• SSRs
  • A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic development, and regulation of gene expression. (biomedcentral.com)
  • We have performed a detailed comparative study of the distribution of SSRs in the sequenced genomes of Arabidopsis thaliana and rice. (biomedcentral.com)
  • SSRs in different genic regions - 5'untranslated region (UTR), 3'UTR, exon, and intron - show distinct patterns of distribution both within and between the two genomes. (biomedcentral.com)
  • Especially notable is the much higher density of SSRs in 5'UTRs compared to the other regions and a strong affinity towards trinucleotide repeats in these regions for both rice and Arabidopsis . (biomedcentral.com)
  • Our work provides insight into the evolution and distribution of SSRs in the two sequenced model plant genomes of monocots and dicots. (biomedcentral.com)
  • Our analyses reveal that the distributions of SSRs appear highly non-random and vary a great deal in different regions of the genes in the genomes. (biomedcentral.com)
  • However, recent research has shown that SSRs have many important functions in terms of development, gene regulation, and evolution. (biomedcentral.com)
  • Most recently, Fondon and Garner [ 3 ] have shown that the fast morphological evolution in domesticated dogs is due to the contraction/expansion of SSRs in the coding regions of the Alx-4 and Runx-2 genes. (biomedcentral.com)
  • 12 ] did a more comprehensive survey of SSRs in Arabidopsis and showed that SSRs in general were more favored in upstream regions of genes and that trinucleotide repeats were the most common repeats found in the coding regions. (biomedcentral.com)
  • In this study, MISA was applied to identify overall 179,681 SSRs in maize reference genome B73, with an average distance of 11.46 Kbp. (biomedcentral.com)
  • Our work provided insight into the non-random distribution spatterns and compositions of SSRs in different regions of maize genome, and also developed more polymorphic SSR markers using next-generation sequencing reads. (biomedcentral.com)
  • The genome-wide SSRs polymorphism markers could be useful for genetic analysis and marker-assisted selection in breeding practice, and it was also proved to be high efficient for molecular marker development via next-generation sequencing reads. (biomedcentral.com)
  • repetitive
  • A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 1-6 or more base pairs) are repeated, typically 5-50 times. (wikipedia.org)
  • The residual fifth is moderately to highly repetitive, and can be divided into two types, depending on whether the individual repeat units are dispersed singularly (interspersed repetitive DNA) or clustered together (satellite DNA). (bmj.com)
  • There are several families of interspersed repetitive DNA, although the two largest are known as short and long interspersed nuclear elements (SINEs and LINEs, respectively), 1 and it is to the SINE family that the frequently mentioned Alu repeat belongs. (bmj.com)
  • regulation of gene ex
  • Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression , organization of chromosome architecture , and signals controlling epigenetic inheritance . (wikipedia.org)
  • Nevertheless, several interesting hypotheses exist suggesting that certain microsatellites may exert subtle influences on the regulation of gene expression. (bmj.com)
  • proteins
  • citation needed] Currently, nine neurologic disorders are known to be caused by an increased number of CAG repeats, typically in coding regions of otherwise unrelated proteins. (wikipedia.org)
  • Many are located in non-coding parts of the human genome and therefore do not produce proteins, but they can also be located in regulatory regions and coding regions. (wikipedia.org)
  • For instance, expansion of CAG repeats in the coding region of HD genes in humans can lead to Huntington's disease, most likely through activation of so-called 'toxic' proteins. (biomedcentral.com)
  • mismatch repair
  • Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. (g3journal.org)
  • The mutation rate for DNA mismatch repair null strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. (g3journal.org)
  • These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells. (g3journal.org)
  • DNA mismatch repair is a highly conserved process that maintains the fidelity of genomes by decreasing the mutation rate 100- to 1000-fold ( Kunkel and Erie 2005 ). (g3journal.org)
  • exons
  • Category II expansions tend to be more phenotypically diverse with heterogeneous expansions that are generally small in magnitude, but also found in the exons of genes. (wikipedia.org)
  • It appeared that 92.23% of all known human genes have STRs in their exons and 99% of STR regions are shorter than 33 bp. (biomedcentral.com)
  • Huntington's
  • Category I includes Huntington's disease (HD) and the spinocerebellar ataxias that are caused by a CAG repeat expansion in protein-coding portions of specific genes. (wikipedia.org)
  • The (CTG.CAG)N repeats in the Huntington's disorder (HD) is ELTD1 one of the most highly variable TRS in the human population . (cancer-basics.com)
  • Although the presence of these subtle mechanisms may be beneficial to a whole population, when they go wrong, as is thought to happen in the case of human trinucleotide repeat associated diseases, such as Huntington's disease, the consequences for the individual can be fatal. (bmj.com)
  • STRs
  • We also demonstrate that STRs are significantly overrepresented in disease-related genes in both human and mouse. (biomedcentral.com)
  • These results are preserved when we limit the analysis to STRs outside known longer tandem repeats. (biomedcentral.com)
  • Based on our findings we conclude that STRs represent hypermutable regions in the human genome that are linked to human disease. (biomedcentral.com)
  • Initially, we annotated the human and mouse genomes with STRs (see Figure 1 for an example and Methods for how STRs are identified). (biomedcentral.com)
  • base pairs
  • Haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization creates a zygote ) consist of three billion DNA base pairs , while diploid genomes (found in somatic cells ) have twice the DNA content. (wikipedia.org)
  • The total length of the human genome is over 3 billion base pairs. (wikipedia.org)
  • Some types of satellite DNA in humans are: A repeated pattern can be between 1 base pair long (a mononucleotide repeat) to several thousand base pairs long[citation needed], and the total size of a satellite DNA block can be several megabases without interruption. (wikipedia.org)
  • AT in ATATATATAT) is repeated at least three times, (3) there are only few base pairs that do not match the periodic motif (see Methods). (biomedcentral.com)
  • somatic
  • 2011) reported a somatic retrotransposition event in the intron of Hdac1 , a histone deacetylase which is a known regulator of L1 expression within the human genome, suggesting how a single transposition event might alter the capacity of a given cell to regulate further insertions . (scienceoveracuppa.com)
  • All of these disorders have reported somatic mosaicism within the mutated genes, such that different extremes of expansion are seen in different organ systems. (scienceoveracuppa.com)
  • genetic
  • Although the transfer of a number of genes from these organelles to the nucleus prevents them from living independently, each still possesses genetic material in the form of double stranded DNA. (wikipedia.org)
  • citation needed] Trinucleotide repeat disorders generally show genetic anticipation, where their severity increases with each successive generation that inherits them. (wikipedia.org)
  • They are also used in genetic linkage analysis to locate a gene or a mutation responsible for a given trait or disease. (wikipedia.org)
  • The increasing availability of DNA amplification by PCR at the beginning of the 1990s triggered a large number of studies using the amplification of microsatellites as genetic markers for forensic medicine, for paternity testing, and for positional cloning to find the gene underlying a trait or disease. (wikipedia.org)
  • Overall, our study provides a comprehensive information on cell wall related genes families in sorghum which offers a valuable resource to develop strategies for altering biomass composition by plant breeding and genetic engineering approaches. (frontiersin.org)
  • 4 , 5 So far, many genes have been attributed to cause this disease, thereby revealing its genetic complexity. (arvojournals.org)
  • however, they are extremely useful in such fields as forensic DNA profiling and genetic linkage analysis, which can be used to search for genes involved in a wide range of disorders. (bmj.com)
  • However, when used to refer to the number of repeating units of genetic information that are sufficient to encode the blueprint for something as complex as a human being, it never ceases to amaze me that this number is big enough! (bmj.com)
  • intron
  • If the repeat is present in an intron it can cause toxic effects by forming spherical clusters called RNA foci in cell nuclei. (wikipedia.org)
  • Their distributions within the genome in different regions were non-random, and the density followed in a descending order of UTR, promotor, intron, intergenic and CDS. (biomedcentral.com)
  • disorders
  • These disorders are characterized by autosomal-dominant mode of inheritance (with the exception of spino-bulbar muscular atrophy, which shows X-linked inheritance), midlife onset, a progressive course, and a correlation of the number of CAG repeats with the severity of disease and the age at onset. (wikipedia.org)
  • Some of these strategies have the potential for future use in gene therapy for trinucleotide repeat disorders. (lidsen.com)
  • TRS disorders typically have large and variable repeat expansions that result in multiple tissue dysfunction or degeneration. (cancer-basics.com)
  • Given the common etiology underlying these varied disorders, for some time it had been a mystery to scientists how glutamine expansion tracts could prove toxic. (scienceoveracuppa.com)
  • Such inclusions are associated with toxicity in some of the trinucleotide repeat disorders. (scienceoveracuppa.com)
  • codons
  • Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame (the grouping of the codons), resulting in a completely different translation from the original. (wikipedia.org)
  • variation
  • However, variation in the length of the repeat is common. (wikipedia.org)
  • Exonic structural variation may have a direct influence on gene products, and hence of interest for e.g. resequencing studies. (biomedcentral.com)
  • These data provide insight into the extent and origin of genome-wide intrastrain HSV-1 variation and present useful methods for expansion to in vivo patient infection studies. (nclockservice.com)
  • chromosomal
  • In fact "functional DNA", consisting of transcribed genes and regions involved either in transcriptional regulation or in maintaining chromosomal structure/integrity, is thought to comprise less than a sixth of the total human genome. (bmj.com)
  • transcription
  • We record that repeats possess the to hinder the binding of transcription elements with their consensus series by changed DNA inhaling and exhaling dynamics in closeness from the binding sites. (cancer-basics.com)
  • Transcription factor 4 ( TCF4 ), that encodes for E2-2 protein, a group of E protein transcription factors known for cellular growth and differentiation, is one such gene that has been associated with this disease. (arvojournals.org)
  • deletions
  • We have found that the gain of novel LCRs is frequently associated with repeat expansion whereas the loss of LCRs is more often due to accumulation of amino acid substitutions as opposed to deletions. (biomedsearch.com)
  • In recent years it has been demonstrated that structural variations, such as indels (insertions and deletions), are common throughout the genome, but the implications of structural variations are still not clearly understood. (biomedcentral.com)
  • A bias toward deletions at homopolymers and insertions at (AT) n microsatellites suggests a different mechanism for mismatch generation at these sites. (g3journal.org)
  • phenotype
  • Thus, the phenotype of traits linked to genes found in either chloroplasts or mitochondria are determined exclusively by the maternal parent. (wikipedia.org)
  • species
  • The five chloroplast genomes ranged from 161,072 bp ( Q. baronii ) to 161,237 bp ( Q. dolicholepis ) in length, and their gene organization and order, and GC content, were similar to those of other Fagaceae species. (frontiersin.org)
  • humans
  • While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, the chimpanzees (approximately 4% ) and bonobos . (wikipedia.org)
  • Nevertheless, even focusing as intended upon microsatellites and their relevance to humans, it should become clear that most of these questions remain ones that will require consideration, even if only in passing. (bmj.com)
  • found
  • The expression of fragility was found to be influenced by the TRS enlargement beyond a threshold of copies in tandem. (cancer-basics.com)
  • Overexpression of Mre11p or Rad50p suppresses the inhibition of DSB repair by CAG 98 and significantly increases the average size of expansions found at the recipient locus. (embopress.org)
  • 7 by conducting genome-wide linkage scan and association with 64 multiplex Caucasian families where they identified rs613872 to be coinciding with the FECD2 locus previously found by Sundin and colleagues. (arvojournals.org)
  • They can be found in any genome (both eukaryote and prokaryote) and in any region (protein coding regions and non-coding regions). (biomedcentral.com)
  • human
  • Human genomes include both protein-coding DNA genes and noncoding DNA . (wikipedia.org)
  • The human genome was the first of all vertebrates to be completely sequenced. (wikipedia.org)
  • As of 2012, thousands of human genomes have been completely sequenced, and many more have been mapped at lower levels of resolution. (wikipedia.org)
  • The human homolog of mbl, MBNL1, which was originally identified as binding CUG repeats in RNA, has since been shown to bind CAG (and CCG) repeats as well. (wikipedia.org)
  • Sequential breakdown of the human genome into component DNA types. (bmj.com)
  • study of ancient expansion, contraction, demographic and migration, analysis of possible racial and human evolutionary history. (blogspot.com)
  • LINE-1 (L1) transposable elements are a family of retrotransposons, some of which are still transpositionally active in the human genome. (scienceoveracuppa.com)
  • PolyQ
  • Furthermore, when the CAG repeat was changed to a repeating series of CAACAG (which also translates to polyQ), toxicity was dramatically reduced. (wikipedia.org)