Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains

Shopland, Lindsay S.; Johnson, Carol V.; Byron, Meg; McNeil, John A.; Lawrence, Jeanne B.

doi:10.1083/jcb.200303131

Cited by 191 publications

(207 citation statements)

References 41 publications

(77 reference statements)

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“…The genes are found outside of the XIST RNA (yellow), which extends beyond the Barr body, the visible manifestation of the heterochromatin. 49,50,58,59) and splicing and transcription factors localize (22,49,51,60,61). The act of silencing and condensing the inner core of Xi may make the existing concentration of protein-coding genes in the peripheral region more pronounced and observable.…”

Section: Discussionmentioning

confidence: 99%

The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences

Clemson

Hall

Byron

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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192

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We investigated whether genes escape X chromosome inactivation by positioning outside of the territory defined by XIST RNA. Results reveal an unanticipated higher order organization of genes and noncoding sequences. All 15 X-linked genes, regardless of activity, position on the border of the XIST RNA territory, which resides outside of the DAPI-dense Barr body. Although more strictly delineated on the inactive X chromosome (Xi), all genes localized predominantly to the outer rim of the Xi and active X chromosome. This outer rim is decorated only by X chromosome DNA paints and is excluded from both the XIST RNA and dense DAPI staining. The only DNA found well within the Barr body and XIST RNA territory was centromeric and Cot-1 DNA; hence, the core of the X chromosome essentially excludes genes and is composed primarily of noncoding repeat-rich DNA. Moreover, we show that this core of repetitive sequences is expressed throughout the nucleus yet is silenced throughout Xi, providing direct evidence for chromosomewide regulation of ''junk'' DNA transcription. Collective results suggest that the Barr body, long presumed to be the physical manifestation of silenced genes, is in fact composed of a core of silenced noncoding DNA. Instead of acting at a local gene level, XIST RNA appears to interact with and silence core architectural elements to effectively condense and shut down the Xi.Barr body ͉ chromosome territory ͉ nuclear organization ͉ XIST ͉ noncoding RNA X inactivation in mammalian females is a prominent example of the formation of facultative heterochromatin during early development, which prevents the deleterious effects of overexpression of X-linked genes. In interphase, the inactive X chromosome (Xi) is found as a condensed heterochromatic Barr body, usually positioned at the nuclear or nucleolar periphery (1-4). Because many genes have been identified that escape X inactivation, packaging differences of sequences at some level within the Xi is presumed (5, 6). Although it is generally assumed that the Barr body is condensed DNA comprising genes normally expressed on the active X chromosome (Xa), the specific makeup of the Barr body has not been investigated.X inactivation is a multistep process initiated by XIST (7-9). Just after XIST RNA sweeps across the chromosome, a defined pattern of chromatin changes including histone modifications, recruitment of macroH2A, and methylation occurs (for review see refs. 10 and 11). We have shown that XIST RNA remains in the nucleus, functionally associated with the inactive chromatin, forming an interphase territory coincident with Xi (12, 13). We incorporated our results into two models for the higher-level organization of the inactive X chromosome (12). In each alternate view, XIST RNA would induce differences in the packaging of the chromatin to facilitate inactivation. In the first model, all genes, regardless of whether they escape from or are subject to X inactivation, would be interspersed throughout the chromosome territory and would not be cytologically disti...

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Section: Discussionmentioning

confidence: 99%

The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences

Clemson

Hall

Byron

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

192

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“…Support for this was shown in live mammalian nuclei where one or more speckles was shown to provide splicing factors to the inducible BK virus and cytomegalovirus immediate early transcripts stably integrated into the baby hamster or rat genomes, respectively (Misteli et al, 1997). More recently, Shopland et al (2003) reported that multiple specific genes and gene-rich R-bands cluster around SC35 domains (speckles) and proposed that the speckles are functional centers for a multitude of clustered genes or local euchromatic neighborhoods.…”

Section: The Organization and Dynamics Of Plant Sr Proteins Are Depenmentioning

confidence: 98%

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Fang

Hearn

Spector

2004

MBoC

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The organization of the pre-mRNA splicing machinery has been extensively studied in mammalian and yeast cells and far less is known in living plant cells and different cell types of an intact organism. Here, we report on the expression, organization, and dynamics of pre-mRNA splicing factors (SR33, SR1/atSRp34, and atSRp30) under control of their endogenous promoters in Arabidopsis. Distinct tissue-specific expression patterns were observed, and differences in the distribution of these proteins within nuclei of different cell types were identified. These factors localized in a cell type-dependent speckled pattern as well as being diffusely distributed throughout the nucleoplasm. Electron microscopic analysis has revealed that these speckles correspond to interchromatin granule clusters. Time-lapse microscopy revealed that speckles move within a constrained nuclear space, and their organization is altered during the cell cycle. Fluorescence recovery after photobleaching analysis revealed a rapid exchange rate of splicing factors in nuclear speckles. The dynamic organization of plant speckles is closely related to the transcriptional activity of the cells. The organization and dynamic behavior of speckles in Arabidopsis cell nuclei provides significant insight into understanding the functional compartmentalization of the nucleus and its relationship to chromatin organization within various cell types of a single organism. INTRODUCTIONPre-mRNA (pre-mRNA) splicing, a process of excision of introns and ligation of exons, is essential for generating mature transcripts and enhancing mRNA export from the nucleus to the cytoplasm. Splicing occurs within a large macromolecular complex called the spliceosome, which is composed of U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles and a large number of non-small nuclear ribonucleoprotein particle proteins (Zhou et al., 2002). The latter include members of the SR (Ser-Arg) family of pre-mRNA splicing factors characterized by one or two N-terminal RNA recognition motifs that interact with the pre-mRNAs and a C-terminal variable-length Arg/Ser(RS)-rich domain that influences its subcellular localization and splicing activity depending upon its phosphorylation levels (for review, see Graveley, 2000).In mammalian cells, pre-mRNA splicing factors are concentrated in 20 -50 distinct nuclear domains called speckles as well as being diffusely distributed throughout the nucleoplasm, and this distribution corresponds to interchromatin granule clusters (IGCs) and perichromatin fibrils (PFs). PFs often extend from the periphery of IGCs or are present in the nucleoplasm at some distance from an IGCs (for review, see Lamond and Spector, 2003). It has been proposed that IGCs are storage and/or modification/reassembly sites for premRNA splicing factors and that splicing factors are recruited from these compartments to the sites of active transcription (PFs) (Jiménez-García and Spector, 1993). Disassembly of IGCs by overexpression of an SR protein kinase Clk/STY disrupts the coo...

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“…They may involve differences between human and rodent nuclear organization. We next sought to analyze whether expressed gene loci colocalize with nuclear splicing factor speckles, as it was observed for several active genes (Nielsen et al 2002;Shopland et al 2003;Chuang et al 2006;Takizawa et al 2008). We codetected splicing speckles together with the oct3/4 gene locus in undifferentiated ES cells, in ES cells after 5 days of differentiation, and in terminally differentiated, postmitotic macrophages.…”

Section: Gene Positioning and Expressionmentioning

confidence: 99%

Three-dimensional positioning of genes in mouse cell nuclei

et al. 2008

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To understand the regulation of the genome, it is necessary to understand its three-dimensional organization in the nucleus. We investigated the positioning of eight gene loci on four different chromosomes, including the β-globin gene, in mouse embryonic stem cells and in in vitro differentiated macrophages by fluorescence in situ hybridization on structurally preserved nuclei, confocal microscopy, and 3D quantitative image analysis. We found that gene loci on the same chromosome can significantly differ from each other and from their chromosome territory in their average radial nuclear position. Radial distribution of a given gene locus can change significantly between cell types, excluding the possibility that positioning is determined solely by the DNA sequence. For the set of investigated gene loci, we found no relationship between radial distribution and local gene density, as it was described for human cell nuclei. We did find, however, correlation with other genomic properties such as GC content and certain repetitive elements such as long terminal repeats or long interspersed nuclear elements. Our results suggest that gene density itself is not a driving force in nuclear positioning. Instead, we propose that other genomic properties play a role in determining nuclear chromatin distribution.

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Clustering of multiple specific genes and gene-rich R-bands around SC-35 domains

Cited by 191 publications

References 41 publications

The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences

The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences

Tissue-specific Expression and Dynamic Organization of SR Splicing Factors inArabidopsis

Three-dimensional positioning of genes in mouse cell nuclei

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