Genome mapping and characterization of the Anopheles gambiae heterochromatin

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dc.contributor.authorSharakhova, Maria V.en
dc.contributor.authorGeorge, Phillipen
dc.contributor.authorBrusentsova, Irina V.en
dc.contributor.authorLeman, Scotland C.en
dc.contributor.authorBailey, Jeffrey A.en
dc.contributor.authorSmith, Christopher D.en
dc.contributor.authorSharakhov, Igor V.en
dc.contributor.departmentEntomologyen
dc.contributor.departmentStatisticsen
dc.date.accessioned2017-01-05T22:14:32Zen
dc.date.available2017-01-05T22:14:32Zen
dc.date.issued2010-08-04en
dc.description.abstractBackground Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized. Results To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin. Conclusions Our results demonstrate that Anopheles polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the An. gambiae heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.en
dc.description.versionPublished versionen
dc.format.extent? - ? (17) page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.citationBMC Genomics. 2010 Aug 04;11(1):459en
dc.identifier.doihttps://doi.org/10.1186/1471-2164-11-459en
dc.identifier.issn1471-2164en
dc.identifier.urihttp://hdl.handle.net/10919/73961en
dc.identifier.volume11en
dc.language.isoenen
dc.publisherBiomed Centralen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000282788400001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderMaria V Sharakhova et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiotechnology & Applied Microbiologyen
dc.subjectGenetics & Heredityen
dc.subjectDROSOPHILA-MELANOGASTER HETEROCHROMATINen
dc.subjectNONHISTONE CHROMOSOMAL PROTEINen
dc.subject2L TELOMERIC REGIONen
dc.subjectPOLYTENE CHROMOSOMESen
dc.subjectNUCLEAR-ENVELOPEen
dc.subjectGENE-EXPRESSIONen
dc.subjectSPATIAL-ORGANIZATIONen
dc.subjectINTERCALARY HETEROCHROMATINen
dc.subject3-DIMENSIONAL ORGANIZATIONen
dc.subjectCHROMODOMAIN PROTEINSen
dc.titleGenome mapping and characterization of the Anopheles gambiae heterochromatinen
dc.title.serialBMC Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Entomologyen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/Scienceen
pubs.organisational-group/Virginia Tech/Science/COS T&R Facultyen
pubs.organisational-group/Virginia Tech/Science/Statisticsen

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