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Avian Lampbrush Chromosomes: a Powerful Tool for Exploration of Genome Expression

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Avian Lampbrush Chromosomes: a Powerful Tool for Exploration of Genome Expression Review Article Cytogenet Genome Res 2009;124:251–267 Accepted after revision: October 14, 2008 DOI: 10.1159/000218130 by A. Houben Avian Lampbrush Chromosomes: a Powerful Tool for Exploration of Genome Expression E. Gaginskaya T. Kulikova A. Krasikova Saint-Petersburg State University, Saint-Petersburg, Russia Key Words some specific features: very long transcription units, deregu- Chicken genome ؒ C h r o m o s o m e o r g a n i z a t i o n ؒ L a m p b r u s h lated termination, and transcription of non-coding satellite chromosomes ؒ Non-coding RNA ؒ Oocyte nucleus ؒ repeats. Here, based on the modern view on a role of RNA ,Oogenesis ؒ T r a n s c r i p t i o n interference machinery in regulation of genome expression we suggest a mechanism of initiation of satellite DNA tran- scription and offer a novel interpretation of the ‘classical’ hy- Abstract pothesis that sought to explain the significance of wide- Lampbrush chromosomes (LBCs) are highly extended biva- spread transcription during oocyte growth. lents that function in the growing oocytes of many animals. Copyright © 2009 S. Karger AG, Basel Due to their distinctive chromomere-loop organization and intense transcriptional activity of lateral loops the LBCs, mainly amphibian ones, have served as a powerful system The investigation of genome structure and function for exploring the general principles of chromosome organi- has been greatly helped by studies of model systems such zation and function. The exploitation of avian LBCs has con- as polytene and lampbrush chromosomes that facilitate siderably broadened the opportunities for comparative exploration of gene activity in vivo. In this respect, giant genome research and for cytogenetic analysis of domestic lampbrush chromosomes (LBCs) deserve special atten- species. In this review we highlight the advantages of avian tion. They represent a special form of meiotic chromo- LBCs for research in different areas including integration of somes, which is assumed during oocyte growth in most genome organization studies with studies on gene activity animals other than mammals [Callan, 1986; Macgregor, in vivo, analysis of co-transcriptional events occurring on na- 1987, 2002] except for some monotremes [Lintern-Moore scent transcripts and investigation of chromosome-associ- et al., 1976]. ated intranuclear domains. Recent findings concerning the LBCs were first observed in 1882 by W. Flemming in organization of transcriptionally active and silent chromatin amphibian oocytes and investigated in detail by J. Rück- together with involvement of cohesin and condensin com- ert in shark oocytes in 1892. Actually, we owe the name plexes into maintenance of structural integrity of LBCs are ‘lampbrush chromosome’ to J. Rückert, who compared presented. The biological significance of the LBC phenom- them with bristled brushes for cleaning oil lamps. The enon is discussed. The intensive transcription on LBCs shows history of discovery and early studies of amphibian LBCs © 2009 S. Karger AG, Basel Alla Krasikova 1424–8581/09/1244–0251$26.00/0 Saint-Petersburg State University Fax +41 61 306 12 34 Oranienbaumskoie sch. 2, Stary Peterhof E-Mail [email protected] Accessible online at: Saint-Petersburg, 198504 (Russia) www.karger.com www.karger.com/cgr Tel. +7 812 450 7311, Fax +7 812 450 7310, E-Mail [email protected] a b c Fig. 1. Avian lampbrush chromosomes (LBCs): general view and scheme of orga- nization. a Chaffinch lampbrush bivalent 2 stained with Coomassie blue R250. Two half-bivalents with a characteristic chro- momere-loop organization are joined at chiasmata (arrows). Terminal giant loops (TGLs) and centromere protein bodies (PBs) associated with avian LBCs are indi- cated. b Quail lampbrush bivalent 3. Im- munostaining with antibodies against the elongating form of RNA polymerase II. Lateral loops representing sites of active transcription are brightly stained. Scale bars = 10 ␮ m. c Schematic drawing of a segment of lampbrush half-bivalent and the enlarged image demonstrating in- volvement of cohesin (red) and condensin (green) complexes into structural mainte- nance of the LBC axes. Sister chromatids (arrowheads), ‘double loop’ bridge (DLB) and transcription units (arrows) are indi- cated. are perfectly described in the monograph by Callan mineral oil maintains its transcriptional activity and can [1986]. Holl [1890] was the first who described avian be efficiently used for analysis of dynamics of fusion pro- LBCs during examination of chicken oocytes. Later the teins within intranuclear structures [Lund and Paine, morphology of chromosomes of that type was investigated 1990; Patel et al., 2008]. in pre-vitellogenic oocytes in other avian species namely Chromosomes in the lampbrush form occur at the Columbiformes, Charadriformes, Strigiformes, Anseri- diplotene stage of meiotic prophase I when the oocyte en- formes, Galliformes and Passeriformes by routine histo- ters the period of cytoplasmic growth (pre-vitellogene- logical technique [Loyez, 1906; van Durme, 1914; Bram- sis). They are highly extended bivalents, in which homol- bell, 1926; Greenfield, 1966; Gaginskaya and Gruzova, ogous chromosomes are united at chiasmata ( fig. 1 a). 1969; Gaginskaya, 1972a, b; Wylie, 1972; Guraya, 1976; Each half-bivalent has characteristic chromomere-loop Gaginskaya and Chin, 1980]. morphology and is represented by an array of discrete The real era of ‘lampbrushology’ began 70 years ago, globules of compact chromatin (chromomeres) with pairs when Duryee [1937] offered the method of LBCs micro- of lateral loops expanded outward [Macgregor, 1984; Cal- dissection from the amphibian germinal vesicle (GV). lan, 1986; Gaginskaya, 1989; Morgan, 2002; Gall et al., The method of microsurgical isolation and spreading of 2004]. Lateral loops correspond to transcriptionally ac- the nuclear content on the microscope slide was then im- tive regions of chromosomes, in which sister chromatids proved and modified by Gall [1954, 1966] and Callan are fully separated ( fig. 1 b). Transcription on lateral loops [Callan and Lloyd, 1960]. Introduction of the technique is very intensive, so that nascent transcripts complexed was possible due to enormous GV size that enables per- with proteins, produce a bulk of RNP matrix, which can formance of various microsurgery manipulations. Fur- be easily visualized in a light microscope. Lateral loops of thermore, telomere regions of LBCs are not attached to normal [according to Callan, 1986], or simple [according the nuclear envelope so that intact chromosomes can be to Morgan, 2002], morphology contain one or several easily isolated [Macgregor and Varley, 1988]. It was dem- transcription units. RNP matrix becomes thicker to- onstrated too that intact GV manually isolated under wards the ends of transcription units due to increase in 252 Cytogenet Genome Res 2009;124:251–267 Gaginskaya/Kulikova/Krasikova the length of transcripts and the quantity of RNP ( fig. 1 c). Chromomere Organization during the In the lateral loops, neighboring transcription units can Lampbrush Phase be orientated in the same or opposite directions. From the very early works on amphibian LBCs, these amazing LBCs provide a well-characterized and original sys- objects have attracted the attention of investigators due tem for precise investigation of chromatin epigenetic to giant size, transcriptional activity, the distinctive chro- modifications, as well as structure and organization of momere-loop organization, and also because of their aes- meiotic bivalents [Macgregor et al., 1997]. Mechanisms thetic beauty. Morgan [2002] summarizes recent data on which establish and maintain structural integrity of the organization and functioning of chromosomes dur- chromosomes of this type during the very long period of ing the lampbrush phase and molecular composition of oocyte growth are still not fully understood. Obviously, specialized nuclear structures – both associated with chromomere-loop configuration of LBCs is sustained by LBCs and extrachromosomal. a high level of transcriptional activity on the one hand After the method of LBCs isolation was adapted to avi- and by a group of chromosomal structural proteins on an oocytes [Koecke and Müller, 1965; Kropotova and the other hand. However, DNA topoisomerase II, which Gaginskaya, 1984; Hutchison, 1987; Solovei et al., 1992], is known to participate in the condensation of mitotic a new promising phase in the lampbrushology began. For chromatin, is not a component of amphibian [Fischer et many reasons, exploration into avian LBCs proved to be al., 1993] or avian [Krasikova et al., 2004] LBCs. highly rewarding. Birds belong to warm-blood amniotes. The main candidates for the role of longitudinal and Moreover, they possess a special intermediate type of oo- transverse molecular clips in LBC axes are proteins of the genesis between the so-called solitary and nutrimental structural maintenance of chromosomes (SMC) group, types [Koschelt and Heider, 1902; Gaginskaya, 1975]. As involved in formation of cohesin and condensin com- with amphibian oocytes, the avian GV has a full set of plexes [Hagstrom and Meyer, 2003; Marko, 2008]. As to LBCs, which are typical diplotene bivalents revealing all cohesins, two subunits of the SMC group and two addi- characteristic features of this chromosome type with well tional proteins, in cooperation sufficient to form a cohe- defined chromomeres and long lateral loops ( fig. 1 a, b). sin complex, were found on the axes of avian LBCs At the same time, in the ovary of adult
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