<i>Sukkula</i>retrotransposon movements in the human genome

Cakmak, B.; Marakli, Sevgi; Gözükırmızı, Nermin

doi:10.1080/13102818.2017.1316684

Cited by 6 publications

(9 citation statements)

References 21 publications

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“…The study conducted by Elkina and colleagues have shown that SIRE1 and BARE-1 are present in the genome of farm animals and have different distribution within genomes. In the previous study of our research group, we determined SIRE1 retrotransposon in the human genome (Cakmak et al, 2017). Table 1 Another study conducted by Metzger and colleagues stated that a selfish endogenous retroelement "Steamer" belonged to soft-shell clam family, also founded within the genome of 19 different bivalve species.…”

Section: Resultsmentioning

confidence: 99%

“…As an example, barley retrotransposons such as BARE-1, Sukkula and SIRE1 have been shown to have active homologues in genomes of other cereals (Bonchev & Parisod, 2013;Cakmak et al, 2015;Cakmak et al, 2017). Recent studies have shown existence of plant retrotransposons in animals (Elkina et al, 2015;Cakmak et al, 2017). The study conducted by Elkina and colleagues have shown that SIRE1 and BARE-1 are present in the genome of farm animals and have different distribution within genomes.…”

Section: Resultsmentioning

confidence: 99%

“…Insertion within or close to a gene could directly disrupt gene function or generate new functions with alternative splicing, alternative promoter control and gene silencing (Xiao et al, 2008;Gonzalez et al, 2017). Recent research demonstrated that retrotransposons are found in virtually all genomes and even that the same retrotransposons could be found in different species (Cakmak et al, 2015;Elkina et al, 2015;Igiebor et al, 2016;Cakmak et al, 2017). Additionally, several retrotransposon studies showed that the same retrotransposon may exhibit polymorphism in different organs within the same organism, especially in plants (Yilmaz et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Origin and distribution of different retrotransposons in different taxa

Guner¹,

Gözükırmızı²

2018

GenApp

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Novel genome analysis technologies enable genomic studies of transposable elements (TEs) in different organisms. Population studies of human genome show thousands of individual TE insertions. These insertions are important source of natural human genetic variation. Researchers are beginning to develop population genomic data sets for evaluating the phenotypic impact of human TE polymorphisms. Because of the evidences of horizontal transfer of retrotransposons between different species genome, in this study we aimed to detect barley retrotransposons (Nikita and BAGY2) in the human genome. Inter retrotransposon amplified polymorphism polymerase chain reaction (IRAP PCR) were used to measure the distribution of Nikita and BAGY2 retroelements in the human genome. Analyses reveals that Nikita and BAGY2 are present in the human genome and show different distribution in the genome. The polymorphism ratios of retroelements suggest that Nikita and BAGY2 have been active retrotransposons in the human genome.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Origin and distribution of different retrotransposons in different taxa

Guner¹,

Gözükırmızı²

2018

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“…We also observed barley specific retrotransposons in endemic Colchium chalcedonicum (Karlık et al, 2019). Recently we were able to find barley specific retrotransposons in human genome (Cakmak et al, 2017. We also tested retrotransposon movements for short term mutagenicity test (Yilmaz et al, 2018).…”

Section: Our Research With Transposonsmentioning

confidence: 99%

Transposons Continue the Amaze

Gözükırmızı

2019

International Journal of Science Letters

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Transposable elements (TEs) were first discovered in maize plants. However, they exist almost in all species with a few exceptions (Plasmodium falciparum, Ashbya gossypii and Kluveromuyces lactis). They are the most important contributors to genome plasticity and evolution and even epigenetic genome regulation. Organisms with large genomes have high transposon percentages. For example, Arabidopsis thaliana has a genome size of 125 Mb which comprises 14% transposons, Homo sapiens (3000 Mb) 45-48.5%, and Hordeum vulgare genome (5300 Mb) has 80%. TEs are classified into two major groups based on their transposition mechanisms: Class I (RNA transposonsretrotransposons) and Class II (DNA transposons). Recent progress in whole-genome sequencing and long-read assembly have resulted in identification of unprecedentedly long transposable units spanning dozens or even hundreds of kilobases, initially in prokaryotic and more recently in eukaryotic systems. All TEs in a cell are named as transposome (mobilome), and transposomics is a new area to work with transposome. Although a number of bioinformatics softwares have recently been developed for the annotation of TEs in sequenced genomes, there are very few computational tools strictly dedicated to the identification of active TEs using genome-wide approaches. In this review article, after a brief introduction and review of the transposable elements, I discussed their effects in gene expression, evolution, recent applications and also share our research on retrotransposons with different organisms.

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“…Therefore, LTR primers designed according to a species can be used to amplify DNA of others. As a result, IRAP gives very valuable information related to the genomes of different species [15,16].…”

Section: Introductionmentioning

confidence: 99%

Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L.

Marakli

2018

Marmara Fen Bilimleri Dergisi

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Transferability of barley retrotransposons (Nikita and Sukkula) were examined in Pimpinella anisum L. seeds by using a retrotransposon-based molecular marker: IRAP (inter-retrotransposon amplified polymorphism). Furthermore, transposons' sequences identified in medically important plants were obtained form NCBI, and multiple alignment analyses were performed to investigate the evolutionary relationships. These two retrotransposons were identified in Pimpinella anisum L., showing homomorphic band profiles. In addition, limited similar sequences were detected as a result of clustal analyses. Till date, no study about retrotransposons evaluation using IRAP as molecular marker has been published in aniseed. Our results are expected to contribute a new perspective for genome architect of medically important plants in addition to aniseed.

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Sukkularetrotransposon movements in the human genome

Cited by 6 publications

References 21 publications

Origin and distribution of different retrotransposons in different taxa

Origin and distribution of different retrotransposons in different taxa

Transposons Continue the Amaze

Transferability of Barley Retrotransposons (Sukkula and Nikita) to Investigate Genetic Structure of Pimpinella anisum L.

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