{"title":"Editorial: C.R., the new Editor-in-Chief of C.R.","authors":"Conly L Rieder","doi":"10.1007/s10577-012-9333-9","DOIUrl":"https://doi.org/10.1007/s10577-012-9333-9","url":null,"abstract":"","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"1-3"},"PeriodicalIF":2.6,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-012-9333-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40219941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Induction of human lampbrush chromosomes.","authors":"Ji-Long Liu, Joseph G Gall","doi":"10.1007/s10577-012-9331-y","DOIUrl":"10.1007/s10577-012-9331-y","url":null,"abstract":"<p><p>We previously demonstrated that sperm heads from amphibians (Xenopus and Rana) and zebrafish (Danio) could form giant lampbrush chromosomes when injected into the nucleus of amphibian oocytes. However, similar experiments with mammalian sperm heads were unsuccessful. Here, we describe a slightly modified procedure and demonstrate that human sperm heads can form giant lampbrush chromosomes when injected into the oocyte nucleus of the frog Xenopus laevis or the newt Notophthalmus viridescens. Human and other mammalian chromosomes do not form recognizable lampbrush chromosomes in their own oocytes or in any somatic cells. These experiments thus demonstrate that the lampbrush condition is an inducible state and that the amphibian oocyte nucleus contains all factors required to remodel the inactive chromatin of a mammalian sperm into a transcriptionally active state. They also demonstrate that absence of lampbrush chromosomes from human oocytes must relate to specific features of mammalian oogenesis, not to permanent genetic or epigenetic changes in the chromatin.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"971-8"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566279/pdf/nihms433685.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40217707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ahmet L Tek, Kazunari Kashihara, Minoru Murata, Kiyotaka Nagaki
{"title":"Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat.","authors":"Ahmet L Tek, Kazunari Kashihara, Minoru Murata, Kiyotaka Nagaki","doi":"10.1007/s10577-011-9247-y","DOIUrl":"https://doi.org/10.1007/s10577-011-9247-y","url":null,"abstract":"<p><p>The centromere plays an essential role for proper chromosome segregation during cell division and usually harbors long arrays of tandem repeated satellite DNA sequences. Although this function is conserved among eukaryotes, the sequences of centromeric DNA repeats are variable. Most of our understanding of functional centromeres, which are defined by localization of a centromere-specific histone H3 (CENH3) protein, comes from model organisms. The components of the functional centromere in legumes are poorly known. The genus Astragalus is a member of the legumes and bears the largest numbers of species among angiosperms. Therefore, we studied the components of centromeres in Astragalus sinicus. We identified the CenH3 homolog of A. sinicus, AsCenH3 that is the most compact in size among higher eukaryotes. A CENH3-based assay revealed the functional centromeric DNA sequences from A. sinicus, called CentAs. The CentAs repeat is localized in A. sinicus centromeres, and comprises an AT-rich tandem repeat with a monomer size of 20 nucleotides.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"969-78"},"PeriodicalIF":2.6,"publicationDate":"2011-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-011-9247-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40138293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Stability of monocentric and dicentric ring minichromosomes in Arabidopsis.","authors":"Etsuko Yokota, Fukashi Shibata, Kiyotaka Nagaki, Minoru Murata","doi":"10.1007/s10577-011-9250-3","DOIUrl":"https://doi.org/10.1007/s10577-011-9250-3","url":null,"abstract":"<p><p>A dicentric ring minichromosome (miniδ) was identified in transgenic Arabidopsis thaliana and added to a wild type as a supernumerary chromosome. This line is relatively stable and has been maintained for generations, notwithstanding its ring and dicentric structure. To determine the mechanism for stable transmission of miniδ, the structure and behavior of two new types of ring minichromosomes (miniδ1 and miniδ1-1) derived from miniδ were investigated. Fluorescence in situ hybridization analysis revealed that miniδ1 is dicentric just like miniδ, whereas miniδ1-1 is monocentric. The estimated sizes of miniδ1 and miniδ1-1 were 3.8~5.0 and 1.7 Mb, respectively. The sizes of the two centromeres on miniδ1 were identical (ca. 270 kb) and similar to that of miniδ1-1 (ca. 250 kb). Miniδ1 was relatively stable during mitosis and meiosis, as is miniδ, whereas miniδ1-1 was unstable during mitosis, and the number of minichromosomes per cell varied. This possibly resulted from misdivision caused by a short centromere on monocentric miniδ1-1. Transmission through the female was quite limited for all three ring minichromosomes (0-3.2%), whereas that through the male was relatively high (15.4-27.3%) compared with that of other supernumerary chromosomes in Arabidopsis. Ring structure without telomeres itself seems not to limit the female transmission.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"999-1012"},"PeriodicalIF":2.6,"publicationDate":"2011-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-011-9250-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40115151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A guided tour of large genome size in animals: what we know and where we are heading.","authors":"France Dufresne, Nicholas Jeffery","doi":"10.1007/s10577-011-9248-x","DOIUrl":"https://doi.org/10.1007/s10577-011-9248-x","url":null,"abstract":"<p><p>The study of genome size diversity is an ever-expanding field that is highly relevant in today's world of rapid and efficient DNA sequencing. Animal genome sizes range from 0.02 to 132.83 pg but the majority of animal genomes are small, with the most of these genome sizes being less than 5 pg. Animals with large genomes (> 10 pg) are scattered within some invertebrates, including the Platyhelminthes, crustaceans, and orthopterans, and also the vertebrates including the Actinopterygii, Chondrichthyes, and some amphibians. In this paper, we explore the connections between organismal phenotype, physiology, and ecology to genome size. We also discuss some of the molecular mechanisms of genome shrinkage and expansion obtained through comparative studies of species with full genome sequences and how this may apply to species with large genomes. As most animal species sequenced to date have been in the small range for genome size (especially invertebrates) due to sequencing costs and to difficulties associated with large genome assemblies, an understanding of the structural composition of large genomes is still lacking. Studies using next-generation sequencing are being attempted for the first time in animals with larger genomes. Such analyses using low genome coverage are providing a glimpse of the composition of repetitive elements in animals with more complex genomes. These future studies will allow a better understanding of factors leading to genomic obesity in animals.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"925-38"},"PeriodicalIF":2.6,"publicationDate":"2011-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-011-9248-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40118566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mitosis - The story : Conly Rieder of the Wadsworth Center, Albany, NY, interviewed at the University of Exeter, UK, by James Wakefield and Herbert Macgregor, October 2010.","authors":"Conly Rieder","doi":"10.1007/s10577-010-9174-3","DOIUrl":"https://doi.org/10.1007/s10577-010-9174-3","url":null,"abstract":"","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"275-90"},"PeriodicalIF":2.6,"publicationDate":"2011-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-010-9174-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39971294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fabian Erdel, Katharina Müller-Ott, Michael Baum, Malte Wachsmuth, Karsten Rippe
{"title":"Dissecting chromatin interactions in living cells from protein mobility maps.","authors":"Fabian Erdel, Katharina Müller-Ott, Michael Baum, Malte Wachsmuth, Karsten Rippe","doi":"10.1007/s10577-010-9155-6","DOIUrl":"https://doi.org/10.1007/s10577-010-9155-6","url":null,"abstract":"<p><p>The genome of eukaryotes is organized into a dynamic nucleoprotein complex referred to as chromatin, which can adopt different functional states. Both the DNA and the protein component of chromatin are subject to various post-translational modifications that define the cell's gene expression program. Their readout and establishment occurs in a spatio-temporally coordinated manner that is controlled by numerous chromatin-interacting proteins. Binding to chromatin in living cells can be measured by a spatially resolved analysis of protein mobility using fluorescence microscopy based approaches. Recent advancements in the acquisition of protein mobility data using fluorescence bleaching and correlation methods provide data sets on diffusion coefficients, binding kinetics, and cellular concentrations on different time and length scales. The combination of different techniques is needed to dissect the complex interplay of diffusive translocations, binding events, and mobility constraints of the chromatin environment. While bleaching techniques have their strength in the characterization of particles that are immobile on the second/minute time scale, a correlation analysis is advantageous to characterize transient binding events with millisecond residence time. The application and synergy effects of the different approaches to obtain protein mobility and interaction maps in the nucleus are illustrated for the analysis of heterochromatin protein 1.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"99-115"},"PeriodicalIF":2.6,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-010-9155-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40076367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A perspective of the dynamic structure of the nucleus explored at the single-molecule level.","authors":"Thomas Dange, Aviva Joseph, David Grünwald","doi":"10.1007/s10577-010-9156-5","DOIUrl":"https://doi.org/10.1007/s10577-010-9156-5","url":null,"abstract":"<p><p>Cellular life can be described as a dynamic equilibrium of a highly complex network of interacting molecules. For this reason, it is no longer sufficient to \"only\" know the identity of the participants in a cellular process, but questions such as where, when, and for how long also have to be addressed to understand the mechanism being investigated. Additionally, ensemble measurements may not sufficiently describe individual steps of molecular mobility, spatial-temporal resolution, kinetic parameters, and geographical mapping. It is vital to investigate where individual steps exactly occur to enhance our understanding of the living cell. The nucleus, home too many highly complex multi-order processes, such as replication, transcription, splicing, etc., provides a complicated, heterogeneous landscape. Its dynamics were studied to a new level of detail by fluorescence correlation spectroscopy (FCS). Single-molecule tracking, while still in its infancy in cell biology, is becoming a more and more attractive method to deduce key elements of this organelle. Here we discuss the potential of tracking single RNAs and proteins in the nucleus. Their dynamics, localization, and interaction rates will be vital to our understanding of cellular life. To demonstrate this, we provide a review of the HIV life cycle, which is an extremely elegant balance of nuclear and cytoplasmic functions and provides an opportunity to study mechanisms deeply integrated within the structure of the nucleus. In summary, we aim to present a specific, dynamic view of nuclear cellular life based on single molecule and FCS data and provide a prospective for the future.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"117-29"},"PeriodicalIF":2.6,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-010-9156-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40069374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christian Joppich, Sabrina Scholz, Günter Korge, Alexander Schwendemann
{"title":"Umbrea, a chromo shadow domain protein in Drosophila melanogaster heterochromatin, interacts with Hip, HP1 and HOAP.","authors":"Christian Joppich, Sabrina Scholz, Günter Korge, Alexander Schwendemann","doi":"10.1007/s10577-008-9002-1","DOIUrl":"https://doi.org/10.1007/s10577-008-9002-1","url":null,"abstract":"<p><p>Drosophila melanogaster HP1-interacting protein (Hip) is a partner of heterochromatin protein 1 (HP1) and is involved in transcriptional epigenetic gene silencing and the formation of heterochromatin. Recently, it has been shown that HP1 interacts with the telomere capping factor HP1/ORC (origin recognition complex)-associated protein (HOAP). Telomeres, complexes of DNA and proteins at the end of linear chromosomes, have been recognized to protect chromosome ends from degradation and fusion events. Both proteins are located at telomeres and prevent telomere fusions. Here, we report the identification and characterization of the Hip-interacting protein Umbrea. We found that Umbrea interacts directly with Hip, HP1 and HOAP in vitro. Umbrea, Hip and HP1 are partners in a protein complex in vivo and completely co-localize in the pericentric heterochromatin and at telomeres. Using a Gal4-induced RNA interference system, we found that after depletion of Umbrea in salivary gland polytene chromosomes, they exhibit multiple telomeric fusions. Taken together, these results suggest that Umbrea cooperates with Hip, HP1 and HOAP and plays a functional role in mediating normal telomere behaviour in Drosophila.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"19-36"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-008-9002-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"27963619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The role of LINEs and CpG islands in dosage compensation on the chicken Z chromosome.","authors":"Esther Melamed, Arthur P Arnold","doi":"10.1007/s10577-009-9068-4","DOIUrl":"https://doi.org/10.1007/s10577-009-9068-4","url":null,"abstract":"<p><p>Most avian Z genes are expressed more highly in ZZ males than ZW females, suggesting that chromosome-wide mechanisms of dosage compensation have not evolved. Nevertheless, a small percentage of Z genes are expressed at similar levels in males and females, an indication that a yet unidentified mechanism compensates for the sex difference in copy number. Primary DNA sequences are thought to have a role in determining chromosome gene inactivation status on the mammalian X chromosome. However, it is currently unknown whether primary DNA sequences also mediate chicken Z gene compensation status. Using a combination of chicken DNA sequences and Z gene compensation profiles of 310 genes, we explored the relationship between Z gene compensation status and primary DNA sequence features. Statistical analysis of different Z chromosomal features revealed that long interspersed nuclear elements (LINEs) and CpG islands are enriched on the Z chromosome compared with 329 other DNA features. Linear support vector machine (SVM) classifiers, using primary DNA sequences, correctly predict the Z compensation status for >60% of all Z-linked genes. CpG islands appear to be the most accurate classifier and alone can correctly predict compensation of 63% of Z genes. We also show that LINE CR1 elements are enriched 2.7-fold on the chicken Z chromosome compared with autosomes and that chicken chromosomal length is highly correlated with percentage LINE content. However, the position of LINE elements is not significantly associated with dosage compensation status of Z genes. We also find a trend for a higher proportion of CpG islands in the region of the Z chromosome with the fewest dosage-compensated genes compared with the region containing the greatest concentration of compensated genes. Comparison between chicken and platypus genomes shows that LINE elements are not enriched on sex chromosomes in platypus, indicating that LINE accumulation is not a feature of all sex chromosomes. Our results suggest that CpG islands are not randomly distributed on the Z chromosome and may influence Z gene dosage compensation status.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"727-36"},"PeriodicalIF":2.6,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-009-9068-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40028349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}