1,721,008 research outputs found
Interphase chromosome positioning in in vitro porcine cells and ex vivo porcine tissues
Full text linkCopyright @ 2012 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and 85 reproduction in any medium, provided the original author and source are credited. The article was made available through the Brunel University Open Access Publishing Fund.BACKGROUND: In interphase nuclei of a wide range of species chromosomes are organised into their own specific locations termed territories. These chromosome territories are non-randomly positioned in nuclei which is believed to be related to a spatial aspect of regulatory control over gene expression. In this study we have adopted the pig as a model in which to study interphase chromosome positioning and follows on from other studies from our group of using pig cells and tissues to study interphase genome re-positioning during differentiation. The pig is an important model organism both economically and as a closely related species to study human disease models. This is why great efforts have been made to accomplish the full genome sequence in the last decade. RESULTS: This study has positioned most of the porcine chromosomes in in vitro cultured adult and embryonic fibroblasts, early passage stromal derived mesenchymal stem cells and lymphocytes. The study is further expanded to position four chromosomes in ex vivo tissue derived from pig kidney, lung and brain. CONCLUSIONS: It was concluded that porcine chromosomes are also non-randomly positioned within interphase nuclei with few major differences in chromosome position in interphase nuclei between different cell and tissue types. There were also no differences between preferred nuclear location of chromosomes in in vitro cultured cells as compared to cells in tissue sections. Using a number of analyses to ascertain by what criteria porcine chromosomes were positioned in interphase nuclei; we found a correlation with DNA content.This study is partly supported by Sygen International PLC
LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin
Full text linkWe have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10) containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A-binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A-binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s) across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A-binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A-associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation
Regional regulation of transcription in the chicken genome
No full textAbstract Background Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis. Results We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes. Conclusions Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution. The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108</p
Investigating the role of nuclear myosin I in the low serum induced repositioning of chromosome 10 in interphase nuclei
No full textThis thesis was submitted for the degree of Master of Philosophy and awarded by Brunel University.The nucleus of mammalian cells has been proven to be highly organised. A recent study on interphase chromosome positioning has identified low serum induced rapid chromosome repositioning. Chromosome 10 initially localised at an intermediate position in normal proliferating human dermal fibroblasts (HDF) was found to relocate to the nuclear periphery 15 minutes after the cells have been incubated in low serum. Whereas chromosome X has remained in
a peripheral position. The relocation of chromosome 10 has been shown to be dependant on both actin and myosin functions. In this project we have further investigated the possible role of nuclear myosin I in chromosome 10 repositioning. Using siRNA to block the expression of the nuclear myosin I
(NMI) we were able to identify this nuclear myosin as necessary for the rapid repositioning of chromosome 10. Furthermore, using image analysis software we investigated the effect of the NMI knock down on the overall nuclear size and shape. The analysis has revealed that while the nuclear size of normal proliferating cells remained unchanged after the low serum incubation both in cells expressing the NMI and NMI depleted cells, the knock down of the
NMI seems to have affected the nuclear shape when the cells were subjected to the serum incubation. On the other hand, the analysis of the chromosome territories area has revealed significant differences in the chromosome territories sizes before and after the low serum incubation, in normal proliferating HDF cells .Part funded by the School of Health Sciences and Social Car
Specific nuclear envelope transmembrane proteins can promote the location of chromosomes to and from the nuclear periphery
No full textBACKGROUND: Different cell types have distinctive patterns of chromosome positioning in the nucleus. Although ectopic affinity-tethering of specific loci can be used to relocate chromosomes to the nuclear periphery, endogenous nuclear envelope proteins that control such a mechanism in mammalian cells have yet to be widely identified. RESULTS: To search for such proteins twenty three nuclear envelope transmembrane proteins were screened for their ability to promote peripheral localization of human chromosomes in HT1080 fibroblasts. Five of these proteins had strong effects on chromosome 5, but individual proteins affected different subsets of chromosomes. The repositioning effects were reversible and the proteins with effects all exhibited highly tissue-restricted patterns of expression. Depletion of two nuclear envelope transmembrane proteins that were preferentially expressed in liver each reduced the normal peripheral positioning of chromosome 5 in liver cells. CONCLUSIONS: The discovery of nuclear envelope transmembrane proteins that can modulate chromosome position and have restricted patterns of expression may enable dissection of the functional relevance of tissue-specific patterns of radial chromosome positioning
Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts
Full text linkThis article has been made available through the Brunel Open Access Publishing Fund.Background: Radial chromosome positioning in interphase nuclei is nonrandom and
can alter according to developmental, differentiation, proliferation, or disease status.
However, it is not yet clear when and how chromosome repositioning is elicited.
Results: By investigating the positioning of all human chromosomes in primary
fibroblasts that have left the proliferative cell cycle, we have demonstrated that in
cells made quiescent by reversible growth arrest, chromosome positioning is altered
considerably. We found that with the removal of serum from the culture medium,
chromosome repositioning took less than 15 minutes, required energy and was
inhibited by drugs affecting the polymerization of myosin and actin. We also
observed that when cells became quiescent, the nuclear distribution of nuclear myosin
1ß was dramatically different from that in proliferating cells. If we suppressed the
expression of nuclear myosin 1ß by using RNA-interference procedures, the
movement of chromosomes after 15 minutes in low serum was inhibited. When high
serum was restored to the serum-starved cultures, chromosome repositioning was
evident only after 24 to 36 hours, and this coincided with a return to a proliferating
distribution of nuclear myosin 1ß.
Conclusions: These findings demonstrate that genome organization in interphase
nuclei is altered considerably when cells leave the proliferative cell cycle and that
repositioning of chromosomes relies on efficient functioning of an active nuclear
motor complex that contains nuclear myosin 1ß.Brunel Open Access Publishing Fun
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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