involve expansion of a trinucleo- FRA3B, at chromosome band 3p14.2, is the most tide or minisatellite repeat as has been observed for highly inducible fragile site in the human genome several of the cloned rare fragile sites. Deletions and (Smeets et al., 1986). The constitutive familial renal cell rearrangements at FRA3B have been observed in a carcinoma-associated translocation t(3;8)(p14.2;q24) number of distinct tumors. The recently identi®ed (hRCC) (Cohen et al., 1979) was localized immedi- putative tumor suppressor gene FHIT spans FRA3B, ately centromeric of FRA3B (Paradee et al., 1995; and various groups have reported identifying deletions in Boldog et al., 1993). Structural rearrangements and this gene in dierent tumors. Using a high density of deletions at FRA3B were reported in a variety of PCR ampli®able markers within FRA3B searching for histologically dierent cancers including lung (Todd et deletions in the FRA3B region, we have analysed 21 al., 1997), breast (Panagopoulos et al., 1996), tumor cell lines derived from renal cell, pancreatic, and esophageal (Wang et al., 1996), ovarian (Ehlen et al., ovarian carcinomas. -
Young, L.J., & Hammock E.A.D. (2007)
Update TRENDS in Genetics Vol.23 No.5 Research Focus On switches and knobs, microsatellites and monogamy Larry J. Young1 and Elizabeth A.D. Hammock2 1 Department of Psychiatry and Behavioral Sciences, Center for Behavioral Neuroscience, 954 Gatewood Road, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA 2 Vanderbilt Kennedy Center and Department of Pharmacology, 465 21st Avenue South, MRBIII, Room 8114, Vanderbilt University, Nashville, TN 37232, USA Comparative studies in voles have suggested that a formation. In male prairie voles, infusion of vasopressin polymorphic microsatellite upstream of the Avpr1a locus facilitates the formation of partner preferences in the contributes to the evolution of monogamy. A recent study absence of mating [7]. The distribution of V1aR in the challenged this hypothesis by reporting that there is no brain differs markedly between the socially monogamous relationship between microsatellite structure and mon- and socially nonmonogamous vole species [8]. Site-specific ogamy in 21 vole species. Although the study demon- pharmacological manipulations and viral-vector-mediated strates that the microsatellite is not a universal genetic gene-transfer experiments in prairie, montane and mea- switch that determines mating strategy, the findings do dow voles suggest that the species differences in Avpr1a not preclude a substantial role for Avpr1a in regulating expression in the brain underlie the species differences in social behaviors associated with monogamy. social bonding among these three closely related species of vole [3,6,9,10]. Single genes and social behavior Microsatellites and monogamy The idea that a single gene can markedly influence Analysis of the Avpr1a loci in the four vole species complex social behaviors has recently received consider- mentioned so far (prairie, montane, meadow and pine voles) able attention [1,2]. -
Evaluation of the Effects of Sequence Length and Microsatellite Instability
Int. J. Biol. Sci. 2019, Vol. 15 2641 Ivyspring International Publisher International Journal of Biological Sciences 2019; 15(12): 2641-2653. doi: 10.7150/ijbs.37152 Research Paper Evaluation of the effects of sequence length and microsatellite instability on single-guide RNA activity and specificity Changzhi Zhao1*, Yunlong Wang2*, Xiongwei Nie1, Xiaosong Han1, Hailong Liu1, Guanglei Li1, Gaojuan Yang1, Jinxue Ruan1, Yunlong Ma1, Xinyun Li1, 3, Huijun Cheng1, Shuhong Zhao1, 3, Yaping Fang2, Shengsong Xie1, 3 1. Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, P. R. China; 2. Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China; 3. The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, P. R. China. *The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. Corresponding authors: Shengsong Xie, Tel: 086-027-87387480; Fax: 086-027-87280408; Email: [email protected]; Yaping Fang, Tel: 86-28-87285078; Fax: 86-28-87284285; Email: [email protected]. © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2019.07.21; Accepted: 2019.09.02; Published: 2019.10.03 Abstract Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology is effective for genome editing and now widely used in life science research. -
Repetitive Elements in Humans
International Journal of Molecular Sciences Review Repetitive Elements in Humans Thomas Liehr Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany; [email protected] Abstract: Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called ‘genetic background’, being able to at least potentially influence disease susceptibilities. Here, the known ‘bad boys’ among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well. Keywords: variable numbers of tandem repeats (VNTRs); microsatellites; minisatellites; small-scale repetitive elements (SSREs); chromosomal heteromorphisms (CHs); higher-order repeat (HOR); retroviral DNA 1. Introduction Citation: Liehr, T. Repetitive In humans, like in other higher species, the genome of one individual never looks 100% Elements in Humans. Int. J. Mol. Sci. alike to another one [1], even among those of the same gender or between monozygotic 2021, 22, 2072. -
MNS16A Tandem Repeat Minisatellite of Human Telomerase Gene: Functional Studies in Colorectal, Lung and Prostate Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 17), pp: 28021-28027 Research Paper MNS16A tandem repeat minisatellite of human telomerase gene: functional studies in colorectal, lung and prostate cancer Philipp Hofer1, Cornelia Zöchmeister1, Christian Behm1, Stefanie Brezina1, Andreas Baierl2, Angelina Doriguzzi1, Vanita Vanas1, Klaus Holzmann1, Hedwig Sutterlüty- Fall1, Andrea Gsur1 1Medical University of Vienna, Institute of Cancer Research, A-1090 Vienna, Austria 2University of Vienna, Department of Statistics and Operations Research, A-1010 Vienna, Austria Correspondence to: Andrea Gsur, email: [email protected] Keywords: genetic variation, MNS16A, functional polymorphism, telomerase, TERT regulation Received: September 23, 2016 Accepted: February 21, 2017 Published: March 03, 2017 Copyright: Hofer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT MNS16A, a functional polymorphic tandem repeat minisatellite, is located in the promoter region of an antisense transcript of the human telomerase reverse transcriptase gene. MNS16A promoter activity depends on the variable number of tandem repeats (VNTR) presenting varying numbers of transcription factor binding sites for GATA binding protein 1. Although MNS16A has been investigated in multiple cancer epidemiology studies with incongruent findings, functional data of only two VNTRs (VNTR-243 and VNTR-302) were available thus far, linking the shorter VNTR to higher promoter activity. For the first time, we investigated promoter activity of all six VNTRs of MNS16A in cell lines of colorectal, lung and prostate cancer using Luciferase reporter assay. -
Genome-Wide Mapping and Characterization of Microsatellites In
www.nature.com/scientificreports OPEN Genome-wide mapping and characterization of microsatellites in the swamp eel genome Received: 14 February 2017 Zhigang Li, Feng Chen, Chunhua Huang, Weixin Zheng, Chunlai Yu, Hanhua Cheng & Accepted: 26 April 2017 Rongjia Zhou Published: xx xx xxxx We described genome-wide screening and characterization of microsatellites in the swamp eel genome. A total of 99,293 microsatellite loci were identified in the genome with an overall density of 179 microsatellites per megabase of genomic sequences. The dinucleotide microsatellites were the most abundant type representing 71% of the total microsatellite loci and the AC-rich motifs were the most recurrent in all repeat types. Microsatellite frequency decreased as numbers of repeat units increased, which was more obvious in long than short microsatellite motifs. Most of microsatellites were located in non-coding regions, whereas only approximately 1% of the microsatellites were detected in coding regions. Trinucleotide repeats were most abundant microsatellites in the coding regions, which represented amino acid repeats in proteins. There was a chromosome-biased distribution of microsatellites in non-coding regions, with the highest density of 203.95/Mb on chromosome 8 and the least on chromosome 7 (164.06/Mb). The most abundant dinucleotides (AC)n was mainly located on chromosome 8. Notably, genomic mapping showed that there was a chromosome-biased association of genomic distributions between microsatellites and transposon elements. Thus, the novel dataset of microsatellites in swamp eel provides a valuable resource for further studies on QTL-based selection breeding, genetic resource conservation and evolutionary genetics. Swamp eel (Monopterus albus) taxonomically belongs to teleosts, the family Synbranchidae of the order Synbranchiformes (Neoteleostei, Teleostei, and Vertebrata). -
Identification and Characterization of a Minisatellite Contained Within A
Klein et al. Mobile DNA (2015) 6:18 DOI 10.1186/s13100-015-0049-1 RESEARCH Open Access Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis Brian A. Klein1,2, Tsute Chen2, Jodie C. Scott2, Andrea L. Koenigsberg1, Margaret J. Duncan2 and Linden T. Hu1* Abstract Background: Repetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes. Such elements are known to be involved in transcriptional regulation, host-pathogen interactions and genome evolution. Results: We identified a minisatellite contained within a miniature inverted-repeat transposable element (MITE) in Porphyromonas gingivalis.TheP. gingivalis minisatellite and associated MITE, named ‘BrickBuilt’, comprises a tandemly repeating twenty-three nucleotide DNA sequence lacking spacer regions between repeats, and with flanking ‘leader’ and ‘tail’ subunits that include small inverted-repeat ends. Forms of the BrickBuilt MITE are found 19 times in thegenomeofP. gingivalis strain ATCC 33277, and also multiple times within the strains W83, TDC60, HG66 and JCVI SC001. BrickBuilt is always located intergenically ranging between 49 and 591 nucleotides from the nearest upstream and downstream coding sequences. Segments of BrickBuilt contain promoter elements with bidirectional transcription capabilities. Conclusions: We performed a bioinformatic analysis of BrickBuilt utilizing existing whole genome sequencing, microarray and RNAseq data, as well as performing in vitro promoter probe assays to determine potential roles, mechanisms and regulation of the expression of these elements and their affect on surrounding loci. The multiplicity, localization and limited host range nature of MITEs and MITE-like elements in P. -
Unfolding of Quadruplex Structure in the G-Rich Strand of the Minisatellite Repeat by the Binding Protein UP1
Unfolding of quadruplex structure in the G-rich strand of the minisatellite repeat by the binding protein UP1 Hirokazu Fukuda*, Masato Katahira†, Naoto Tsuchiya*, Yoshiaki Enokizono†, Takashi Sugimura*, Minako Nagao*, and Hitoshi Nakagama*‡ *Biochemistry Division, National Cancer Center Research Institute, 1-1, Tsukiji 5, Chuo-ku, Tokyo 104-0045, Japan; and †Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan Contributed by Takashi Sugimura, July 31, 2002 The mouse hypervariable minisatellite (MN) Pc-1 consists of tan- the other four, MNBP-D, MNBP-E, MNBP-F, and MNBP-G, to dem repeats of d(GGCAG) and flanked sequences. We have previ- the complementary C-rich strand. ously demonstrated that single-stranded d(GGCAG)n folds into the In this article, we document isolation of cDNA clones encod- intramolecular folded-back quadruplex structure under physiolog- ing MNBP-B and characterization of a recombinant MNBP-B. ical conditions. Because DNA polymerase progression in vitro is Sequences of seven proteolytic peptides of purified MNBP-B blocked at the repeat, the characteristic intramolecular quadruplex were determined, and cDNA clones were subsequently isolated. structure of the repeat, at least in part, could be responsible for the MNBP-B was revealed to be identical to the single-stranded hypermutable feature of Pc-1 and other MNs with similar repetitive DNA binding protein, UP1 (17), which is a proteolytic product units. On the other hand, we have isolated six MN Pc-1 binding corresponding to the N-terminal 195 aa of the 34-kDa hetero- proteins (MNBPs) from nuclear extracts of NIH 3T3 cells. -
Variation in MHC Class II B Genes in Marbled Murrelets: Implications for Delineating Conservation Units C
bs_bs_banner Animal Conservation. Print ISSN 1367-9430 Variation in MHC class II B genes in marbled murrelets: implications for delineating conservation units C. Vásquez-Carrillo1*, V. Friesen2, L. Hall3 & M. Z. Peery1 1 Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, USA 2 Department of Biology, Queen’s University, Kingston, Ontario Canada 3 Department of Environmental Science, Policy, and Management, University of California-Berkeley, Berkeley, CA, USA Keywords Abstract adaptive genetic variation; major histocompatibility complex; marbled Conserving genetic variation is critical for maintaining the evolutionary potential murrelet; conservation units; neutral genetic and viability of a species. Genetic studies seeking to delineate conservation units, variation; selection. however, typically focus on characterizing neutral genetic variation and may not identify populations harboring local adaptations. Here, variation at two major Correspondence histocompatibility complex (MHC) class II B genes was characterized in four Catalina Vásquez-Carrillo, Department of populations of marbled murrelets Brachyramphus marmoratus, a threatened Biology, University of Miami, 1301 Memorial species in which little neutral genetic population structure has been detected. High Drive, Coral Gables, FL, 33124, USA. diversity, as well as evidence of balancing selection, was detected in exon 2 of these Tel: 305-284-3013; Fax: 305 284 3039 genes. Genetic population structure based on MHC markers was uncorrelated to Email: [email protected] genetic structure estimated with neutral markers, suggesting that selection played a more important role in shaping population structure at these markers than Editor: Jeff Johnson genetic drift. A high proportion of alleles and inferred peptides were unique to a single population, with the Aleutian Islands and southeast Alaska having the Received 15 March 2013; accepted 1 highest richness of both. -
FANCJ Suppresses Microsatellite Instability and Lymphomagenesis Independent of the Fanconi Anemia Pathway
Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press FANCJ suppresses microsatellite instability and lymphomagenesis independent of the Fanconi anemia pathway Kenichiro Matsuzaki,1 Valerie Borel,1 Carrie A. Adelman,1 Detlev Schindler,2 and Simon J. Boulton1 1DNA Damage Response Laboratory, Clare Hall Laboratories, The Francis Crick Institute, South Mimms EN6 3LD, United Kingdom; 2Department of Human Genetics, Biozentrum, University of Wurzburg, 97074 Wurzburg, Germany Microsatellites are short tandem repeat sequences that are highly prone to expansion/contraction due to their propensity to form non-B-form DNA structures, which hinder DNA polymerases and provoke template slippage. Although error correction by mismatch repair plays a key role in preventing microsatellite instability (MSI), which is a hallmark of Lynch syndrome, activities must also exist that unwind secondary structures to facilitate replication fidelity. Here, we report that Fancj helicase-deficient mice, while phenotypically resembling Fanconi anemia (FA), are also hypersensitive to replication inhibitors and predisposed to lymphoma. Whereas metabolism of G4-DNA − − structures is largely unaffected in Fancj / mice, high levels of spontaneous MSI occur, which is exacerbated by − − replication inhibition. In contrast, MSI is not observed in Fancd2 / mice but is prevalent in human FA-J patients. Together, these data implicate FANCJ as a key factor required to counteract MSI, which is functionally distinct from its role in the FA pathway. [Keywords: DNA repair; FANCJ; Fanconi anemia; genome stability; microsatellite instability] Supplemental material is available for this article. Received September 30, 2015; revised version accepted November 13, 2015. Maintenance of genome integrity during DNA replication which are caused by mutations in DNA mismatch repair is of vital importance to ensure that daughter cells inherit (MMR) genes. -
Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene As Molecular Biomarker of Epilepsy. Sex Diff
International Journal of Molecular Sciences Article Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene as Molecular Biomarker of Epilepsy. Sex Differences in Seizure Types and Symptoms Irina O. Suchkova 1 , Elena V. Borisova 2 and Eugene L. Patkin 1,* 1 Laboratory of Molecular Cytogenetics of Mammalian Development, Department of Molecular Genetics, Institute of Experimental Medicine of the Russian Academy of Sciences, St. Petersburg 197376, Russia; [email protected] 2 Department of Neurology, Clinic of Institute of Experimental Medicine, St. Petersburg 197376, Russia; [email protected] * Correspondence: [email protected] Received: 9 November 2020; Accepted: 27 November 2020; Published: 2 December 2020 Abstract: Epilepsy is a neurological disease with different clinical forms and inter-individuals heterogeneity, which may be associated with genetic and/or epigenetic polymorphisms of tandem-repeated noncoding DNA. These polymorphisms may serve as predictive biomarkers of various forms of epilepsy. ACAP3 is the protein regulating morphogenesis of neurons and neuronal migration and is an integral component of important signaling pathways. This study aimed to carry out an association analysis of the length polymorphism and DNA methylation of the UPS29 minisatellite of the ACAP3 gene in patients with epilepsy. We revealed an association of short UPS29 alleles with increased risk of development of symptomatic and cryptogenic epilepsy in women, and also with cerebrovascular pathologies, structural changes in the brain, neurological status, and the clinical pattern of seizures in both women and men. The increase of frequency of hypomethylated UPS29 alleles in men with symptomatic epilepsy, and in women with both symptomatic and cryptogenic epilepsy was observed.