Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.

Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interb...

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Autores principales:	Igor F Zhimulev, Tatyana Yu Zykova, Fyodor P Goncharov, Varvara A Khoroshko, Olga V Demakova, Valeriy F Semeshin, Galina V Pokholkova, Lidiya V Boldyreva, Darya S Demidova, Vladimir N Babenko, Sergey A Demakov, Elena S Belyaeva
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c81f43e2788d4156909a9eea04f748c3
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spelling	oai:doaj.org-article:c81f43e2788d4156909a9eea04f748c32021-11-25T06:06:45ZGenetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.1932-620310.1371/journal.pone.0101631https://doaj.org/article/c81f43e2788d4156909a9eea04f748c32014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25072930/?tool=EBIhttps://doaj.org/toc/1932-6203Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5' ends of housekeeping genes. As a rule, interbands display preferential "head-to-head" orientation of genes. They are enriched for "broad" class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5'-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called "grey" bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.Igor F ZhimulevTatyana Yu ZykovaFyodor P GoncharovVarvara A KhoroshkoOlga V DemakovaValeriy F SemeshinGalina V PokholkovaLidiya V BoldyrevaDarya S DemidovaVladimir N BabenkoSergey A DemakovElena S BelyaevaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e101631 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Igor F Zhimulev Tatyana Yu Zykova Fyodor P Goncharov Varvara A Khoroshko Olga V Demakova Valeriy F Semeshin Galina V Pokholkova Lidiya V Boldyreva Darya S Demidova Vladimir N Babenko Sergey A Demakov Elena S Belyaeva Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
description	Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5' ends of housekeeping genes. As a rule, interbands display preferential "head-to-head" orientation of genes. They are enriched for "broad" class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5'-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called "grey" bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.
format	article
author	Igor F Zhimulev Tatyana Yu Zykova Fyodor P Goncharov Varvara A Khoroshko Olga V Demakova Valeriy F Semeshin Galina V Pokholkova Lidiya V Boldyreva Darya S Demidova Vladimir N Babenko Sergey A Demakov Elena S Belyaeva
author_facet	Igor F Zhimulev Tatyana Yu Zykova Fyodor P Goncharov Varvara A Khoroshko Olga V Demakova Valeriy F Semeshin Galina V Pokholkova Lidiya V Boldyreva Darya S Demidova Vladimir N Babenko Sergey A Demakov Elena S Belyaeva
author_sort	Igor F Zhimulev
title	Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
title_short	Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
title_full	Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
title_fullStr	Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
title_full_unstemmed	Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.
title_sort	genetic organization of interphase chromosome bands and interbands in drosophila melanogaster.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/c81f43e2788d4156909a9eea04f748c3
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_version_	1718414189440008192

Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster.

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