Dieses Ergebnis aus BASE kann Gästen nicht angezeigt werden. Login für vollen Zugriff.

Here and there: the double-side transgene localization ; Здесь и там: двусторонняя локализация интеграций трансгена

Title:	Here and there: the double-side transgene localization ; Здесь и там: двусторонняя локализация интеграций трансгена
Authors:	P. A. Salnikov; A. A. Khabarova; G. S. Koksharova; R. V. Mungalov; P. S. Belokopytova; I. E. Pristyazhnuk; A. R. Nurislamov; P. Somatich; M. M. Gridina; V. S. Fishman; П. А. Сальников; А. А. Хабарова; Г. С. Кокшарова; Р. В. Мунгалов; П. С. Белокопытова; И. Е. Пристяжнюк; А. Р. Нурисламов; П Соматич; М. М. Гридина; В. С. Фишман
Contributors:	We gratefully thank the Center for Shared Use of Microscopic Analysis of Biological Objects SB RAS and Center for Shared Use of Flow Cytometry SB RAS for providing metaphase chromosomes analysis and FACS sorting facilities (supported by budget project No. 0259-2021- 0016). Computational data analysis was performed on the high-throughput nodes of the Novosibirsk State University. Generation of plasmid vectors, derivation, and expansion of cell lines, molecular analysis, and NGS sequencing were supported by Russian Science Foundation grant No. 19-74-00102. Conflict of interest. The authors declare no conflict of interest
Source:	Vavilov Journal of Genetics and Breeding; Том 25, № 6 (2021); 607-612 ; Вавиловский журнал генетики и селекции; Том 25, № 6 (2021); 607-612 ; 2500-3259 ; 10.18699//VJ21.06
Publisher Information:	Institute of Cytology and Genetics of Siberian Branch of the RAS
Publication Year:	2021
Collection:	Vavilov Journal of Genetics and Breeding / Вавиловский журнал генетики и селекции
Subject Terms:	транспозон «Спящая красавица»; genome-wide screening; transgene mapping; sleeping beauty transposon; полногеномный скрининг; локализация трансгена
Description:	Random transgene integration is a powerful tool for developing new genome-wide screening approaches. These techniques have already been used for functional gene annotation by transposon-insertion sequencing, for identification of transcription factor binding sites and regulatory sequences, and for dissecting chromatin position effects. Precise localization of transgenes and accurate artifact filtration are essential for this type of method. To date, many mapping assays have been developed, including Inverse-PCR, TLA, LAM-PCR, and splinkerette PCR. However, none of them is able to ensure localization of both transgene’s flanking regions simultaneously, which would be necessary for some applications. Here we proposed a cheap and simple NGS-based approach that overcomes this limitation. The developed assay requires using intentionally designed vectors that lack recognition sites of one or a set of restriction enzymes used for DNA fragmentation. By looping and sequencing these DNA fragments, we obtain special data that allows us to link the two flanking regions of the transposon. This can be useful for precise insertion mapping and for screening approaches in the field of chromosome engineering, where chromosomal recombination events between transgenes occur in a cell population. To demonstrate the method’s feasibility, we applied it for mapping SB transposon integration in the human HAP1 cell line. Our technique allowed us to efficiently localize genomic transposon integrations, which was confirmed via PCR analysis. For practical application of this approach, we proposed a set of recommendations and a normalization strategy. The developed method can be used for multiplex transgene localization and detection of rearrangements between them. ; Полногеномные скрининговые методы, основанные на случайной интеграции экзогенных генетических конструкций, – новейший класс инструментов, открывающий возможности для изучения широкого спектра геномных процессов. Данный подход уже был применен к функциональному аннотированию ...
Document Type:	article in journal/newspaper
File Description:	application/pdf
Language:	English
Relation:	https://vavilov.elpub.ru/jour/article/view/3132/1542; Akhtar W., de Jong J., Pindyurin A.V., Pagie L., Meuleman W., de Ridder J., Berns A., Wessels L.F., van Lohuizen M., van Steensel B. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell. 2013;154(4):914-927. DOI 10.1016/j.cell.2013.07.018.; Cain A.K., Barquist L., Goodman A.L., Paulsen I.T., Parkhill J., van Opijnen T. A decade of advances in transposon-insertion sequencing. Nat. Rev. Genet. 2020;21(9):526-540. DOI 10.1038/s41576-020-0244-x.; de Vree P.J., de Wit E., Yilmaz M., van de Heijning M., Klous P., Verstegen M.J., Wan Y., Teunissen H., Krijger P.H., Geeven G., Eijk P.P., Sie D., Ylstra B., Hulsman L.O., van Dooren M.F., van Zutven L.J., van den Ouweland A., Verbeek S., van Dijk K.W., Cornelissen M., Das A.T., Berkhout B., Sikkema-Raddatz B., van den Berg E., van der Vlies P., Weening D., den Dunnen J.T., Matusiak M., Lamkanfi M., Ligtenberg M.J., ter Brugge P., Jonkers J., Foekens J.A., Martens J.W., van der Luijt R., van Amstel H.K., van Min M., Splinter E., de Laat W. Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping. Nat. Biotechnol. 2014;32(10):1019-1025. DOI 10.1038/nbt.2959.; Deutschbauer A., Price M.N., Wetmore K.M., Shao W., Baumohl J.K., Xu Z., Nguyen M., Tamse R., Davis R.W., Arkin A.P. Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet. 2011;7(11):e1002385. DOI 10.1371/journal.pgen.1002385.; Dymond J., Boeke J. The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Bioeng. Bugs. 2012;3(3):168-171. DOI 10.4161/bbug.19543.; Francke U., Hsieh C.L., Kelly D., Lai E., Popko B. Induced reciprocal translocation in transgenic mice near sites of transgene integration. Mamm. Genome. 1992;3(4):209-126. DOI 10.1007/BF00355721.; Friedrich M.J., Rad L., Bronner I.F., Strong A., Wang W., Weber J., Mayho M., Ponstingl H., Engleitner T., Grove C., Pfaus A., Saur D., Cadiñanos J., Quail M.A., Vassiliou G.S., Liu P., Bradley A., Rad R. Genome-wide transposon screening and quantitative insertion site sequencing for cancer gene discovery in mice. Nat. Protoc. 2017; 12(2):289-309. DOI 10.1038/nprot.2016.164.; Gabriel R., Kutschera I., Bartholomae C.C., von Kalle C., Schmidt M. Linear amplification mediated PCR-localization of genetic elements and characterization of unknown flanking DNA. J. Vis. Exp. 2014; (88):e51543. DOI 10.3791/51543.; Goh K.G.K., Phan M.D., Forde B.M., Chong T.M., Yin W.F., Chan K.G., Ulett G.C., Sweet M.J., Beatson S.A., Schembri M.A. Genome-wide discovery of genes required for capsule production by uropathogenic Escherichia coli. mBio. 2017;8(5):e01558-17. DOI 10.1128/mBio.01558-17.; Goodman A.L., Wu M., Gordon J.I. Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nat. Protoc. 2011;6(12):1969-1980. DOI 10.1038/nprot.2011.417.; Hochrein L., Mitchell L.A., Schulz K., Messerschmidt K., MuellerRoeber B. L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast. Nat. Commun. 2018;9(1):1931. DOI 10.1038/s41467-017-02208-6.; Laboulaye M.A., Duan X., Qiao M., Whitney I.E., Sanes J.R. Mapping transgene insertion sites reveals complex interactions between mouse transgenes and neighboring endogenous genes. Front. Mol. Neurosci. 2018;11:385. DOI 10.3389/fnmol.2018.00385.; Li H., Durbin R. Fast and accurate short read alignment with BurrowsWheeler transform. Bioinformatics. 2009;25(14):1754-1760. DOI 10.1093/bioinformatics/btp324.; Li S., Jia S., Hou L., Nguyen H., Sato S., Holding D., Cahoon E., Zhang C., Clemente T., Yu B. Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy. J. Exp. Bot. 2019; 70(15):3825-3833. DOI 10.1093/jxb/erz202.; Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011;17:10-12. DOI 10.14806/ej.17.1.200.; Moudgil A., Wilkinson M.N., Chen X., He J., Cammack A.J., Vasek M.J., Lagunas T.J., Qi Z.,Lalli M.A., Guo C., Morris S.A., Dougherty J.D., Mitra R.D. Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells. Cell. 2020;182(4):992-1008.e21. DOI 10.1016/ j.cell.2020.06.037.; Nicholls P.K., Bellott D.W., Cho T.J., Pyntikova T., Page D.C. Locating and characterizing a transgene integration site by nanopore sequencing. G3 (Bethesda). 2019;9(5):1481-1486. DOI 10.1534/g3.119.300582.; Park D., Park S.H., Ban Y.W., Kim Y.S., Park K.C., Kim N.S., Kim J.K., Choi I.Y. A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data. BMC Biotechnol. 2017;17(1):67. DOI 10.1186/s12896-017-0386-x.; Pindyurin A.V., de Jong J., Akhtar W. TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes. Genomics. 2015;106(3):171-177. DOI 10.1016/j.ygeno.2015.06.009.; Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-842. DOI 10.1093/bioinformatics/btq033.; Robinson J.T., Thorvaldsdóttir H., Winckler W., Guttman M., Lander E.S., Getz G., Mesirov J.P. Integrative genomics viewer. Nat. Biotechnol. 2011;29(1):24-26. DOI 10.1038/nbt.1754.; Smith A.J., De Sousa M.A., Kwabi-Addo B., Heppell-Parton A., Impey H., Rabbitts P. A site-directed chromosomal translocation induced in embryonic stem cells by Cre-loxP recombination. Nat. Genet. 1995;9(4):376-385. DOI 10.1038/ng0495-376.; Uemura M., Niwa Y., Kakazu N., Adachi N., Kinoshita K. Chromosomal manipulation by site-specific recombinases and fluorescent protein-based vectors. PLoS One. 2010;5(3):e9846. DOI 10.1371/journal.pone.0009846.; Wang H., Mayhew D., Chen X., Johnston M., Mitra R.D. “Calling cards” for DNA-binding proteins in mammalian cells. Genetics. 2012;190(3):941-949. DOI 10.1534/genetics.111.137315.; Wang W., Bartholomae C.C., Gabriel R., Deichmann A., Schmidt M. The LAM-PCR method to sequence LV integration sites. Methods Mol. Biol. 2016;1448:107-120. DOI 10.1007/978-1-4939-3753-0_9.; Zastrow-Hayes G.M., Lin H., Sigmund A.L., Hoffman J.L., Alarcon C.M., Hayes K.R., Richmond T.A., Jeddeloh J.A., May G.D., Beatty M.K. Southern-by-sequencing: A robust screening approach for molecular characterization of genetically modified crops. Plant Genome. 2015;8(1):1-15. DOI 10.3835/plantgenome2014.08.0037.; Zhang R., Yin Y., Zhang Y., Li K., Zhu H., Gong Q., Wang J., Hu X., Li N. Molecular characterization of transgene integration by nextgeneration sequencing in transgenic cattle. PLoS One. 2012;7(11): e50348. DOI 10.1371/journal.pone.0050348.; https://vavilov.elpub.ru/jour/article/view/3132
DOI:	10.18699/VJ21.068
Availability:	https://vavilov.elpub.ru/jour/article/view/3132; https://doi.org/10.18699/VJ21.068
Rights:	Authors who publish with this journal agree to the following terms:Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access). ; Авторы, публикующие в данном журнале, соглашаются со следующим:Авторы сохраняют за собой авторские права на работу и предоставляют журналу право первой публикации работы на условиях лицензии Creative Commons Attribution License, которая позволяет другим распространять данную работу с обязательным сохранением ссылок на авторов оригинальной работы и оригинальную публикацию в этом журнале.Авторы сохраняют право заключать отдельные контрактные договорённости, касающиеся не-эксклюзивного распространения версии работы в опубликованном здесь виде (например, размещение ее в институтском хранилище, публикацию в книге), со ссылкой на ее оригинальную публикацию в этом журнале.Авторы имеют право размещать их работу в сети Интернет (например в институтском хранилище или персональном сайте) до и во время процесса рассмотрения ее данным журналом, так как это может привести к продуктивному обсуждению и большему количеству ссылок на данную работу (См. The Effect of Open Access).
Accession Number:	edsbas.DF9BEABD
Database:	BASE