Transcriptional contribution of nuclear lamina protein emerin and BAF in Drosophila ovaries
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ABSTRACT:
PROVIDER: PRJNA705972 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13827131.fastq.gz | Fastqsanger.gz | |||
| SRR13827132.fastq.gz | Fastqsanger.gz | |||
| SRR13827133_1.fastq.gz | Fastqsanger.gz | |||
| SRR13827133_2.fastq.gz | Fastqsanger.gz | |||
| SRR13827134_1.fastq.gz | Fastqsanger.gz |
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Project description:Nuclear lamina (NL) contributes to tissue homeostasis. In Drosophila, compromised NL blocks differentiation and causes loss of germline stem cells (GSCs) due to activation of the Chk2 checkpoint kinase. Checkpoint activation occurs upon loss of the NL protein Drosophila emerin or its partner Barrier-to-autointegration factor (BAF). As NL has long been thought to interact with specific genomic loci and regulate transcription, we examined transcriptional changes in emerin-/- and baf KD ovaries. We found thousands of genes are mis-regulated upon loss of emerin or BAF in GSCs. Remarkably, more than 90% of mis-regulated genes are shared between emerin-/- and baf KD. Finally, we show that transcriptional changes are downstream of Chk2 activation, as transcription are restored in chk2, emerin double mutant ovaries.
2021-12-01 | GSE168062 | GEO
Project description:The nuclear lamina (NL) is a filamentous layer lining the inner-nuclear-membrane (INM) that aids in the organization of the genome in large domains of low transcriptional activity. Recently, it was shown that the single-cell genome-NL interactions are much more dynamic than previously anticipated, which challenges the concept of the NL as a safe guard for transcriptional repressed genes. Here we discuss the role of the NL in light of these new findings and introduce Lamin A and BAF as potential modulators of LAD positioning BAF-chromatin and Lamin B2-chromatin interactions were assayed in human HT1080 by DamID on Nimblegen microarrays, with two biological replicates each, that were hybridized in a dye-swap design.
2014-02-15 | E-GEOD-55066 | biostudies-arrayexpress
Project description:The nuclear lamina (NL) is a filamentous layer lining the inner-nuclear-membrane (INM) that aids in the organization of the genome in large domains of low transcriptional activity. Recently, it was shown that the single-cell genome-NL interactions are much more dynamic than previously anticipated, which challenges the concept of the NL as a safe guard for transcriptional repressed genes. Here we discuss the role of the NL in light of these new findings and introduce Lamin A and BAF as potential modulators of LAD positioning
2014-02-15 | GSE55066 | GEO
Project description:Entry into mitosis is triggered by mitotic kinases that phosphorylate multiple proteins to induce profound cellular changes including nuclear envelope breakdown, chromosome condensation and spindle assembly. Conversely, mitotic exit requires protein dephosphorylation as cells return to their interphase organization. Protein Phosphatase 2A in complex with its B55/Tws regulatory subunit (PP2A-B55) is known to play a crucial role in this transition. However, the precise events and substrates that it regulates are incompletely understood. We used proteomic approaches in Drosophila to identify proteins that interact with PP2A-B55 and are dephosphorylated in a PP2A-B55 dependent manner. Among several candidates, we identified Otefin (also known as Emerin) as a target of PP2A-B55 in the process of nuclear envelope reformation after mitosis. Emerin is a protein of the inner nuclear membrane that interacts with the DNA-binding protein Barrier-to-Autointegration Factor (BAF) via a LEM domain. Our results indicate that phosphorylation of Emerin at Ser50 and Ser54 near its LEM domain negatively regulates its association with BAF, Lamin and additional Emerin. Using live imaging, we show that dephosphorylation of Emerin at the identified sites determines the timing of nuclear envelope reformation. Genetic rescue experiments indicate that this regulation is required in vivo during embryonic development. Phosphoregulation of the Emerin-BAF complex formation by PP2A-B55 appears as a key event of mitotic exit that is likely to be conserved across species.
2023-08-10 | PXD041030 | Pride
Project description:Entry into mitosis is triggered by mitotic kinases that phosphorylate multiple proteins to induce profound cellular changes including nuclear envelope breakdown, chromosome condensation and spindle assembly. Conversely, mitotic exit requires protein dephosphorylation as cells return to their interphase organization. Protein Phosphatase 2A in complex with its B55/Tws regulatory subunit (PP2A-B55) is known to play a crucial role in this transition. However, the precise events and substrates that it regulates are incompletely understood. We used proteomic approaches in Drosophila to identify proteins that interact with PP2A-B55 and are dephosphorylated in a PP2A-B55 dependent manner. Among several candidates, we identified Otefin (also known as Emerin) as a target of PP2A-B55 in the process of nuclear envelope reformation after mitosis. Emerin is a protein of the inner nuclear membrane that interacts with the DNA-binding protein Barrier-to-Autointegration Factor (BAF) via a LEM domain. Our results indicate that phosphorylation of Emerin at Ser50 and Ser54 near its LEM domain negatively regulates its association with BAF, Lamin and additional Emerin. Using live imaging, we show that dephosphorylation of Emerin at the identified sites determines the timing of nuclear envelope reformation. Genetic rescue experiments indicate that this regulation is required in vivo during embryonic development. Phosphoregulation of the Emerin-BAF complex formation by PP2A-B55 appears as a key event of mitotic exit that is likely to be conserved across species.
2023-08-10 | PXD041091 | Pride
Project description:Entry into mitosis is triggered by mitotic kinases that phosphorylate multiple proteins to induce profound cellular changes including nuclear envelope breakdown, chromosome condensation and spindle assembly. Conversely, mitotic exit requires protein dephosphorylation as cells return to their interphase organization. Protein Phosphatase 2A in complex with its B55/Tws regulatory subunit (PP2A-B55) is known to play a crucial role in this transition. However, the precise events and substrates that it regulates are incompletely understood. We used proteomic approaches in Drosophila to identify proteins that interact with PP2A-B55 and are dephosphorylated in a PP2A-B55 dependent manner. Among several candidates, we identified Otefin (also known as Emerin) as a target of PP2A-B55 in the process of nuclear envelope reformation after mitosis. Emerin is a protein of the inner nuclear membrane that interacts with the DNA-binding protein Barrier-to-Autointegration Factor (BAF) via a LEM domain. Our results indicate that phosphorylation of Emerin at Ser50 and Ser54 near its LEM domain negatively regulates its association with BAF, Lamin and additional Emerin. Using live imaging, we show that dephosphorylation of Emerin at the identified sites determines the timing of nuclear envelope reformation. Genetic rescue experiments indicate that this regulation is required in vivo during embryonic development. Phosphoregulation of the Emerin-BAF complex formation by PP2A-B55 appears as a key event of mitotic exit that is likely to be conserved across species.
2023-08-10 | PXD041032 | Pride
Project description:The nuclear lamina (NL) is thought to aid in the spatial organization of interphase chromosomes by providing an anchoring platform for hundreds of large genomic regions named lamina associated domains (LADs). Recently, a new live-cell imaging approach demonstrated directly that LAD-NL interactions are dynamic and in part stochastic. Here we discuss implications of these new findings and introduce Lamin A and BAF as potential modulators of stochastic LAD positioning.
| S-EPMC4049918 | biostudies-literature
Project description:The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, so-called lamin associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2β to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina as well as identified putative LAD proximal proteins. Our analysis identifies many heterochromatin related proteins related to H3K9 methylation processes as well as many proteins related to cell cycle regulation identifying important proteins essential for LAD function.
2021-03-09 | PXD012943 | Pride
Project description:Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of mammalian SWI/SNF/BAF complexes in neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here we report that BCL7A is a modulator of the SWI/SNF/BAF complex and stimulates the genome-wide occupancy of the ATPase BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway and mitochondrial bioenergetics in differentiating NPCs. Together, our findings uncover the unique mechanistic contribution of BCL7A-containing SWI/SNF/BAF complex in mitochondria-driven NPC commitment, thereby providing a better understanding of the cell-intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis and cognitive flexibility.
2022-10-15 | GSE210756 | GEO
Project description:Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of mammalian SWI/SNF/BAF complexes in neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here we report that BCL7A is a modulator of the SWI/SNF/BAF complex and stimulates the genome-wide occupancy of the ATPase BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway and mitochondrial bioenergetics in differentiating NPCs. Together, our findings uncover the unique mechanistic contribution of BCL7A-containing SWI/SNF/BAF complex in mitochondria-driven NPC commitment, thereby providing a better understanding of the cell-intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis and cognitive flexibility.
2022-10-15 | GSE210759 | GEO