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Demakova OV, Demakov SA, Boldyreva LV, Zykova TY, Levitsky VG, Semeshin VF, Pokholkova GV, Sidorenko DS, Goncharov FP, Belyaeva ES, Zhimulev IF. Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes. Chromosoma 2019; 129:25-44. [PMID: 31820086 DOI: 10.1007/s00412-019-00728-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
In Drosophila melanogaster, the chromatin of interphase polytene chromosomes appears as alternating decondensed interbands and dense black or thin gray bands. Recently, we uncovered four principle chromatin states (4НММ model) in the fruit fly, and these were matched to the structures observed in polytene chromosomes. Ruby/malachite chromatin states form black bands containing developmental genes, whereas aquamarine chromatin corresponds to interbands enriched with 5' regions of ubiquitously expressed genes. Lazurite chromatin supposedly forms faint gray bands and encompasses the bodies of housekeeping genes. In this report, we test this idea using the X chromosome as the model and MSL1 as a protein marker of the lazurite chromatin. Our bioinformatic analysis indicates that in the X chromosome, it is only the lazurite chromatin that is simultaneously enriched for the proteins and histone marks associated with exons, transcription elongation, and dosage compensation. As a result of FISH and EM mapping of a dosage compensation complex subunit, MSL1, we for the first time provide direct evidence that lazurite chromatin forms faint gray bands. Our analysis proves that overall most of housekeeping genes typically span from the interbands (5' region of the gene) to the gray band (gene body). More rarely, active lazurite chromatin and inactive malachite/ruby chromatin may be found within a common band, where both the housekeeping and the developmental genes reside together.
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Affiliation(s)
- Olga V Demakova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Sergey A Demakov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Lidiya V Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Tatyana Yu Zykova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Victor G Levitsky
- Novosibirsk State University, Novosibirsk, 630090, Russia.,Institute of Cytology and Genetics, SB RAS, 630090, Novosibirsk, Russia
| | - Valeriy F Semeshin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Galina V Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Darya S Sidorenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Fedor P Goncharov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Elena S Belyaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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Kotlikova IV, Demakova OV, Semeshin VF, Shloma VV, Boldyreva LV, Kuroda MI, Zhimulev IF. The Drosophila dosage compensation complex binds to polytene chromosomes independently of developmental changes in transcription. Genetics 2006; 172:963-74. [PMID: 16079233 PMCID: PMC1456256 DOI: 10.1534/genetics.105.045286] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2005] [Accepted: 07/22/2005] [Indexed: 11/18/2022] Open
Abstract
In Drosophila, the dosage compensation complex (DCC) mediates upregulation of transcription from the single male X chromosome. Despite coating the polytene male X, the DCC pattern looks discontinuous and probably reflects DCC dynamic associations with genes active at a given moment of development in a salivary gland. To test this hypothesis, we compared binding patterns of the DCC and of the elongating form of RNA polymerase II (PolIIo). We found that, unlike PolIIo, the DCC demonstrates a stable banded pattern throughout larval development and escapes binding to a subset of transcriptionally active areas, including developmental puffs. Moreover, these proteins are not completely colocalized at the electron microscopy level. These data combined imply that simple recognition of PolII machinery or of general features of active chromatin is either insufficient or not involved in DCC recruitment to its targets. We propose that DCC-mediated site-specific upregulation of transcription is not the fate of all active X-linked genes in males. Additionally, we found that DCC subunit MLE associates dynamically with developmental and heat-shock-induced puffs and, surprisingly, with those developing within DCC-devoid regions of the male X, thus resembling the PolIIo pattern. These data imply that, independently of other MSL proteins, the RNA-helicase MLE might participate in general transcriptional regulation or RNA processing.
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Affiliation(s)
- I V Kotlikova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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Kelley RL. Path to equality strewn with roX. Dev Biol 2004; 269:18-25. [PMID: 15081354 DOI: 10.1016/j.ydbio.2004.01.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2003] [Revised: 01/12/2004] [Accepted: 01/26/2004] [Indexed: 11/29/2022]
Abstract
Male flies hypertranscribe most genes along their single X chromosome to match the output of females with two X chromosomes. This is mediated by chromatin modifications carried out by the MSL complex composed of noncoding roX RNA and at least five MSL proteins. New results indicate that one of these subunits, the MOF acetyltransferase, not only acts on histone H4, but on itself and MSL3. Cycles of covalent modifications of the MSL subunits may determine the proper level of hypertranscription or control cis spreading along the chromosome. The MSL complex binds to the roX genes, the very source of the RNA component of the complex. New details of how this interaction occurs hint at a possible autoregulatory function. Finally, despite intensive efforts, the molecular mechanism by which the MSL complex distinguishes the X from the autosomes remains a mystery. The MSL complex is able to spread epigenetically from the site of roX transcription, and recent work has defined the conditions that control local cis spreading. However, it is equally clear that soluble MSL complex can distinguish the X chromosome from autosomes. Reconciling all these findings into a unified model presents a challenge.
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Affiliation(s)
- Richard L Kelley
- Department of Molecular, Cellular Biology and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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Zhimulev IF, Belyaeva ES, Semeshin VF, Koryakov DE, Demakov SA, Demakova OV, Pokholkova GV, Andreyeva EN. Polytene Chromosomes: 70 Years of Genetic Research. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 241:203-75. [PMID: 15548421 DOI: 10.1016/s0074-7696(04)41004-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Polytene chromosomes were described in 1881 and since 1934 they have served as an outstanding model for a variety of genetic experiments. Using the polytene chromosomes, numerous biological phenomena were discovered. First the polytene chromosomes served as a model of the interphase chromosomes in general. In polytene chromosomes, condensed (bands), decondensed (interbands), genetically active (puffs), and silent (pericentric and intercalary heterochromatin as well as regions subject to position effect variegation) regions were found and their features were described in detail. Analysis of the general organization of replication and transcription at the cytological level has become possible using polytene chromosomes. In studies of sequential puff formation it was found for the first time that the steroid hormone (ecdysone) exerts its action through gene activation, and that the process of gene activation upon ecdysone proceeds as a cascade. Namely on the polytene chromosomes a new phenomenon of cellular stress response (heat shock) was discovered. Subsequently chromatin boundaries (insulators) were discovered to flank the heat shock puffs. Major progress in solving the problems of dosage compensation and position effect variegation phenomena was mainly related to studies on polytene chromosomes. This review summarizes the current status of studies of polytene chromosomes and of various phenomena described using this successful model.
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia
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