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Anopheles mosquitoes reveal new principles of 3D genome organization in insects

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dc.contributor.authorLukyanchikova, Varvaraen
dc.contributor.authorNuriddinov, Miroslaven
dc.contributor.authorBelokopytova, Polinaen
dc.contributor.authorTaskina, Alenaen
dc.contributor.authorLiang, Jiangtaoen
dc.contributor.authorReijnders, Maarten J. M. F.en
dc.contributor.authorRuzzante, Livioen
dc.contributor.authorFeron, Romainen
dc.contributor.authorWaterhouse, Robert M.en
dc.contributor.authorWu, Yangen
dc.contributor.authorMao, Chunhongen
dc.contributor.authorTu, Zhijian Jakeen
dc.contributor.authorSharakhov, Igor V.en
dc.contributor.authorFishman, Veniaminen
dc.date.accessioned2022-06-13T16:20:21Zen
dc.date.available2022-06-13T16:20:21Zen
dc.date.issued2022-04-12en
dc.description.abstractChromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for similar to 100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.en
dc.description.notesThe following reagents were obtained through BEI Resources, NIAID, NIH: An. coluzzii, Strain MOPTI, Eggs, MRA-763, contributed by Gregory C. Lanzaro; An. merus, Strain MAF, MRA-1156, contributed by Maureen Coetzee; An. atroparvus, Strain EBRO, Eggs, MRA-493, contributed by Carlos Aranda and Mark Q. Benedict; An. albimanus, Strain STECLA, Eggs, MRA-126, contributed by Mark Q. Benedict. All computations were performed using nodes of the high-throughput cluster of the Novosibirsk State University, and bioinformatics resource center of the Institute of Cytology and Genetics. We are sincerely grateful to Nariman Battulin for fruitful discussions. This work was supported by the NSF grant MCB-1715207, NIH NIAID grants R21AI135298 and R21AI159382, and the USDA National Institute of Food and Agriculture Hatch project 223822 to IVS. The reported study of An. atroparvus was partly funded by RFBR according to the research project no 19-34-50051 to IVS and VL. PacBio sequencing of An. merus was funded by a grant from the University of Lausanne Department of Ecology and Evolution to RMW and NIH grants AI133571 and AI121284 to Z.T. M.J.M.F.R., L.R., R.F., and R.M.W. were supported by Novartis Foundation for medical-biological research grant #18B116 and Swiss National Science Foundation grants PP00P3_170664 and PP00P3_202669. V.L. was partly supported by the Fulbright Foreign Student Program, Grantee ID: 15161026. Hi-C data analysis was supported by the Ministry of Education and Science of Russian Federation, grant #2019-0546 (FSUS-2020-0040). ChIP-seq data analysis was supported by project 121031800061-7 (Mechanisms of genetic control of development, physiological processes and behavior in animals).en
dc.description.sponsorshipNSF [MCB-1715207]; NIH NIAID [R21AI135298, R21AI159382]; USDA National Institute of Food and Agriculture Hatch project [223822]; RFBR [19-34-50051]; University of Lausanne Department of Ecology and Evolution; NIH [AI133571, AI121284]; Novartis Foundation [18B116]; Swiss National Science Foundation [PP00P3_170664, PP00P3_202669]; Fulbright Foreign Student Program [15161026]; Ministry of Education and Science of Russian Federation [2019-0546 (FSUS-2020-0040)]; [121031800061-7]en
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1038/s41467-022-29599-5en
dc.identifier.eissn2041-1723en
dc.identifier.issue1en
dc.identifier.other1960en
dc.identifier.pmid35413948en
dc.identifier.urihttp://hdl.handle.net/10919/110758en
dc.identifier.volume13en
dc.language.isoenen
dc.publisherNature Portfolioen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectAsian malaria mosquitoen
dc.subjectHi-C revealsen
dc.subjectinversion breakpointsen
dc.subjectchromatinen
dc.subjectpolycomben
dc.subjectmapen
dc.subjectarchitectureen
dc.subjectalignmenten
dc.subjectpredictionen
dc.subjectevolutionen
dc.titleAnopheles mosquitoes reveal new principles of 3D genome organization in insectsen
dc.title.serialNature Communicationsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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