Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV) with small insertions and deletions (INDELs) sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS) with LIM-kinase 1-dependent cognitive defects. The Drosophila melanogaster mutant agnts3 has unusual architecture of the agnostic locus harboring LIMK1: it is a hotspot of chromosome breaks, ectopic contacts, underreplication, and recombination. Here, we present the analysis of LIMK1-containing locus sequencing data in agnts3 and three D. melanogaster wild-type strains-Canton-S, Berlin, and Oregon-R. We found multiple strain-specific SVs, namely, single base changes and small INDEls. The specific feature of agnts3 is 28 bp A/T-rich insertion in intron 1 of LIMK1 and the insertion of mobile S-element from Tc1/mariner superfamily residing ~460 bp downstream LIMK1 3'UTR. Neither of SVs leads to amino acid substitutions in agnts3 LIMK1. However, they apparently affect the nucleosome distribution, non-canonical DNA structure formation and transcriptional factors binding. Interestingly, the overall expression of miRNAs including the biomarkers for human neurological diseases, is drastically reduced in agnts3 relative to the wild-type strains. Thus, LIMK1 DNA structure per se, as well as the pronounced changes in total miRNAs profile, probably lead to LIMK1 dysregulation and complex behavioral dysfunctions observed in agnts3 making this mutant a simple plausible Drosophila model for WBS.

Department of Biochemical Genetics of Animals Institute of Molecular Genetics Russian Academy of SciencesMoscow Russia

Department of Biophysical Chemistry and Molecular Oncology Institute of Biophysics Academy of Sciences of the Czech RepublicBrno Czechia

Department of Human and Animal Anatomy and Physiology Herzen State Pedagogical UniversitySt Petersburg Russia

Department of Molecular Mechanisms of Biological Adaptation Engelhardt Institute of Molecular Biology Russian Academy of SciencesMoscow Russia

Department of Molecular Mechanisms of Development Koltzov Institute of Developmental Biology Russian Academy of SciencesMoscow Russia

Department of Neurogenetics Pavlov Institute of Physiology Russian Academy of SciencesSt Petersburg Russia

Zobrazit více v PubMed

Arnold K., Bordoli L., Kopp J., Schwede T. (2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195–201. 10.1093/bioinformatics/bti770 PubMed DOI

Bacolla A., Jaworski A., Larson J., Jakupciak J., Chuzhanova N., Abeysinghe S., et al. . (2004). Breakpoints of gross deletions coincide with non-B DNA conformations. Proc. Natl. Acad. Sci. U.S.A. 101, 14162–14167. 10.1073/pnas.0405974101 PubMed DOI PMC

Belyaeva E., Zhimulev I., Volkova E., Alekseyenko A., Moshkin Y., Koryakov D. (1998). Su(UR)ES: a gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proc. Natl. Acad. Sci. U.S.A. 95, 7532–7537. 10.1073/pnas.95.13.7532 PubMed DOI PMC

Bhattacharya A., Ziebarth J., Cui Y. (2012). Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PLoS ONE 7:e46176. 10.1371/journal.pone.0046176 PubMed DOI PMC

Brázda V., Kolomazník J., Lýsek J., Hároníková L., Coufal J., Št'astný J. (2016). Palindrome analyser - A new web-based server for predicting and evaluating inverted repeats in nucleotide sequences. Biochem. Biophys. Res. Commun. 478, 1739–1745. 10.1016/j.bbrc.2016.09.015 PubMed DOI

Brázda V., Laister R., Jagelská E., Arrowsmith C. (2011). Cruciform structures are a common DNA feature important for regulating biological processes. BMC Mol. Biol. 12:33. 10.1186/1471-2199-12-33 PubMed DOI PMC

Cao D.-D., Li L., Chan W.-Y. (2016). MicroRNAs: key regulators in the central nervous system and their implication in neurological diseases. Int. J. Mol. Sci. 17:E842. 10.3390/ijms17060842 PubMed DOI PMC

Carvalho C., Lupski J. (2016). Mechanisms underlying structural variant formation in genomic disorders. Nat. Rev. Genet. 17, 224–238. 10.1038/nrg.2015.25 PubMed DOI PMC

Chawla G., Sokol N. (2012). Hormonal activation of let-7-C microRNAs via EcR is required for adult Drosophila melanogaster morphology and function. Development. 139, 1788–1797. 10.1242/dev.077743 PubMed DOI PMC

Chen D., Fu L.-Y., Zhang Z., Li G., Zhang H., Jiang L., et al. . (2014). Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res. 42, 3028–3043. 10.1093/nar/gkt1294 PubMed DOI PMC

Cordaux R., Udit S., Batzer M., Feschotte C. (2006). Birth of a chimeric primate gene by capture of the transposase gene from a mobile element. Proc. Natl. Acad. Sci. U.S.A. 103, 8101–8106. 10.1073/pnas.0601161103 PubMed DOI PMC

Coufal J., Jagelská E., Liao J., Brázda V. (2013). Preferential binding of p53 tumor suppressor to p21 promoter sites that contain inverted repeats capable of forming cruciform structure. Biochem. Biophys. Res. Commun. 441, 83–88. 10.1016/j.bbrc.2013.10.015 PubMed DOI

Cridland J., Thornton K., Long A. (2015). Gene expression variation in Drosophila melanogaster due to rare transposable element insertion alleles of large effect. Genetics 199, 85–93. 10.1534/genetics.114.170837 PubMed DOI PMC

Cusco I., Corominas R., Bayés M., Flores R., Rivera-Brugués N., Campuzano V., et al. . (2008). Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion. Genome Res. 18, 683–694. 10.1101/gr.073197.107 PubMed DOI PMC

Deniz O., Flores O., Battistini F., Pérez A., Soler-López M., Orozco M. (2011). Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics 12:489. 10.1186/1471-2164-12-489 PubMed DOI PMC

Feng Y., Huang W., Meng W., Jegga A. G., Wang Y., Cai W., et al. . (2014). Heat shock improves Sca-1+ stem cell survival and directs ischemic cardiomyocytes toward a prosurvival phenotype via exosomal transfer: a critical role for HSF1/miR-34a/HSP70 pathway. Stem Cells 32, 462–472. 10.1002/stem.1571 PubMed DOI PMC

Feschotte C. (2008). Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9, 397–405. 10.1038/nrg2337 PubMed DOI PMC

Field Y., Kaplan N., Fondufe-Mittendorf Y., Moore I. K., Sharon E., Lubling Y., et al. . (2008). Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 4:e1000216. 10.1371/journal.pcbi.1000216 PubMed DOI PMC

Funikov S., Ryazansky S., Kanapin A., Logacheva M., Penin A., Snezhkina A., et al. . (2016). Interplay between RNA interference and heat shock response systems in Drosophila melanogaster. Open Biol. 6:E160224. 10.1098/rsob.160224 PubMed DOI PMC

Ghosh T., Soni K., Scaria V., Halimani M., Bhattacharjee C., Pillai B. (2008). MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene. Nucleic Acids Res. 36, 6318–6332. 10.1093/nar/gkn624 PubMed DOI PMC

Gil E., Bosch A., Lampe D., Lizcano J., Perales J., Danos O., et al. . (2013). Functional characterization of the human mariner transposon Hsmar2. PLoS ONE 8:e73227. 10.1371/journal.pone.0073227 PubMed DOI PMC

Gouy M., Guindon S., Gascuel O. (2010). SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 27, 221–224. 10.1093/molbev/msp259 PubMed DOI

Guex N., Peitsch M. (1997). SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18, 2714–2723. 10.1002/elps.1150181505 PubMed DOI

Hastings P., Lupski J., Rosenberg S., Ira G. (2009). Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551–564. 10.1038/nrg2593 PubMed DOI PMC

Hawley R. (1980). Chromosomal sites necessary for normal levels of meiotic recombination in Drosophila melanogaster. I. Evidence for and mapping of the sites. Genetics 94, 625–646. PubMed PMC

Hehir-Kwa J. Y., Rodríguez-Santiago B., Vissers L. E., de Leeuw N., Pfundt R., Buitelaar J. K., et al. . (2011). De novo copy number variants associated with intellectual disability have a paternal origin and age bias. Am. J. Med. Genet. A 158A, 1493–1497. 10.1136/jmedgenet-2011-100147 PubMed DOI

Heinemeyer T., Wingender E., Reuter I., Hermjakob H., Kel A. E., Kel O. V., et al. . (1998). Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26, 362–367. 10.1093/nar/26.1.362 PubMed DOI PMC

Hirsch E. (2006). How to judge animal models of Parkinson's disease in terms of neuroprotection. J. Neural Transm. Suppl. 70, 255–260. 10.1007/978-3-211-45295-0_39 PubMed DOI

Hoogenraad C., Akhmanova A., Galjart N., De Zeeuw C. (2004). LIMK1 and CLIP-115: linking cytoskeletal defects to Williams syndrome. Bioessays 26, 141–150. 10.1002/bies.10402 PubMed DOI

Humphrey W., Dalke A., Schulten K. (1996). VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38, 27–28. 10.1016/0263-7855(96)00018-5 PubMed DOI

Ibáñez-Ventoso C., Vora M., Driscoll M. (2008). Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS ONE 3:e2818. 10.1371/journal.pone.0002818 PubMed DOI PMC

Inagaki H., Ohye T., Kogo H., Kato T., Bolor H., Taniguchi M., et al. (2009). Chromosomal instability mediated by non-B DNA: cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans. Genome Res. 19, 191–198. 10.1101/gr.079244.108 PubMed DOI PMC

Johnson R., Noble W., Tartaglia G. G., Buckley N. (2012). Neurodegeneration as an RNA disorder. Prog. Neurobiol. 99, 293–315. 10.1016/j.pneurobio.2012.09.006 PubMed DOI PMC

Kaminskaya A., Nikitina E., Medvedeva A., Gerasimenko M., Chernikova D., Savateeva-Popova E. (2015). Influence of limk1 gene polymorphism on learning acquisition and memory formation with pCREB distribution and aggregate formation in neuromuscular junctions in Drosophila melanogaster. Genetika 51, 685–693. 10.1134/S1022795415060071 PubMed DOI

Kaminskaya A., Nikitina E., Payalina T., Molotkov D., Zakharov G., Popov A., et al. . (2012). Effect of the LIM kinase 1 isoform ratio on Drosophila melanogaster courtship behavior: a complex approach. Russ. J. Genet. Appl. Res. 2, 367–377. 10.1134/S2079059712050024 PubMed DOI

Kertesz M., Iovino N., Unnerstall U., Gaul U., Segal E. (2007). The role of site accessibility in microRNA target recognition. Nat. Genet. 39, 1278–1284. 10.1038/ng2135 PubMed DOI

Kim Y.-J., Kim D.-N. (2016). Structural basis for elastic mechanical properties of the DNA double helix. PLoS ONE 11:e0153228. 10.1371/journal.pone.0153228 PubMed DOI PMC

Kirov G., Pocklington A. J., Holmans P., Ivanov D., Ikeda M., Ruderfer D., et al. . (2012). De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia. Mol. Psychiatry 17, 142–153. 10.1038/mp.2011.154 PubMed DOI PMC

Kosikov K. (1936). A new duplication in the Drosophila melanogaster X chromosome and its evolutionary significance. Dokl. Akad. Nauk SSSR 3, 297–300.

Kozomara A., Griffiths-Jones S. (2014). miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 42, D68–D73. 10.1093/nar/gkt1181 PubMed DOI PMC

Kucherenko M., Shcherbata H. (2013). Steroids as external temporal codes act via microRNAs and cooperate with cytokines in differential neurogenesis. Fly 7, 173–183. 10.4161/fly.25241 PubMed DOI PMC

Kumar D. (2008). Disorders of the genome architecture: a review. Genomic Med. 2, 69–76. 10.1007/s11568-009-9028-2 PubMed DOI PMC

Li G., Ruan X., Auerbach R., Sandhu K. S., Zheng M., Wang P., et al. . (2012). Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98. 10.1016/j.cell.2011.12.014 PubMed DOI PMC

Lushnikov S., Dmitriev A., Fedoseev A., Zakharov G., Zhuravlev A., Medvedeva A., et al. (2014). Low-frequency dynamics of DNA in Brillouin light scattering spectra. JETP Lett. 98, 735–741. 10.1134/S0021364013240168 DOI

Maciotta S., Meregalli M., Torrente Y. (2013). The involvement of microRNAs in neurodegenerative diseases. Front. Cell Neurosci. 7:0265. 10.3389/fncel.2013.00265 PubMed DOI PMC

Marinescu V., Kohane I., Riva A. (2005). MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC Bioinformatics 6:79. 10.1186/1471-2105-6-79 PubMed DOI PMC

Mattick J. (2011). The central role of RNA in human development and cognition. FEBS Lett. 585, 1600–1616. 10.1016/j.febslet.2011.05.001 PubMed DOI

Medrano-Fernández A., Barco A. (2016). Nuclear organization and 3D chromatin architecture in cognition and neuropsychiatric disorders. Mol. Brain 9:E83. 10.1186/s13041-016-0263-x PubMed DOI PMC

Medvedeva A., Molotkov D., Nikitina E., Popov A., Karagodin D., Baricheva E., et al. . (2008). Systemic regulation of genetic and cytogenetic processes by a signal cascade of actin remodeling: locus agnostic in Drosophila. Russ. J. Genet. 44, 669–681. 10.1134/S1022795408060069 PubMed DOI

Medvedeva A., Savvateeva E. (1991). The effects of the agnostic gene ts-mutations that control calmodulin functions and learning ability on ectopic pairing of Drosophila polytene chromosomes. Dokl. Akad. Nauk SSSR 318, 733–736. PubMed

Meng Y., Zhang Y., Tregoubov V., Janus C., Cruz L., Jackson M., et al. . (2002). Abnormal spine morphology and enhanced LTP in LIMK-1 knockout mice. Neuron 35, 121–133. 10.1016/S0896-6273(02)00758-4 PubMed DOI

Mills R., Luttig C., Larkins C., Beauchamp A., Tsui C., Pittard S., et al. . (2006). An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182–1190. 10.1101/gr.4565806 PubMed DOI PMC

Morris K., Mattick J. (2014). The rise of regulatory RNA. Nat. Rev. Genet. 15, 423–437. 10.1038/nrg3722 PubMed DOI PMC

Mullaney J., Mills R., Pittard S., Devine S. (2010). Small insertions and deletions (INDELs) in human genomes. Hum. Mol. Genet. 19, R131–R136. 10.1093/hmg/ddq400 PubMed DOI PMC

Nehammer C., Podolska A., Mackowiak S. D., Kagias K., Pocock R. (2015). Specific microRNAs regulate heat stress responses in Caenorhabditis elegans. Sci. Rep. 5:8866. 10.1038/srep08866 PubMed DOI PMC

Nikitina E., Medvedeva A., Zakharov G., Savvateeva-Popova E. (2014a). The Drosophila agnostic Locus: involvement in the formation of cognitive defects in williams syndrome. Acta Nat. 6, 53–61. PubMed PMC

Nikitina E., Medvedeva A., Zakharov G., Savvateeva-Popova E. (2014b). Williams syndrome as a model for elucidation of the pathway genes - the brain - cognitive functions: genetics and epigenetics. Acta Nat. 6, 9–22. PubMed PMC

Ohnishi O. (1977). Spontaneous and ethyl methanesulfonate-induced mutations controlling viability in Drosophila melanogaster. II. Homozygous effect of polygenic mutations. Genetics 87, 529–545. PubMed PMC

Ostertag E., Kazazian H. (2001). Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35, 501–538. 10.1146/annurev.genet.35.102401.091032 PubMed DOI

Pérez Jurado L. A. (2003). Williams–Beuren syndrome: a model of recurrent genomic mutation. Horm. Res. 59, 106–113. PubMed

Plank J., Dean A. (2014). Enhancer function: mechanistic and genome-wide insights come together. Mol. Cell. 55, 5–14. 10.1016/j.molcel.2014.06.015 PubMed DOI PMC

Qiu L., LeBel R., Storm D., Chen X. (2016). Type 3 adenylyl cyclase: a key enzyme mediating the cAMP signaling in neuronal cilia. Int. J. Physiol. Pathophysiol. Pharmacol. 8, 95–108. PubMed PMC

Quinlan A., Hall I. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842. 10.1093/bioinformatics/btq033 PubMed DOI PMC

Reiter L., Liehr T., Rautenstrauss B., Robertson H., Lupski J. (1999). Localization of mariner DNA transposons in the human genome by PRINS. Genome Res. 9, 839–843. 10.1101/gr.9.9.839 PubMed DOI PMC

Robinson M., McCarthy D., Smyth G. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140. 10.1093/bioinformatics/btp616 PubMed DOI PMC

Rokavec M., Li H., Jiang L., Hermeking H. (2014). The p53/miR-34 axis in development and disease. J. Mol. Cell Biol. 6, 214–230. 10.1093/jmcb/mju003 PubMed DOI

Ruby G., Stark A., Johnston W., Kellis M., Bartel D., Lai E. (2007). Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17, 1850–1864. 10.1101/gr.6597907 PubMed DOI PMC

Sandelin A., Wasserman W., Lenhard B. (2004). ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res. 32, W249–W252. 10.1093/nar/gkh372 PubMed DOI PMC

Savvateeva E., Kamyshev N. (1981). Behavioral effects of temperature sensitive mutations affecting metabolism of cAMP in D. melanogaster. Pharm. Biochem. Behav. 14, 603–611. 10.1016/0091-3057(81)90119-2 PubMed DOI

Savvateeva-Popova E., Peresleni A., Scharagina L., Medvedeva A., Korochkina S., Grigorieva I., et al. . (2004). Architecture of the X chromosome, expression of LIM Kinase 1, and recombination in the agnostic mutants of Drosophila: a model for human williams syndrome. Russ. J. Genet. 40, 605–624. 10.1023/B:RUGE.0000033308.97306.9a PubMed DOI

Savvateeva-Popova E., Peresleny A., Scharagina L., Tokmacheva E., Medvedeva A., Kamyshev N., et al. (2002). Complex study of Drosophila mutants in the agnostic locus: a model for coupling chromosomal architecture and cognitive functions. J. Evol. Biochem. Physiol. 38, 706–733. 10.1023/A:1023003625014 PubMed DOI

Savvateeva-Popova E., Popov A., Grossman A., Nikitina E., Medvedeva A., Molotkov D., et al. . (2008). Non-coding RNA as a trigger of neuropathologic disorder phenotypes in transgenic Drosophila. J. Neural Transm. 115, 1629–1642. 10.1007/s00702-008-0078-8 PubMed DOI

Schwede T., Kopp J., Guex N., Peitsch M. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381–3385. 10.1093/nar/gkg520 PubMed DOI PMC

Tassabehji M., Metcalfe K., Karmiloff-Smith A., Carette M. J., Grant J., Dennis N., et al. . (1999) Williams syndrome: use of chromosomal microdeletions as a tool to dissect cognitive physical phenotypes. Am. J. Hum. Genet. 64, 118–125. 10.1086/302214 PubMed DOI PMC

Valero M. C., de Luis O., Cruces J., Pérez Jurado L. A. (2000). Fine-scale comparative mapping of the human 7q11.23 region and the orthologous region on mouse chromosome 5G: the low-copy repeats that flank the Williams-Beuren syndrome deletion arose at breakpoint sites of an evolutionary inversion(s). Genomics 69, 1–13. 10.1006/geno.2000.6312 PubMed DOI

Venderova K., Kabbach G., Abdel-Messih E., Zhang Y., Parks R., Imai Y., et al. . (2009). Leucine-Rich Repeat Kinase 2 interacts with Parkin, DJ-1 and PINK-1 in a Drosophila melanogaster model of Parkinson's disease. Hum. Mol. Genet. 18, 4390–4404. 10.1093/hmg/ddp394 PubMed DOI

Wells R. (2007). Non-B DNA conformations, mutagenesis and disease. Trends Biochem. Sci. 32, 271–278. 10.1016/j.tibs.2007.04.003 PubMed DOI

Wells R. (2009). Discovery of the role of Non-B DNA structures in mutagenesis and human genomic disorders. J. Biol. Chem. 284, 8997–9009. 10.1074/jbc.X800010200 PubMed DOI PMC

Xamena N., Creus A., Macros R. (1985). Effect of intercalating mutagens on crossing over in Drosophila melanogaster females. Experientia 41, 1078–1081. 10.1007/BF01952152 DOI

Xi L., Fondufe-Mittendorf Y., Xia L., Flatow J., Widom J., Wang J.-P. (2010). Predicting nucleosome positioning using a duration Hidden Markov Model. BMC Bioinformatics 11:346. 10.1186/1471-2105-11-346ss PubMed DOI PMC

Zhang Y., Wong C.-H., Birnbaum R., Li G., Favaro R., Ngan C. Y., et al. . (2013). Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations. Nature 504, 306–310. 10.1038/nature12716 PubMed DOI PMC

Zhimulev I., Semeshin V., Kulichkov V., Belyaeva E. (1982). Intercalary heterochromatin in Drosophila. Chromosoma 87, 197–228. 10.1007/BF00338489 DOI

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids