Molecular characterization of the singed wings locus of Drosophila melanogaster.

BACKGROUND: Hormones frequently guide animal development via the induction of cascades of gene activities, whose products further amplify an initial hormonal stimulus. In Drosophila the transformation of the larva into the pupa and the subsequent metamorphosis to the adult stage is triggered by changes in the titer of the steroid hormone 20-hydroxyecdysone. singed wings (swi) is the only gene known in Drosophila melanogaster for which mutations specifically interrupt the transmission of the regulatory signal from early to late ecdysone inducible genes. RESULTS: We have characterized singed wings locus, showing it to correspond to EG:171E4.2 (CG3095). swi encodes a predicted 68.5-kDa protein that contains N-terminal histidine-rich and threonine-rich domains, a cysteine-rich C-terminal region and two leucine-rich repeats. The SWI protein has a close homolog in D. melanogaster, defining a new family of SWI-like proteins, and is conserved in D. pseudoobscura. A lethal mutation, swit476, shows a severe disruption of the ecdysone pathway and is a C>Y substitution in one of the two conserved CysXCys motifs that are common to SWI and the Drosophila Toll-4 protein. CONCLUSIONS: It is not entirely clear from the present molecular analysis how the SWI protein may function in the ecdysone induced cascade. Currently all predictions agree in that SWI is very unlikely to be a nuclear protein. Thus it probably exercises its control of "late" ecdysone genes indirectly. Apparently the genetic regulation of ecdysone signaling is much more complex then was previously anticipated.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster

<p>Abstract</p> <p>Background</p> <p>Despite many efforts, little is known about distribution and interactions of chromatin proteins which contribute to the specificity of chromomeric organization of interphase chromosomes. To address this issue, we used publicly available datasets from several recent Drosophila genome-wide mapping and annotation projects, in particular, those from modENCODE project, and compared molecular organization of 13 interband regions which were accurately mapped previously.</p> <p>Results</p> <p>Here we demonstrate that in interphase chromosomes of <it>Drosophila </it>cell lines, the interband regions are enriched for a specific set of proteins generally characteristic of the "open" chromatin (RNA polymerase II, CHRIZ (CHRO), BEAF-32, BRE1, dMI-2, GAF, NURF301, WDS and TRX). These regions also display reduced nucleosome density, histone H1 depletion and pronounced enrichment for ORC2, a pre-replication complex component. Within the 13 interband regions analyzed, most were around 3-4 kb long, particularly those where many of said protein features were present. We estimate there are about 3500 regions with similar properties in chromosomes of <it>D. melanogaster </it>cell lines, which fits quite well the number of cytologically observed interbands in salivary gland polytene chromosomes.</p> <p>Conclusions</p> <p>Our observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a universal principle of interphase chromosome organization.</p

Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome

<p>Abstract</p> <p>Background</p> <p>Eukaryotic genomes are organized in extended domains with distinct features intimately linking genome structure, replication pattern and chromatin state. Recently we identified a set of long late replicating euchromatic regions that are underreplicated in salivary gland polytene chromosomes of <it>D. melanogaster</it>.</p> <p>Results</p> <p>Here we demonstrate that these underreplicated regions (URs) have a low density of <it>P</it>-<it>element </it>and <it>piggyBac </it>insertions compared to the genome average or neighboring regions. In contrast, <it>Minos</it>-based transposons show no paucity in URs but have a strong bias to testis-specific genes. We estimated the suppression level in 2,852 stocks carrying a single <it>P</it>-<it>element </it>by analysis of eye color determined by the mini-<it>white </it>marker gene and demonstrate that the proportion of suppressed transgenes in URs is more than three times higher than in the flanking regions or the genomic average. The suppressed transgenes reside in intergenic, genic or promoter regions of the annotated genes. We speculate that the low insertion frequency of <it>P-elemen</it>ts and <it>piggyBac</it>s in URs partially results from suppression of transgenes that potentially could prevent identification of transgenes due to complete suppression of the marker gene. In a similar manner, the proportion of suppressed transgenes is higher in loci replicating late or very late in Kc cells and these loci have a lower density of <it>P-elements </it>and <it>piggyBac </it>insertions. In transgenes with two marker genes suppression of mini-<it>white </it>gene in eye coincides with suppression of <it>yellow </it>gene in bristles.</p> <p>Conclusions</p> <p>Our results suggest that the late replication domains have a high inactivation potential apparently linked to the silenced or closed chromatin state in these regions, and that such inactivation potential is largely maintained in different tissues.</p

Identical Functional Organization of Nonpolytene and Polytene Chromosomes in Drosophila melanogaster

Salivary gland polytene chromosomes demonstrate banding pattern, genetic meaning of which is an enigma for decades. Till now it is not known how to mark the band/interband borders on physical map of DNA and structures of polytene chromosomes are not characterized in molecular and genetic terms. It is not known either similar banding pattern exists in chromosomes of regular diploid mitotically dividing nonpolytene cells. Using the newly developed approach permitting to identify the interband material and localization data of interband-specific proteins from modENCODE and other genome-wide projects, we identify physical limits of bands and interbands in small cytological region 9F13-10B3 of the X chromosome in D. melanogaster, as well as characterize their general molecular features. Our results suggests that the polytene and interphase cell line chromosomes have practically the same patterns of bands and interbands reflecting, probably, the basic principle of interphase chromosome organization. Two types of bands have been described in chromosomes, early and late-replicating, which differ in many aspects of their protein and genetic content. As appeared, origin recognition complexes are located almost totally in the interbands of chromosomes

Overexpression of the SuUR gene induces reversible modifications at pericentric, telomeric and intercalary heterochromatin of Drosophila melanogaster polytene chromosomes

The SuUR (suppressor of underreplication) gene controls late replication and underreplication of DNA in Drosophila melanogaster polytene chromosomes: its mutation suppresses DNA underreplication whereas additional doses of the normal allele strongly enhances underreplication. The SuUR protein is localized in late replicating and underreplicating regions. The N-terminal part of the SuUR protein shares modest similarity with the ATPase/helicase domain of SWI2/SNF2 chromatin remodeling factors, suggesting a role in modification of chromatin structure. Here we describe novel structural modifications of polytene chromosomes (swellings) and show that SuUR controls chromatin organization in polytene chromosomes. The swellings develop as the result of SuUR ectopic expression in the transgene system Sgs3-GAL4; UAS-SuUR(+). They are reminiscent of chromosome puffs and appear in similar to190 regions of intercalary, pericentric and telomeric heterochromatin; some of them attain tremendous size. The swellings are temperature sensitive: they are maximal at 29C and are barely visible at 18degreesC. Shifting from 29degreesC to 18degreesC results in the complete recovery of the normal structure of chromosomes. The swellings are transcriptionally inactive, since they do not incorporate [H-3]uridine. The SuUR protein is not visualized in regions of maximally developed swellings. Regular ecdysone-inducible puffs are not induced in cells where these swellings are apparent

Late Replication Domains in Polytene and Non-Polytene Cells of Drosophila melanogaster

In D. melanogaster polytene chromosomes, intercalary heterochromatin (IH) appears as large dense bands scattered in euchromatin and comprises clusters of repressed genes. IH displays distinctly low gene density, indicative of their particular regulation. Genes embedded in IH replicate late in the S phase and become underreplicated. We asked whether localization and organization of these late-replicating domains is conserved in a distinct cell type. Using published comprehensive genome-wide chromatin annotation datasets (modENCODE and others), we compared IH organization in salivary gland cells and in a Kc cell line. We first established the borders of 60 IH regions on a molecular map, these regions containing underreplicated material and encompassing ∼12% of Drosophila genome. We showed that in Kc cells repressed chromatin constituted 97% of the sequences that corresponded to IH bands. This chromatin is depleted for ORC-2 binding and largely replicates late. Differences in replication timing between the cell types analyzed are local and affect only sub-regions but never whole IH bands. As a rule such differentially replicating sub-regions display open chromatin organization, which apparently results from cell-type specific gene expression of underlying genes. We conclude that repressed chromatin organization of IH is generally conserved in polytene and non-polytene cells. Yet, IH domains do not function as transcription- and replication-regulatory units, because differences in transcription and replication between cell types are not domain-wide, rather they are restricted to small “islands” embedded in these domains. IH regions can thus be defined as a special class of domains with low gene density, which have narrow temporal expression patterns, and so displaying relatively conserved organization

The problems of genetic support of dividing the black kite (Milvus migrans) into subspecies

The black kite Milvus migrans is a common bird of prey demonstrating remarkable ecological plasticity. It inhabits a variety of habitats and is an increasingly synanthropic species. The black kite is widespread in Eurasia, Africa, Australia and adjacent islands. Palearctic kites migrate to Africa, India and China in winter, but kites of Africa and Australia are partly sedentary and partly seasonal migrants. The wide range and high mobility are the reasons of a complex population structure of the black kite. Commonly five to seven M. migrans subspecies are distinguished, each of which is widespread over extensive areas and has more or less an apparent phenotype. Recently, studies of genetic differences between black kite populations started to emerge. On the grounds of earlier studies of mitochondrial and nuclear genes of this species, we check whether there is a genetic support for separation of the black kite subspecies. Recent studies of some mitochondrial loci substantiate the recognition of at least the European (M. m. migrans), Asian (M. m. lineatus and M. m. govinda), African (M. m. aegyptius and M. m. parasitus), and Australian (M. m. affinis) black kite subspecies. Furthermore, the mitochondrial haplotype difference suggests that the African yellow-billed kite, including M. m. aegyptius and M. m. parasitus, should be a separate species as already proposed, or even two separate species

Polytene chromosomes reflect functional organization of the Drosophila genome

Polytene chromosomes of Drosophila melanogaster are a convenient model for studying interphase chromosomes of eukaryotes. They are giant in size in comparison with diploid cell chromosomes and have a pattern of cross stripes resulting from the ordered chromatid arrangement. Each region of polytene chromosomes has a unique banding pattern. Using the model of four chromatin types that reveals domains of varying compaction degrees, we were able to correlate the physical and cytological maps of some polytene chromosome regions and to show the main properties of genetic and molecular organization of bands and interbands, that we describe in this review. On the molecular map of the genome, the interbands correspond to decompacted aquamarine chromatin and 5’ ends of ubiquitously active genes. Gray bands contain lazurite and malachite chromatin, intermediate in the level of compaction, and, mainly, coding parts of genes. Dense black transcriptionally inactive bands are enriched in ruby chromatin. Localization of several dozens of interbands on the genome molecular map allowed us to study in detail their architecture according to the data of whole genome projects. The distribution of proteins and regulatory elements of the genome in the promoter regions of genes localized in the interbands shows that these parts of interbands are probably responsible for the formation of open chromatin that is visualized in polytene chromosomes as interbands. Thus, the permanent genetic activity of interbands and gray bands and the inactivity of genes in black bands are the basis of the universal banding pattern in the chromosomes of all Drosophila tissues. The smallest fourth chromosome of Drosophila with an atypical protein composition of chromatin is a special case.  Using the model of four chromatin states and fluorescent in situ hybridization, its cytological map was refined and the genomic coordinates of all bands and interbands were determined. It was shown that, in spite of the peculiarities of this chromosome, its band organization in general corresponds to the rest of the genome. Extremely long genes of different Drosophila chromosomes do not fit the common scheme, since they can occupy a series of alternating bands and interbands (up to nine chromosomal structures) formed by parts of these genes

ГЛУБИННОЕ СТРОЕНИЕ САЛАИРСКОГО СКЛАДЧАТО-ПОКРОВНОГО СООРУЖЕНИЯ (СЕВЕРО-ЗАПАД ЦЕНТРАЛЬНО-АЗИАТСКОГО СКЛАДЧАТОГО ПОЯСА) ПО ДАННЫМ МАГНИТОТЕЛЛУРИЧЕСКОГО ЗОНДИРОВАНИЯ

The Salair fold-nappe terrane (a.k.a. Salair orogen, Salair) is the northwestern part of the Altai-Sayan folded area of the Central Asian Orogenic Belt. It is composed of Cambrian – Early Ordovician volcanic rocks and island-arc sedimentary deposits. In plan, Salair is a horseshoe-shaped structure with the northeast-facing convex side, which is formed by the outcrops of the Early Paleozoic folded basement. Its inner part is the Khmelev basin composed of Upper Devonian – Lower Carboniferous sandstones and siltstones. The Early Paleozoic volcanic rocks and sediments of Salair are overthrusted onto the Devonian-Permian sediments of the Kuznetsk basin. The Paleozoic thrusts, that were reactivated at the neotectonic stage, are observed in the modern relief as tectonic steps. Our study of the Salair deep structure was based on the data from two profiles of magnetotelluric sounding. These 175-km and 125-km long profiles go across the strike of the Salair structure and the western part of the Kuznetsk basin. Profile 1 detects a subhorizontal zone of increased conductivity (100–500 Ohm·m) at the depths of 8–15 km. At the eastern part of Profile 1, this zone gently continues upward, towards a shallow conducting zone that corresponds to the sediments of the Kuznetsk basin. Two high-resistance bodies (1000–7000 Ohm⋅m) are detected at the depths of 0–6 km in the middle of the section. They are separated by a subvertical conducting zone corresponding to the Kinterep thrust. The main features are the subhorizontal positions and the flattened forms of crustal conductivity anomalies. At the central part of Profile 2, there is a high-resistance block (above 150000 Ohm⋅m) over the entire depth range of the section, from the surface to the depths of about 20 km. In the eastern part of Profile 2, a shallow zone of increased conductivity corresponds to the sediments of the Kuznetsk basin. The subhorizontal mid-crust layer of increased conductivity, which is detected in the Salair crust, is typical of intracontinental orogens. The distribution pattern of electrical conductivity anomalies confirms the Salair thrust onto the Kuznetsk basin. The northern part of the Khmelev basin is characterized by high resistivity, which can be explained by abundant covered Late Permian granite massifs in that part of the Khmelev basin. The Kinterep thrust located in the northeastern part of the Khmelev basin is manifested in the deep geoelectric crust structure as a conducting zone, which can be considered as an evidence of the activity of this fault.Салаирское покровно-складчатое сооружение (Салаирский ороген, Салаир) расположено на северо-западе Алтае-Саянской складчатой области Центрально-Азиатского складчатого пояса и сложено кембрийско-раннеордовикскими вулканогенными и осадочными отложениями островодужного происхождения. В плане Салаир имеет форму подковы, обращенной выпуклой стороной на северо-восток. Во внутренней части этой дугообразной структуры, образованной выходами раннепалеозойского складчатого фундамента, находится Хмелевский прогиб, выполненный терригенными отложениями верхнего девона – нижнего карбона. По системе чешуйчатых надвигов раннепалеозойские отложения Салаира надвинуты на девонско-пермское осадочное выполнение Кузнецкого прогиба. Палеозойские надвиги местами реактивированы на неотектоническом этапе и выражены в современном рельефе тектоногенными уступами. С целью изучения глубинного строения Салаира было пройдено два профиля магнитотеллурического зондирования. Профили имеют длину 175 и 125 км. Они ориентированы вкрест простирания основных структур и пересекают Салаир и западную часть Кузнецкого прогиба. На первом профиле выделяется субгоризонтально залегающая зона повышенной проводимости с удельным электрическим сопротивлением (УЭС) 100–500 Ом⋅м, в диапазоне глубин 8–15 км. В восточной части профиля она полого воздымается в направлении малоглубинной проводящей зоны, соответствующей осадочному выполнению Кузнецкого прогиба. Два высокоомных тела со значениями УЭС 1000–7000 Ом⋅м залегают на глубинах 0–6 км в средней части разреза и разделены субвертикальной проводящей зоной, соответствующей Кинтерепскому надвигу. Главной чертой разреза является субгоризонтальное залегание и уплощенная форма коровых неоднородностей электропроводности. Центральную часть второго профиля занимает высокоомный блок (УЭС более 150000 Ом⋅м), распространяющийся на всю глубину разреза – от поверхности до глубин около 20 км. Восточную часть разреза занимает малоглубинная зона повышенной проводимости, соответствующая осадочному выполнению Кузнецкого прогиба. Земная кора Салаира содержит субгоризонтально залегающую зону повышенной проводимости, типичную для внутриконтинентальных орогенов. Картина распределения аномалий электропроводности подтверждает наличие надвига Салаира на Кузнецкий прогиб. Северная часть Хмелевского прогиба характеризуется высокими значениями УЭС, что может быть объяснено широким развитием невскрытых позднепермских гранитоидных массивов в этой части прогиба. Расположенный в северо-восточной части Хмелевского прогиба Кинтерепский надвиг проявлен в глубинной геоэлектрической структуре земной коры в виде проводящей зоны, что может рассматриваться как свидетельство активности данного разлома