Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology最新文献

{"title":"Transcription and ncRNAs: at the cent(rome)re of kinetochore assembly and maintenance.","authors":"Kristin C Scott","doi":"10.1007/s10577-013-9387-3","DOIUrl":"https://doi.org/10.1007/s10577-013-9387-3","url":null,"abstract":"<p><p>Centromeres are sites of chromosomal spindle attachment during mitosis and meiosis. Centromeres are defined, in part, by a distinct chromatin landscape in which histone H3 is replaced by the conserved histone H3 variant, CENP-A. Sequences competent for centromere formation and function vary among organisms and are typically composed of repetitive DNA. It is unclear how such diverse genomic signals are integrated with the epigenetic mechanisms that govern CENP-A incorporation at a single locus on each chromosome. Recent work highlights the intriguing possibility that the transcriptional properties of centromeric core DNA contribute to centromere identity and maintenance through cell division. Moreover, core-derived noncoding RNAs (ncRNAs) have emerged as active participants in the regulation and control of centromere activity in plants and mammals. This paper reviews the transcriptional properties of eukaryotic centromeres and discusses the known roles of core-derived ncRNAs in chromatin integrity, kinetochore assembly, and centromere activity.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"643-51"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9387-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39974516","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":"Epigenetic regulation by long noncoding RNAs in plants.","authors":"Jae Bok Heo,&nbsp;Yong-Suk Lee,&nbsp;Sibum Sung","doi":"10.1007/s10577-013-9392-6","DOIUrl":"https://doi.org/10.1007/s10577-013-9392-6","url":null,"abstract":"<p><p>Many eukaryotes, including plants, produce a large number of long noncoding RNAs (lncRNAs).Growing number of lncRNAs are being reported to have regulatory roles in various developmental processes.Emerging mechanisms underlying the function of lncRNAs indicate that lncRNAs are versatile regulatory molecules. They function as potent cis- and trans-regulators of gene expression, including the formation of modular scaffolds that recruit chromatin-modifying complexes to target chromatin. LncRNAs have also been reported in plants. Here, we describe our current understanding on potential roles of lncRNA in plants.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"685-93"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9392-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31866545","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":"Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response.","authors":"Bayly S Wheeler","doi":"10.1007/s10577-013-9394-4","DOIUrl":"https://doi.org/10.1007/s10577-013-9394-4","url":null,"abstract":"<p><p>Transposons are mobile genetic elements that are a major constituent of most genomes. Organisms regulate transposable element expression, transposition, and insertion site preference, mitigating the genome instability caused by uncontrolled transposition. A recent burst of research has demonstrated the critical role of small non-coding RNAs in regulating transposition in fungi, plants, and animals. While mechanistically distinct, these pathways work through a conserved paradigm. The presence of a transposon is communicated by the presence of its RNA or by its integration into specific genomic loci. These signals are then translated into small non-coding RNAs that guide epigenetic modifications and gene silencing back to the transposon. In addition to being regulated by the host, transposable elements are themselves capable of influencing host gene expression. Transposon expression is responsive to environmental signals, and many transposons are activated by various cellular stresses. TEs can confer local gene regulation by acting as enhancers and can also confer global gene regulation through their non-coding RNAs. Thus, transposable elements can act as stress-responsive regulators that control host gene expression in cis and trans.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"587-600"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9394-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31882364","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":"The role of chromosomal retention of noncoding RNA in meiosis.","authors":"Da-Qiao Ding,&nbsp;Tokuko Haraguchi,&nbsp;Yasushi Hiraoka","doi":"10.1007/s10577-013-9389-1","DOIUrl":"https://doi.org/10.1007/s10577-013-9389-1","url":null,"abstract":"<p><p>Meiosis is a process of fundamental importance for sexually reproducing eukaryotes. During meiosis, homologous chromosomes pair with each other and undergo homologous recombination, ultimately producing haploid sets of recombined chromosomes that will be inherited by the offspring. Compared with the extensive progress that has been made in understanding the molecular mechanisms underlying recombination, how homologous sequences pair with each other is still poorly understood. The diversity of the underlying mechanisms of pairing present in different organisms further increases the complexity of this problem. Involvement of meiosis-specific noncoding RNA in the pairing of homologous chromosomes has been found in the fission yeast Schizosaccharomyces pombe. Although different organisms may have developed other or additional systems that are involved in chromosome pairing, the findings in S. pombe will provide new insights into understanding the roles of noncoding RNA in meiosis.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"665-72"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9389-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40278629","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":"Maintenance of epigenetic information: a noncoding RNA perspective.","authors":"Tanmoy Mondal,&nbsp;Chandrasekhar Kanduri","doi":"10.1007/s10577-013-9385-5","DOIUrl":"https://doi.org/10.1007/s10577-013-9385-5","url":null,"abstract":"<p><p>Along the lines of established players like chromatin modifiers and transcription factors, noncoding RNA (ncRNA) are now widely accepted as one of the key regulatory molecules in epigenetic regulation of transcription. With increasing evidence of ncRNAs in the establishment of gene silencing through their ability to interact with major chromatin modifiers, in the current review, we discuss their prospective role in the area of inheritance and maintenance of these established silenced states which can be reversible or irreversible in nature. In addition, we attempt to understand and speculate how these RNA dependent or independent maintenance mechanisms differ between each other in a developmental stage, tissue, and gene-specific manner in different biological contexts by utilizing known/unknown regulatory factors.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"615-25"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9385-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39975227","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":"Molecular versatility: the many faces and functions of noncoding RNA.","authors":"Brian P Chadwick,&nbsp;Kristin C Scott","doi":"10.1007/s10577-013-9397-1","DOIUrl":"https://doi.org/10.1007/s10577-013-9397-1","url":null,"abstract":"","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"555-9"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9397-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31907783","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":"Long noncoding RNA-based chromatin control of germ cell differentiation: a yeast perspective.","authors":"Edwige Hiriart,&nbsp;André Verdel","doi":"10.1007/s10577-013-9393-5","DOIUrl":"https://doi.org/10.1007/s10577-013-9393-5","url":null,"abstract":"<p><p>Germ cell differentiation, the cellular process by which a diploid progenitor cell produces by meiotic divisions haploid cells, is conserved from the unicellular yeasts to mammals. Over the recent years, yeast germ cell differentiation process has proven to be a powerful biological system to identify and study several long noncoding RNAs (lncRNAs) that play a central role in regulating cellular differentiation by acting directly on chromatin. Remarkably, in the well-studied budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe, the lncRNA-based chromatin regulations of germ cell differentiation are quite different. In this review, we present an overview of these regulations by focusing on the mechanisms and their respective functions both in S. cerevisiae and in S. pombe. Part of these lncRNA-based chromatin regulations may be conserved in other eukaryotes and play critical roles either in the context of germ cell differentiation or, more generally, in the development of multicellular organisms.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"653-63"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9393-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31879572","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":"Long noncoding RNAs as metazoan developmental regulators.","authors":"Jamila I Horabin","doi":"10.1007/s10577-013-9382-8","DOIUrl":"https://doi.org/10.1007/s10577-013-9382-8","url":null,"abstract":"<p><p>The study of long noncoding RNAs (lncRNAs) is still in its infancy with more putative RNAs identified than those with ascribed functions. Defined as transcripts that are longer than 200 nucleotides without a coding sequence, their numbers are on the rise and may well challenge protein coding transcripts in number and diversity. lncRNAs are often expressed at low levels and their sequences are frequently poorly conserved, making it unclear if they are transcriptional noise or bonafide effectors. Despite these limitations, inroads into their functions are being made and it is clear they make a contribution in regulating all aspects of biology. The early verdict on their activity, however, suggests the majority function as chromatin modifiers. A good proportion show a connection to disease highlighting their importance and the need to determine their function. The focus of this review is on lncRNAs which influence developmental processes which in itself covers a large range of known activities.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"673-84"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9382-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40259001","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":"Long nonoding RNAs in the X-inactivation center.","authors":"Emily Maclary,&nbsp;Michael Hinten,&nbsp;Clair Harris,&nbsp;Sundeep Kalantry","doi":"10.1007/s10577-013-9396-2","DOIUrl":"https://doi.org/10.1007/s10577-013-9396-2","url":null,"abstract":"<p><p>The X-inactivation center is a hotbed of functional long noncoding RNAs in eutherian mammals. These RNAs are thought to help orchestrate the epigenetic transcriptional states of the two X-chromosomes in females as well as of the single X-chromosome in males. To balance X-linked gene expression between the sexes, females undergo transcriptional silencing of most genes on one of the two X-chromosomes in a process termed X-chromosome inactivation. While one X-chromosome is inactivated, the other X-chromosome remains active. Moreover, with a few notable exceptions, the originally established epigenetic transcriptional profiles of the two X-chromosomes is maintained as such through many rounds of cell division, essentially for the life of the organism. The stable and divergent transcriptional fates of the two X-chromosomes, despite residing in a shared nucleoplasm, make X-inactivation a paradigm of epigenetic transcriptional regulation. Originally proposed in 1961 by Mary Lyon, the X-inactivation hypothesis has been validated through much experimentation. In the last 25 years, the discovery and functional characterization has firmly established X-linked long noncoding RNAs as key players in choreographing X-chromosome inactivation.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"601-614"},"PeriodicalIF":2.6,"publicationDate":"2013-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9396-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39977667","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":"Subchromosomal karyotype evolution in Equidae.","authors":"P Musilova,&nbsp;S Kubickova,&nbsp;J Vahala,&nbsp;J Rubes","doi":"10.1007/s10577-013-9346-z","DOIUrl":"https://doi.org/10.1007/s10577-013-9346-z","url":null,"abstract":"<p><p>Equidae is a small family which comprises horses, African and Asiatic asses, and zebras. Despite equids having diverged quite recently, their karyotypes underwent rapid evolution which resulted in extensive differences among chromosome complements in respective species. Comparative mapping using whole-chromosome painting probes delineated genome-wide chromosome homologies among extant equids, enabling us to trace chromosome rearrangements that occurred during evolution. In the present study, we performed subchromosomal comparative mapping among seven Equidae species, representing the whole family. Region-specific painting and bacterial artificial chromosome probes were used to determine the orientation of evolutionarily conserved segments with respect to centromere positions. This allowed assessment of the configuration of all fusions occurring during the evolution of Equidae, as well as revealing discrepancies in centromere location caused by centromere repositioning or inversions. Our results indicate that the prevailing type of fusion in Equidae is centric fusion. Tandem fusions of the type telomere-telomere occur almost exclusively in the karyotype of Hartmann's zebra and are characteristic of this species' evolution. We revealed inversions in segments homologous to horse chromosomes 3p/10p and 13 in zebras and confirmed inversions in segments 4/31 in African ass, 7 in horse and 8p/20 in zebras. Furthermore, our mapping results suggested that centromere repositioning events occurred in segments homologous to horse chromosomes 7, 8q, 10p and 19 in the African ass and an element homologous to horse chromosome 16 in Asiatic asses. Centromere repositioning in chromosome 1 resulted in three different chromosome types occurring in extant species. Heterozygosity of the centromere position of this chromosome was observed in the kiang. Other subtle changes in centromere position were described in several evolutionary conserved chromosomal segments, suggesting that tiny centromere repositioning or pericentric inversions are quite frequent in zebras and asses.</p>","PeriodicalId":347802,"journal":{"name":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","volume":" ","pages":"175-87"},"PeriodicalIF":2.6,"publicationDate":"2013-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10577-013-9346-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40228047","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}