Dataset Information

Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines.

ABSTRACT:

Background

Strains from a collection of Drosophila GFP protein trap lines express GFP in the normal tissues where the endogenous protein is present. This collection can be used to screen for proteins distributed in the nucleus in a non-uniform pattern.

Methodology/principal findings

We analyzed four lines that show peripheral or punctate nuclear staining. One of these lines affects an uncharacterized gene named CG11138. The CG11138 protein shows a punctate distribution in the nuclear periphery similar to that of Drosophila insulator proteins but does not co-localize with known insulators. Interestingly, mutations in Lamin proteins result in alterations in CG11138 localization, suggesting that this protein may be a novel component of the nuclear lamina. A second line affects the Decondensation factor 31 (Df31) gene, which encodes a protein with a unique nuclear distribution that appears to segment the nucleus into four different compartments. The X-chromosome of males is confined to one of these compartments. We also find that Drosophila Nucleoplasmin (dNlp) is present in regions of active transcription. Heat shock leads to loss of dNlp from previously transcribed regions of polytene chromosome without redistribution to the heat shock genes. Analysis of Stonewall (Stwl), a protein previously found to be necessary for the maintenance of germline stem cells, shows that Stwl is present in a punctate pattern in the nucleus that partially overlaps with that of known insulator proteins. Finally we show that Stwl, dNlp, and Df31 form part of a highly interactive network. The properties of other components of this network may help understand the role of these proteins in nuclear biology.

Conclusions/significance

These results establish screening of GFP protein trap alleles as a strategy to identify factors with novel cellular functions. Information gained from the analysis of CG11138 Stwl, dNlp, and Df31 sets the stage for future studies of these proteins.

SUBMITTER: Rohrbaugh M

PROVIDER: S-EPMC3547006 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines.

Rohrbaugh Margaret M Clore Alyssia A Davis Julia J Johnson Sharonta S Jones Brian B Jones Keith K Kim Joanne J Kithuka Bramwel B Lunsford Krystal K Mitchell Joy J Mott Brian B Ramos Edward E Tchedou Maza R MR Acosta Gilbert G Araujo Mark M Cushing Stuart S Duffy Gabriel G Graves Felicia F Griffin Kyler K Gurudatta B V BV Jackson Deaundra D Jaimes Denis D Jamison Kendall K Jones Khali K Kelley Dhaujee D Kilgore Marquita M Laramore Derica D Le Thuy T Mazhar Bakhtawar B Mazhar Muhammad M MM McCrary Britney B Miller Teanndras T Moreland Celethia C Mullins Alex A Munye Elyas E Okoorie Sheila S Pittman Elisha E Roberts Nikkita N Rose De'Warren D Rowland Alex A Shagarabi Anwar A Smith Jamela J Stallworth Tayler T Stroud Nicole N Sung Elizabeth E Sung Kai K Takenaka Naomi N Torre Eduardo E Veira Jarvis J Vu Kim K Wagstaff William W Wood Ashley M AM Wu Karen K Yang Jingping J Corces Victor G VG

PloS one 20130116 1

<h4>Background</h4>Strains from a collection of Drosophila GFP protein trap lines express GFP in the normal tissues where the endogenous protein is present. This collection can be used to screen for proteins distributed in the nucleus in a non-uniform pattern.<h4>Methodology/principal findings</h4>We analyzed four lines that show peripheral or punctate nuclear staining. One of these lines affects an uncharacterized gene named CG11138. The CG11138 protein shows a punctate distribution in the nucl ...[more]

PMID: 23341925

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Project description:Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogaster cell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism's genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and then tested for correlations between nucleosome positioning, transcription factor binding motifs, and gene expression. Nucleosomes in all cell lines were positioned in accordance with previously known DNA-nucleosome interactions, with helically repeating A/T di-nucleotide pairs arranged within nucleosomal DNAs and AT-rich pentamers generally excluded from nucleosomal DNA. Nucleosome organization in all cell lines differed markedly from in vitro reconstituted chromatin, with highly expressed genes showing strong nucleosome organization around transcriptional start sites. Importantly, comparative analysis identified genomic regions that exhibited cell line-specific nucleosome enrichment or depletion. Further analysis of these regions identified 91 out of 16,384 possible heptamer sequences that showed differential nucleosomal occupation between cell lines, and 49 of the heptamers matched one or more known transcription factor binding sites. These results demonstrate that there is differential nucleosome positioning between these Drosophila cell lines and therefore identify a system that could be used to investigate the functional significance of differential nucleosomal positioning in cell type specification.

Dataset Information

Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines.

Background

Methodology/principal findings

Conclusions/significance

Publications

Identification and characterization of proteins involved in nuclear organization using Drosophila GFP protein trap lines.

Similar Datasets

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