TY  - JOUR
AB  - Holocentric chromosomes occur in a number of independent eukaryotic lineages, and they form holokinetic kinetochores along the entire poleward chromatid surfaces. Due to this alternative chromosome structure, Luzula elegans sister chromatids segregate already in anaphase I followed by the segregation of the homologues in anaphase II. However, not yet known is the localization and dynamics of cohesin and the structure of the synaptonemal complex (SC) during meiosis. We show here that the α-kleisin subunit of cohesin localizes at the centromeres of both mitotic and meiotic metaphase chromosomes and that it, thus, may contribute to assemble the centromere in L. elegans. This localization and the formation of a tripartite SC structure indicate that the prophase I behaviour of L. elegans is similar as in monocentric species.
AU  - Ma, W.*
AU  - Schubert, V.*
AU  - Martis, M.M.
AU  - Hause, G.*
AU  - Liu, Z.*
AU  - Shen, Y.*
AU  - Conrad, U.*
AU  - Shi, W.*
AU  - Scholz, U.*
AU  - Taudien, S.*
AU  - Cheng, Z.*
AU  - Houben, A.*
C1  - 48896
C2  - 41487
CY  - Dordrecht
SP  - 393-405
TI  - The distribution of α-kleisin during meiosis in the holocentromeric plant Luzula elegans.
JO  - Chromosome Res.
VL  - 24
IS  - 3
PB  - Springer
PY  - 2016
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - 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.
AU  - Kölbl, A.C.*
AU  - Weigl, D.*
AU  - Mulaw, M.A.
AU  - Thormeyer, T.*
AU  - Bohlander, S.K.
AU  - Cremer, T.*
AU  - Dietzel, S.*
C1  - 26400
C2  - 32211
SP  - 735-752
TI  - The radial nuclear positioning of genes correlates with features of megabase-sized chromatin domains.
JO  - Chromosome Res.
VL  - 20
IS  - 6
PB  - Springer
PY  - 2012
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - We used chicken retinospheroids (RS) to study the nuclear architecture of vertebrate cells in a three-dimensional (3D) cell culture system. The results showed that the different neuronal cell types of RS displayed an extreme form of radial nuclear organization. Chromatin was arranged into distinct radial zones which became already visible after DAPI staining. The distinct zones were enriched in different chromatin modifications and in different types of chromosomes. Active isoforms of RNA polymerase II were depleted in the outermost zone. Also chromocenters and nucleoli were radially aligned in the nuclear interior. The splicing factor SC35 was enriched at the central zone and did not show the typical speckled pattern of distribution. Evaluation of neuronal and non-neuronal chicken tissues showed that the highly ordered form of radial nuclear organization was also present in neuronal chicken tissues. Furthermore, the data revealed that the neuron-specific nuclear organization was remodeled when cells spread on a flat substrate. Monolayer cultures of a chicken cell line did not show this extreme form of radial organization. Rather, such monolayer cultures displayed features of nuclear organization which have been described before for many different types of monolayer cells. The finding that an extreme form radial nuclear organization, which has not been described before, is present in RS and tissues, but not in cells spread on a flat substrate, suggests that it would be important to complement studies on nuclear architecture performed with monolayer cells by studies on 3D cell culture systems and tissues.
AU  - Berchtold, D.*
AU  - Fesser, S.*
AU  - Bachmann, G.*
AU  - Kaiser, A.*
AU  - Eilert, J.C.*
AU  - Frohns, F.*
AU  - Sadoni, N.*
AU  - Muck, J.*
AU  - Kremmer, E.
AU  - Eick, D.
AU  - Layer, P.G.*
AU  - Zink, D.*
C1  - 6127
C2  - 28439
CY  - Dordrecht
SP  - 165-182
TI  - Nuclei of chicken neurons in tissues and three-dimensional cell cultures are organized into distinct radial zones.
JO  - Chromosome Res.
VL  - 19
IS  - 2
PB  - Springer
PY  - 2011
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - A new experimental approach was designed to test different predictions of current models of the nuclear architecture with respect to the topography of transcription. We constructed a plasmid, termed pIndi, which carries a reporter gene coding for a red cytoplasmic fluorescent reporter protein. Transcription of the reporter gene is regulated by the inducible promoter of the human immunodeficiency virus (HIV) and is strongly dependent on the HIV-1 Tat protein. Expressing the red fluorescent reporter protein allowed us to distinguish between cells with active and silent reporter genes. Importantly, transient transfection resulted in the clustering of plasmids, forming one or several extra-chromosomal pIndi bodies. Repetitive lac operator sequences in pIndi allowed us to visualize these bodies in living cells by the binding of LacI proteins tagged with a fluorescent protein. Using this model, we analyzed the three-dimensional nuclear topography of pIndi bodies with active or silent reporter genes. Our results are compatible with predictions of the chromosome territory-interchromatin compartment (CT-IC) model. We demonstrate that pIndi bodies localize in the IC, both in the silent and active state. Activation of transgene transcription resulted in the recruitment of RNA polymerase II and NFkappaB and a closer positioning to splicing speckles.
AU  - Meggendorfer, M.
AU  - Weierich, C.*
AU  - Wolff, H.
AU  - Brack-Werner, R.
AU  - Cremer, T.*
C1  - 5950
C2  - 27638
SP  - 401-417
TI  - Functional nuclear topography of transcriptionally inducible extra-chromosomal transgene clusters.
JO  - Chromosome Res.
VL  - 18
IS  - 4
PB  - Springer
PY  - 2010
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - DNA replication initiates from origins of replication following a strict sequential activation programme and a conserved temporal order of activation. The number of replication initiation sites varies between species, according to the complexity of the genomes, with an average spacing of 100,000 bp. In contrast to yeast genomes, the location and definition of origins in mammalian genomes has been elusive. Historically, mammalian replication initiation sites have been mapped in situ by systematically searching specific genomic loci for sites that preferentially initiated DNA replication, potential origins by start-site mapping and autonomously replicating sequence experiments, and potential ORC and pre-replicative complex (pre-RC) sites by chromatin immunoprecipitation (ChIP) using antibodies for pre-RC proteins. In the past decade, ChIP has become an important method for analyzing protein/DNA interactions. Classically, ChIP is combined with Southern blotting or PCR. Recently, whole genome-ChIP methods have been very successful in unicellular eukaryotes to understand molecular mechanisms coordinating replication initiation and its flexibility in response to environmental changes. However, in mammalian systems, ChIP with pre-RC antibodies has often been challenging and genome-wide studies are scarce. In this review, we will appraise the progress that has been made in understanding replication origin organization using immunoprecipitation of the ORC and Mcm2-7 complexes. A special focus will be on the advantages and disadvantages of genome-wide ChIP-technologies and their potential impact on understanding metazoan replicators.
AU  - Schepers, A.
AU  - Papior, P.
C1  - 1142
C2  - 27241
SP  - 63-77
TI  - Why are we where we are? Understanding replication origins and initiation sites in eukaryotes using ChIP-approaches.
JO  - Chromosome Res.
VL  - 18
IS  - 1
PB  - Springer
PY  - 2010
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - We analysed the nuclear organization of the Polycomb/Trithorax group response element (PRE/TRE) Fab-7 and of other PRE/TREs in larval tissues of D. melanogaster. The results show that pairing/clustering of transgenic and endogenous Fab-7 elements and of other endogenous PRE/TREs occurs only to a limited degree in a highly locus-specific and tissue-specific manner. However, transgenic Fab-7 elements as well as the Fab-7-regulated Abd-B gene and other endogenous loci preferentially occupied defined nuclear regions. Preferred association with the nuclear periphery was observed in the inactive state. However, also in the active state, Fab-7 was often found associated with the nuclear periphery as well as with the boundary of heterochromatin in a fly line- and tissue-specific manner. The boundary between heterochromatin and euchromatin revealed a highly complex architecture in the three-dimensional nuclear space with a close juxtaposition of active and repressed domains. The results suggest that such complex architectures create nuclear microenvironments sustaining specific states of activity of defined PRE/TREs. However, the data also show that the positional behaviour of the transgenic Fab-7 element does not apply to PRE/TREs in general. Altogether, this finding and the highly locus-, tissue-, and fly line-specific behaviour with regard to nuclear positioning and pairing/clustering suggest that the relationships between nuclear organization and functional regulation of PRE/TREs are highly complex and that simple models making general predictions might not be appropriate.
AU  - Fedorova, E.*
AU  - Sadoni, N.*
AU  - Dahlsveen, I.K.*
AU  - Koch, J.*
AU  - Kremmer, E.
AU  - Eick, D.
AU  - Paro, R.*
AU  - Zink, D.*
C1  - 3207
C2  - 25691
SP  - 649-673
TI  - The nuclear organization of Polycomb/Trithorax group response elements in larval tissues of Drosophila melanogaster.
JO  - Chromosome Res.
VL  - 16
IS  - 4
PB  - Springer
PY  - 2008
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - For many years whole chromosome painting probes have been the work-horses in a large variety of clinical and research molecular cytogenetic applications. In recent years painting probes have been complemented by an increasing number of further region-specific probes, which allow the specific staining of centromeres, subtelomeres or other regions within the genome. This development of new probe sets was greatly facilitated by the Human Genome Project from which well-characterized probes for any region within the genome have emerged. Furthermore, the evolution of different multicolor fluorescence in situ hybridization (FISH) technologies now allows the cohybridization of multiple DNA-probes of different colors. These developments have paved the way for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. Using appropriate instrumentation and image processing, the analysis can be performed two-dimensionally on metaphase spreads or three-dimensionally in intact interphase nuclei. Here we summarize some of the most recent developments and discuss the application of painting probes in different scenarios.
AU  - Langer, S.
AU  - Kraus, J.
AU  - Jentsch, I.*
AU  - Speicher, M.R.
C1  - 2323
C2  - 21819
SP  - 15-23
TI  - Multicolor chromosome painting in diagnostic and research applications.
JO  - Chromosome Res.
VL  - 12
IS  - 1
PY  - 2004
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - Fluorescence in situ hybridization (FISH) plays an essential role in research and clinical diagnostics. The versatility and resolution of FISH depends critically on the probe set used. Here, we describe an improved approach for the generation of specific DNA probes from single copies of chromosomes. Single chromosomes or single chromosomal regions were microdissected by laser pressure catapulting and amplified using linker-adaptor PCR. The probes were labeled and tested in various scenarios including multicolor-FISH experiments employing up to seven different fluorochromes. FISH confirmed the specific and even staining of the respective chromosomal regions. Furthermore, the capability of these probes to detect even small translocations (<3 Mb) suggests that the dissected regions are completely represented in the generated painting probes.
AU  - Thalhammer, S.*
AU  - Langer, S.*
AU  - Speicher, M.R.
AU  - Heckl, W.M.*
AU  - Geigl, J.B.
C1  - 2996
C2  - 21814
SP  - 337-343
TI  - Generation of chromosome painting probes from single chromosomes by laser microdissection and linker-adaptor PCR.
JO  - Chromosome Res.
VL  - 12
IS  - 4
PY  - 2004
SN  - 0967-3849
ER  - 

TY  - JOUR
AB  - Karyotyping of mouse chromosomes is a skillful art, which is laborious work even for experienced cytogeneticists. With the growing number of mouse models for human diseases, there is an increasing demand for automated mouse karyotyping systems. Here, such a karyotyping system for mouse chromosomes based on the multiplex-fluorescence in-situ hybridization (M-FISH) technology is shown. The system was tested on a number of individual mice with numerical and structural aberrations and its reproducibility and robustness verified. Mouse M-FISH should be a valuable tool for the analysis of chromosomal rearrangements in mice.
AU  - Jentsch, I.*
AU  - Adler, I.-D.
AU  - Carter, N.P.*
AU  - Speicher, M.R.*
C1  - 23582
C2  - 31387
SP  - 211-214
TI  - Karyotyping mouse chromosomes by multiplex-FISH (M-FISH).
JO  - Chromosome Res.
VL  - 9
IS  - 3
PB  - Kluwer Academic Publishers
PY  - 2001
SN  - 0967-3849
ER  -