ALBERT

Description:    Chicken ( Gallus gallus domesticus , GGA) and Japanese quail ( Coturnix coturnix japonica , CCO) karyotypes are very similar. They have identical chromosome number (2 n  = 78) and show a high degree of synteny. Centromere positions on the majority of orthologous chromosomes are different in these two species. To explore the nature of this divergence, we used high-resolution comparative fluorescent in situ hybridization mapping on giant lampbrush chromosomes (LBCs) from growing oocytes. We applied 41 BAC clones specific for GGA1, 2, 3, 11, 12, 13, 14, and 15 to chicken and quail LBCs. This approach allowed us to rule out a pericentric inversion earlier proposed to explain the difference between GGA1 and CCO1. In addition to a well-established large-scale pericentric inversion that discriminates GGA2 and CCO2, we identified another, smaller one in the large inverted region. For the first time, we described in detail inversions that distinguish GGA3 from CCO3 and GGA11 from CCO11. Despite the newly identified and confirmed inversions, our data suggest that, in chicken and Japanese quail, the difference in centromere positions is not mainly caused by pericentric inversions but is instead due to centromere repositioning events and the formation of new centromeres. We also consider the formation of short arms of quail microchromosomes by heterochromatin accumulation as a third scenario that could explain the discrepancy in centromeric indexes. Content Type Journal Article Pages 1-16 DOI 10.1007/s10577-012-9319-7 Authors Anna Zlotina, Saint-Petersburg State University, Oranienbaumskoe sh., 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Svetlana Galkina, Saint-Petersburg State University, Oranienbaumskoe sh., 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Alla Krasikova, Saint-Petersburg State University, Oranienbaumskoe sh., 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Richard P. M. A. Crooijmans, Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands Martien A. M. Groenen, Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands Elena Gaginskaya, Saint-Petersburg State University, Oranienbaumskoe sh., 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Svetlana Deryusheva, Saint-Petersburg State University, Oranienbaumskoe sh., 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description:    We have identified novel nuclear bodies, which we call pearls, in the giant oocyte nuclei of Xenopus laevis and Xenopus tropicalis . Pearls are attached to the lampbrush chromosomes at specific loci that are transcribed by RNA polymerase III, and they disappear after inhibition of polymerase III activity. Pearls are enriched for small Cajal body-specific RNAs (scaRNAs), which are guide RNAs that modify specific nucleotides on splicing snRNAs. Surprisingly, snRNAs themselves are not present in pearls, suggesting that pearls are not functionally equivalent to Cajal bodies in other systems, which contain both snRNAs and scaRNAs. We suggest that pearls may function in the processing of RNA polymerase III transcripts, such as tRNA, 5S rRNA, and other short non-coding RNAs. Content Type Journal Article Pages 1-17 DOI 10.1007/s10577-012-9320-1 Authors Zehra F. Nizami, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA Joseph G. Gall, Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description:    Exploration into morphofunctional organisation of centromere DNA sequences is important for understanding the mechanisms of kinetochore specification and assembly. In-depth epigenetic analysis of DNA fragments associated with centromeric nucleosome proteins has demonstrated unique features of centromere organisation in chicken karyotype: there are both mature centromeres, which comprise chromosome-specific homogeneous arrays of tandem repeats, and recently evolved primitive centromeres, which consist of non-tandemly organised DNA sequences. In this work, we describe the arrangement and transcriptional activity of chicken centromere repeats for Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 and non-repetitive centromere sequences of chromosomes 5, 27, and Z using highly elongated lampbrush chromosomes, which are characteristic of the diplotene stage of oogenesis. The degree of chromatin packaging and fine spatial organisations of tandemly repetitive and non-tandemly repetitive centromeric sequences significantly differ at the lampbrush stage. Using DNA/RNA FISH, we have demonstrated that during the lampbrush stage, DNA sequences are transcribed within the centromere regions of chromosomes that lack centromere-specific tandem repeats. In contrast, chromosome-specific centromeric repeats Cen1, Cen2, Cen3, Cen4, Cen7, Cen8, and Cen11 do not demonstrate any transcriptional activity during the lampbrush stage. In addition, we found that CNM repeat cluster localises adjacent to non-repetitive centromeric sequences in chicken microchromosome 27 indicating that centromere region in this chromosome is repeat-rich. Cross-species FISH allowed localisation of the sequences homologous to centromeric DNA of chicken chromosomes 5 and 27 in centromere regions of quail orthologous chromosomes. Content Type Journal Article Pages 1-14 DOI 10.1007/s10577-012-9321-0 Authors Alla Krasikova, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Tatsuo Fukagawa, Department of Genetics, National Institute of Genetics, Mishima, Japan Anna Zlotina, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg, 198504 Russia Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description: A Tribute to Simon W.L. Chan, PhD (1974–2012) Content Type Journal Article Pages 1-2 DOI 10.1007/s10577-012-9314-z Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description:    A nonrandom radial nuclear organization of genes has been well documented. This study provides further evidence that radial positioning depends on features of corresponding ∼1 Mbp chromatin domains (CDs), which represent the basic units of higher-order chromatin organization. We performed a quantitative three-dimensional analysis of the radial nuclear organization of three genes located on chromosome 1 in a DG75 Burkitt lymphoma-derived cell line. Quantitative real-time polymerase chain reaction revealed similar transcription levels for the three selected genes, whereas the total expression strength (TES) calculated as the sum of transcription of all genes annotated within a surrounding window of about 1 Mbp DNA differed for each region. Radial nuclear position of the studied CDs correlated with TES, i.e., the domain with the highest TES occupied the most interior position. Positions of CDs with stable TES values were stably maintained even under experimental conditions, resulting in genome-wide changes of the expression levels of many other genes. Our results strongly support the hypothesis that knowledge of the local chromatin environment is essential to predict the radial nuclear position of a gene. Content Type Journal Article Pages 1-18 DOI 10.1007/s10577-012-9309-9 Authors Alexandra C. Kölbl, Department Biologie II, Ludwig-Maximilians-Universität München, 82152 Planegg, Martinsried, Germany Daniela Weigl, Department Biologie II, Ludwig-Maximilians-Universität München, 82152 Planegg, Martinsried, Germany Medhanie Mulaw, Medizinische Klinik und Poliklinik III, Ludwig-Maximilians-Universität München, Munich, Germany Tobias Thormeyer, Department Biologie II, Ludwig-Maximilians-Universität München, 82152 Planegg, Martinsried, Germany Stefan K. Bohlander, Medizinische Klinik und Poliklinik III, Ludwig-Maximilians-Universität München, Munich, Germany Thomas Cremer, Department Biologie II, Ludwig-Maximilians-Universität München, 82152 Planegg, Martinsried, Germany Steffen Dietzel, Department Biologie II, Ludwig-Maximilians-Universität München, 82152 Planegg, Martinsried, Germany Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description:    We have examined transcription loops on lampbrush chromosomes of the newt Notophthalmus by superresolution microscopy. Because of the favorable, essentially two-dimensional morphology of these loops, an average optical resolution in the x – y plane of about 50 nm was achieved. We analyzed the distribution of the multifunctional RNA-binding protein CELF1 on specific loops. CELF1 distribution is consistent with a model in which individual transcripts are tightly folded and hence closely packed against the loop axis. Content Type Journal Article Pages 1-7 DOI 10.1007/s10577-012-9306-z Authors Rainer Kaufmann, Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany Christoph Cremer, Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany Joseph G. Gall, Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description:    Ring chromosomes and small supernumerary marker chromosomes (sSMC) are enigmatic types of derivative chromosomes, in which the telomeres are thought to play a crucial role in their formation and stabilization. Considering that there are only a few studies that evaluate the presence of telomeric sequences in ring chromosomes and on sSMC, here, we analyzed 14 ring chromosomes and 29 sSMC for the presence of telomeric sequences through fluorescence in situ hybridization (FISH). The results showed that ring chromosomes can actually fall into two groups: the ones with or without telomeres. Additionally, telomeric signals were detectable at both ends of centric and neocentric sSMC with inverted duplication shape, as well as in complex sSMC. Apart from that, generally both ring- and centric minute-shaped sSMC did not present telomeric sequences neither detectable by FISH nor by a second protein-directed immunohistochemical approach. However, the fact that telomeres are absent does not automatically mean that the sSMC has a ring shape, as often deduced in the previous literature. Overall, the results obtained by FISH studies directed against telomeres need to be checked carefully by other approaches. Content Type Journal Article Pages 1-11 DOI 10.1007/s10577-012-9316-x Authors Roberta Santos Guilherme, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Elisabeth Klein, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Claudia Venner, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Ahmed B. Hamid, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Samarth Bhatt, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Maria Isabel Melaragno, Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, 04023-900 São Paulo, SP, Brazil Marianne Volleth, Institut für Humangenetik, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany Anna Polityko, National Medical Center, ‘Mother and Child’, Orlovskaya Str. 66, 220053 Minsk, Belarus Anna Kulpanovich, National Medical Center, ‘Mother and Child’, Orlovskaya Str. 66, 220053 Minsk, Belarus Nadezda Kosyakova, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Thomas Liehr, Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, 07743 Jena, Germany Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849

Description:    Flow cytometry (FCM) has been widely used in plant science to determine the amount of nuclear DNA, either in absolute units or in relative terms, as an indicator of ploidy. The requirement for fresh material in some applications, however, limits the value of FCM in field research, including plant biosystematics, ecology and population biology. Dried plant samples have proven to be a suitable alternative in some cases (large-scale ploidy screening) although tissue dehydration is often associated with a decrease in the quality of FCM analysis. The present study tested, using time-scale laboratory and in situ field experiments, the applicability of glycerol-treated nuclear suspension for DNA flow cytometry. We demonstrate that plant nuclei preserved in ice-cold buffer + glycerol solution remain intact for at least a few weeks and provide estimates of nuclear DNA content that are highly comparable and of similar quality to those obtained from fresh tissue. The protocol is compatible with both DAPI and propidium iodide staining, and allows not only the determination of ploidy level but also genome size in absolute units. Despite its higher laboriousness, glycerol-preserved nuclei apparently represent the most reliable way of sample preservation for genome size research. We assume that the protocol will provide a vital alternative to other preservation methods, especially when stringent criteria on the quality of FCM analysis are required. Content Type Journal Article Pages 303-315 DOI 10.1007/s10577-012-9277-0 Authors Filip Kolář, Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic Magdalena Lučanová, Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic Jakub Těšitel, Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic João Loureiro, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, P.O. Box 3046, 3001-455 Coimbra, Portugal Jan Suda, Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849 Journal Volume Volume 20 Journal Issue Volume 20, Number 2

Description:    Several recent studies have produced comparative maps of genes on amniote sex chromosomes, revealing homology of gene content and arrangement across lineages as divergent as mammals and lizards. For example, the chicken Z chromosome, which shares homology with the sex chromosomes of all birds, monotremes, and a gecko, is a striking example of stability of genome organization and retention, or independent acquisition, of function in sex determination. In other lineages, such as snakes and therian mammals, well conserved but independently evolved sex chromosome systems have arisen. Among lizards, novel sex chromosomes appear frequently, even in congeneric species. Here, we review recent gene mapping data, examine the evolutionary relationships of amniote sex chromosomes and argue that gene content can predispose some chromosomes to a specialized role in sex determination. Content Type Journal Article Pages 7-19 DOI 10.1007/s10577-011-9266-8 Authors Denis O’Meally, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia Tariq Ezaz, Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia Arthur Georges, Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia Stephen D. Sarre, Wildlife Genetics Laboratory, Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia Jennifer A. Marshall Graves, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849 Journal Volume Volume 20 Journal Issue Volume 20, Number 1

Description:    Three xenarthrans species Chaetophractus villosus , Chaetophractus vellerosus , and Zaedyus pichiy have been used for the analysis of the structure, behavior, and immunochemical features of the XY body during pachytene. In all these species, the sex chromosomes form an XY body easily identifiable in thin sections by the special and regular packing of the chromatin fibers of the internal region of the XY body (“differential” regions) and those of the peripheral region (synaptic region). Spermatocyte spreads show a complete synapsis between the X- and the Y-axis, which lasts up to the end of pachytene. From the early pachytene substages to the late ones, the X-axis develops prominent branches, which in late pachytene span the synaptic region. Synapsis is regular as shown by SYCP1 labeling. Axial development is followed by SYCP3 labeling and in the asynaptic region of the X-axis by BRCA1. Gamma-H2AX labels exclusively the differential (asynaptic) region of the X chromosome. A single focus is labeled by MLH1 in the synaptic region. The location of this MLH1 focus spans from 0.3 to 1.6 μm from the telomere in the analyzed xenarthrans, covering approximately half of the Y-axis length. It is concluded that xenarthrans, as basal placental mammals, harbor the largest pseudoautosomal regions of presently analyzed mammals, and shows the typical features of meiotic sex chromosome inactivation (MSCI). Content Type Journal Article Pages 293-302 DOI 10.1007/s10577-012-9273-4 Authors Roberta B. Sciurano, 2da. Cátedra de Histología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10 (C1121ABG), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina Mónica I. Rahn, 2da. Cátedra de Histología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10 (C1121ABG), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina Luis Rossi, 2da. Cátedra de Histología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10 (C1121ABG), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina Juan Pablo Luaces, 2da. Cátedra de Histología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10 (C1121ABG), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina María Susana Merani, 2da. Cátedra de Histología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10 (C1121ABG), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina Alberto J. Solari, 2da. Cátedra de Histología, Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10 (C1121ABG), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina Journal Chromosome Research Online ISSN 1573-6849 Print ISSN 0967-3849 Journal Volume Volume 20 Journal Issue Volume 20, Number 2