{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T20:04:52Z","timestamp":1762113892829,"version":"build-2065373602"},"reference-count":49,"publisher":"MDPI AG","issue":"16","license":[{"start":{"date-parts":[[2021,8,13]],"date-time":"2021-08-13T00:00:00Z","timestamp":1628812800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002261","name":"Russian Foundation for Basic Research","doi-asserted-by":"publisher","award":["N 20-015-00300 A"],"award-info":[{"award-number":["N 20-015-00300 A"]}],"id":[{"id":"10.13039\/501100002261","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the State Program of the Russian Federation 47 GP &quot;Scientific and Technological Development of the Russian Federation&quot; (2019-2030) (63.1)","award":["No number"],"award-info":[{"award-number":["No number"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Chromatin 3D structure plays a crucial role in regulation of gene activity. Previous studies have envisioned spatial contact formations between chromatin domains with different epigenetic properties, protein compositions and transcription activity. This leaves specific DNA sequences that affect chromosome interactions. The Drosophila melanogaster polytene chromosomes are involved in non-allelic ectopic pairing. The mutant strain agnts3, a Drosophila model for Williams\u2013Beuren syndrome, has an increased frequency of ectopic contacts (FEC) compared to the wild-type strain Canton-S (CS). Ectopic pairing can be mediated by some specific DNA sequences. In this study, using our Homology Segment Analysis software, we estimated the correlation between FEC and frequency of short matching DNA fragments (FMF) for all sections of the X chromosome of Drosophila\u00a0CS and agnts3 strains. With fragment lengths of 50 nucleotides (nt), CS showed a specific FEC\u2013FMF correlation for 20% of the sections involved in ectopic contacts. The correlation was unspecific in agnts3, which may indicate the alternative epigenetic mechanisms affecting FEC in the mutant strain. Most of the fragments that specifically contributed to FMF were related to 1.688 or 372-bp middle repeats. Thus, middle repetitive DNA may serve as an organizer of ectopic pairing.<\/jats:p>","DOI":"10.3390\/ijms22168713","type":"journal-article","created":{"date-parts":[[2021,8,13]],"date-time":"2021-08-13T09:22:38Z","timestamp":1628846558000},"page":"8713","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Chromatin Structure and \u201cDNA Sequence View\u201d: The Role of Satellite DNA in Ectopic Pairing of the Drosophila X Polytene Chromosome"],"prefix":"10.3390","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2673-4283","authenticated-orcid":false,"given":"Aleksandr V.","family":"Zhuravlev","sequence":"first","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gennadii A.","family":"Zakharov","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia"},{"name":"EPAM Systems Inc., Saint Petersburg 197110, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterina V.","family":"Anufrieva","sequence":"additional","affiliation":[{"name":"Faculty of Biology, Herzen State Pedagogical University of Russia, 191186 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna V.","family":"Medvedeva","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ekaterina A.","family":"Nikitina","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia"},{"name":"Faculty of Biology, Herzen State Pedagogical University of Russia, 191186 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena V.","family":"Savvateeva-Popova","sequence":"additional","affiliation":[{"name":"Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,8,13]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1083\/jcb.145.6.1119","article-title":"Differences in the Localization and Morphology of Chromosomes in the Human Nucleus","volume":"145","author":"Croft","year":"1999","journal-title":"J. Cell Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1007\/s00412-016-0580-y","article-title":"Chromosomal Aneuploidies Induced upon Lamin B2 Depletion Are Mislocalized in the Interphase Nucleus","volume":"126","author":"Ranade","year":"2017","journal-title":"Chromosoma"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"4475","DOI":"10.1128\/MCB.00208-07","article-title":"The Three-Dimensional Structure of Human Interphase Chromosomes Is Related to the Transcriptome Map","volume":"27","author":"Goetze","year":"2007","journal-title":"Mol. Cell. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e192","DOI":"10.1371\/journal.pbio.0050192","article-title":"Myc Dynamically and Preferentially Relocates to a Transcription Factory Occupied by Igh","volume":"5","author":"Osborne","year":"2007","journal-title":"PLoS Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e138","DOI":"10.1371\/journal.pbio.0040138","article-title":"Intermingling of Chromosome Territories in Interphase Suggests Role in Translocations and Transcription-Dependent Associations","volume":"4","author":"Branco","year":"2006","journal-title":"PLoS Biol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/j.cell.2008.03.004","article-title":"Chromatin Dynamics and Gene Positioning","volume":"132","author":"Kumaran","year":"2008","journal-title":"Cell"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1038\/ng1423","article-title":"Active Genes Dynamically Colocalize to Shared Sites of Ongoing Transcription","volume":"36","author":"Osborne","year":"2004","journal-title":"Nat. Genet."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1002\/bies.201100142","article-title":"Banding Patterns in Drosophila Melanogaster Polytene Chromosomes Correlate with DNA-Binding Protein Occupancy","volume":"34","author":"Zhimulev","year":"2012","journal-title":"Bioessays"},{"key":"ref_9","first-page":"1","article-title":"Polytene Chromosomes, Heterochromatin, and Position Effect Variegation","volume":"37","author":"Zhimulev","year":"1998","journal-title":"Adv. Genet."},{"key":"ref_10","first-page":"338","article-title":"Banding Pattern of Polytene Chromosomes as a Representation of Universal Principles of Chromatin Organization into Topological Domains","volume":"83","author":"Kolesnikova","year":"2018","journal-title":"Biochemistry"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"e101631","DOI":"10.1371\/journal.pone.0101631","article-title":"Genetic Organization of Interphase Chromosome Bands and Interbands in Drosophila Melanogaster","volume":"9","author":"Zhimulev","year":"2014","journal-title":"PLoS ONE"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e0195207","DOI":"10.1371\/journal.pone.0195207","article-title":"Similarity in Replication Timing between Polytene and Diploid Cells Is Associated with the Organization of the Drosophila Genome","volume":"13","author":"Kolesnikova","year":"2018","journal-title":"PLoS ONE"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1083\/jcb.102.1.112","article-title":"Spatial Organization of Chromosomes in the Salivary Gland Nuclei of Drosophila Melanogaster","volume":"102","author":"Hochstrasser","year":"1986","journal-title":"J. Cell Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1101\/gad.179804.111","article-title":"A Decade of 3C Technologies: Insights into Nuclear Organization","volume":"26","year":"2012","journal-title":"Genes Dev."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1016\/j.cell.2015.10.026","article-title":"Stable Chromosome Condensation Revealed by Chromosome Conformation Capture","volume":"163","author":"Eagen","year":"2015","journal-title":"Cell"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.cell.2012.01.010","article-title":"Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome","volume":"148","author":"Sexton","year":"2012","journal-title":"Cell"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1007\/s00412-006-0063-7","article-title":"DNA Underreplication in Intercalary Heterochromatin Regions in Polytene Chromosomes of Drosophila Melanogaster Correlates with the Formation of Partial Chromosomal Aberrations and Ectopic Pairing","volume":"115","author":"Belyaeva","year":"2006","journal-title":"Chromosoma"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"9","DOI":"10.32607\/20758251-2014-6-1-9-22","article-title":"Williams Syndrome as a Model for Elucidation of the Pathway Genes\u2014the Brain\u2014Cognitive Functions: Genetics and Epigenetics","volume":"6","author":"Nikitina","year":"2014","journal-title":"Acta Nat."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"53","DOI":"10.32607\/20758251-2014-6-2-53-61","article-title":"The Drosophila Agnostic Locus: Involvement in the Formation of Cognitive Defects in Williams Syndrome","volume":"6","author":"Nikitina","year":"2014","journal-title":"Acta Nat."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1002\/med.20230","article-title":"LIM Kinases Are Attractive Targets with Many Macromolecular Partners and Only a Few Small Molecule Regulators","volume":"32","author":"Manetti","year":"2012","journal-title":"Med. Res. Rev."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"123","DOI":"10.3389\/fgene.2017.00123","article-title":"Drosophila Model for the Analysis of Genesis of LIM-Kinase 1-Dependent Williams-Beuren Syndrome Cognitive Phenotypes: INDELs, Transposable Elements of the Tc1\/Mariner Superfamily and MicroRNAs","volume":"8","author":"Zhuravlev","year":"2017","journal-title":"Front. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1134\/S1022795408060069","article-title":"Systemic Regulation of Genetic and Cytogenetic Processes by a Signal Cascade of Actin Remodeling: Locus Agnostic in Drosophila","volume":"44","author":"Medvedeva","year":"2008","journal-title":"Russ. J. Genet."},{"key":"ref_23","unstructured":"Zhuravlev, A., and Zakharov, G. (2021, July 30). Homology Segment Analysis. Available online: https:\/\/bitbucket.org\/beneor\/homology-segment-analysis\/src\/master\/."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Medvedeva, A., Tokmatcheva, E., Kaminskaya, A., Vasileva, S., Nikitina, E., Zhuravlev, A., Zakharov, G., Zatsepina, O., and Savvateeva-Popova, E. (2021). Parent-of-Origin Effects on Nuclear Chromatin Organization and Behavior in Drosophila Model for Williams-Beuren Syndrome. Vavilovskii Zhurnal Genet. Selektsii, in press.","DOI":"10.18699\/VJ21.054"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2843","DOI":"10.1073\/pnas.84.9.2843","article-title":"Cloning and Characterization of a Dispersed, Multicopy, X Chromosome Sequence in Drosophila Melanogaster","volume":"84","author":"Waring","year":"1987","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"4129","DOI":"10.1534\/g3.120.401727","article-title":"Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny","volume":"10","author":"Hanlon","year":"2020","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"16460","DOI":"10.1073\/pnas.1410534111","article-title":"SiRNAs from an X-Linked Satellite Repeat Promote X-Chromosome Recognition in Drosophila Melanogaster","volume":"111","author":"Menon","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1083\/jcb.201404097","article-title":"Repetitive Centromeric Satellite RNA Is Essential for Kinetochore Formation and Cell Division","volume":"207","author":"Erhardt","year":"2014","journal-title":"J. Cell Biol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.tjem.2018.08.001","article-title":"User\u2019s guide to correlation coefficients","volume":"18","author":"Akoglu","year":"2018","journal-title":"Turk. J. Emerg. Med."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1023\/B:RUGE.0000033308.97306.9a","article-title":"Architecture of the X Chromosome, Expression of LIM Kinase 1, and Recombination in the Agnostic Mutants of Drosophila: A Model for Human Williams Syndrome","volume":"40","author":"Peresleni","year":"2004","journal-title":"Russ. J. Genet."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1007\/BF00338489","article-title":"Intercalary Heterochromatin in Drosophila","volume":"87","author":"Zhimulev","year":"1982","journal-title":"Chromosoma"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"312","DOI":"10.3389\/fcell.2020.00312","article-title":"Functional Significance of Satellite DNAs: Insights From Drosophila","volume":"8","author":"Shatskikh","year":"2020","journal-title":"Front. Cell Dev. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1073\/pnas.83.3.696","article-title":"Multiplicity of Satellite DNA Sequences in Drosophila Melanogaster","volume":"83","author":"Lohe","year":"1986","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1534\/g3.116.035352","article-title":"Comparative Analysis of Satellite DNA in the Drosophila Melanogaster Species Complex","volume":"7","author":"Jagannathan","year":"2017","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1093\/nar\/20.5.1113","article-title":"A Superfamily of Drosophila Satellite Related (SR) DNA Repeats Restricted to the X Chromosome Euchromatin","volume":"20","author":"DiBartolomeis","year":"1992","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1023\/A:1023003625014","article-title":"Complex Study of Drosophila Mutants in the Agnostic Locus: A Model for Coupling Chromosomal Architecture and Cognitive Functions","volume":"38","author":"Peresleny","year":"2002","journal-title":"J. Evol. Biochem. Physiol."},{"key":"ref_37","first-page":"33","article-title":"Genetic Control of Second Messenger Systems and Their Role in Learning. Usp","volume":"17","author":"Savvateeva","year":"1991","journal-title":"Sovr. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2332","DOI":"10.1242\/jcs.02960","article-title":"The Chromodomain Protein, Chromator, Interacts with JIL-1 Kinase and Regulates the Structure of Drosophila Polytene Chromosomes","volume":"119","author":"Rath","year":"2006","journal-title":"J. Cell. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1093\/genetics\/165.3.1183","article-title":"Heterochromatic Self-Association, a Determinant of Nuclear Organization, Does Not Require Sequence Homology in Drosophila","volume":"165","author":"Sage","year":"2003","journal-title":"Genetics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1007\/s11055-018-0632-2","article-title":"A Weakened Geomagnetic Field: Effects on Genomic Transcriptiln Activity, Learning, and Memory in Drosophila Melanogaster","volume":"48","author":"Nikitina","year":"2018","journal-title":"Neurosci. Behav. Phys."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.neuint.2014.03.012","article-title":"The Interplay between MicroRNAs and Histone Deacetylases in Neurological Diseases","volume":"77","author":"Bourassa","year":"2014","journal-title":"Neurochem. Int."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"398","DOI":"10.3389\/fgene.2018.00398","article-title":"The Nature of Actin-Family Proteins in Chromatin-Modifying Complexes","volume":"9","author":"Kumar","year":"2018","journal-title":"Front. Genet."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1016\/j.neuron.2017.05.039","article-title":"The Biology of Forgetting-A Perspective","volume":"95","author":"Davis","year":"2017","journal-title":"Neuron"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1093\/emboj\/20.4.812","article-title":"Ectopic HP1 Promotes Chromosome Loops and Variegated Silencing in Drosophila","volume":"20","author":"Seum","year":"2001","journal-title":"EMBO J."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/35065132","article-title":"Methylation of Histone H3 Lysine 9 Creates a Binding Site for HP1 Proteins","volume":"410","author":"Lachner","year":"2001","journal-title":"Nature"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1534\/genetics.107.071720","article-title":"Transcription of the 1.688 Satellite DNA Family Is under the Control of RNA Interference Machinery in Drosophila Melanogaster Ovaries","volume":"176","author":"Usakin","year":"2007","journal-title":"Genetics"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1016\/0092-8674(84)90422-7","article-title":"A Structural Basis for Variegating Position Effects","volume":"37","author":"Tartof","year":"1984","journal-title":"Cell"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1080\/15476286.2015.1086864","article-title":"Identification of the Drosophila X Chromosome: The Long and Short of It","volume":"12","author":"Menon","year":"2015","journal-title":"RNA Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","article-title":"Ensembl 2018","volume":"46","author":"Zerbino","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/16\/8713\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T06:45:36Z","timestamp":1760165136000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/22\/16\/8713"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,13]]},"references-count":49,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2021,8]]}},"alternative-id":["ijms22168713"],"URL":"https:\/\/doi.org\/10.3390\/ijms22168713","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2021,8,13]]}}}