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The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [RNA-seq]

ABSTRACT: The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [RNA-seq]

PROVIDER: PRJNA915344 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22878562_1.fastq.gz	Fastqsanger.gz
	SRR22878562_2.fastq.gz	Fastqsanger.gz
	SRR22878563_1.fastq.gz	Fastqsanger.gz
	SRR22878563_2.fastq.gz	Fastqsanger.gz
	SRR22878564_1.fastq.gz	Fastqsanger.gz

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The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [RNA-seq]

Project description:Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips, accumulates at the nuclear envelope and interacts with further components of the nuclear lamina. To investigate effects of defective lamina components on gene expression, we analysed the transcriptomes of 4 day old wild-type, gbpl3-5, crwn4-1, crwn1-1crwn4-1, as well as gbpl3-5 mutants expressing GBPL3-GFP or the GTPase-dead GBPL3(K83A)-GFP under control of the AtGBPL3-promoter.

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The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing

Project description:The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing

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The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [ChIP-Seq]

Project description:The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [ChIP-Seq]

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The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing [ChIP-Seq]

Project description:Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips and accumulates at the nuclear envelope. Furthermore, fluorescent lifetime imaging experiments in the presence or absence of the chromatin-labelling dye Sytox-Orange suggested that GBPL3 might be able to interact with chromatin. Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) revealed only few GBPL3-associated chromatin domains, which were concentrated particularly within or near centromeric regions.

2022-12-23 | GSE221668 | GEO

The large GTPase AtGBPL3 links nuclear envelope formation to lamina-associated gene silencing

Project description:This SuperSeries is composed of the SubSeries listed below.

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Effect of truncation mutants of the trypanosomatid nuclear lamina protein NUP-1 on the whole cell proteome in T. brucei

Project description:The nuclear lamina has multiple functions, including maintaining nuclear structural integrity and differential gene expression. Correct spatial and temporal lamina assembly is essential to meet these and other roles. Recently, it emerged that multiple lamina systems exist that are likely products of independent origins, while all these systems share remarkably analogous functions. Several lamina proteins are known in trypanosomes, two of which, NUP-1 and NUP-2, are essential, coiled-coil proteins with a molecular mass 450 and 250 kDa, respectively. Sequence analysis indicates distinct quaternary structures when compared to the ~60 kDa lamin proteins of multiple lineages, including metazoa. To uncover organisational principles of the trypanosome lamina we generated NUP-1 deletion mutants (N=N-terminal domain; C= C-terminal domain; NC: fusion of the N- and C-terminal domain with entire repeat region deletedd))designed to identify domains of NUP-1 responsible for oligomerisation. We find that both N- and C-termini act as interaction domains and disruption of these interactions impacts additional components of the lamina, the nuclear envelope and nucleoporin TbNup98. By contrast there is remarkably little impact on transcription, crucially including silencing of telomeric variant surface glycoprotein genes. These data indicate that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and suggest an architecture distinct to the lamin system is based on a ‘hub and spoke’ configuration.

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Large intestine lamina propria CD45 positive cells

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Project description:This SuperSeries is composed of the following subset Series: GSE35777: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [Tiling Array] GSE36048: A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq] Refer to individual Series

2012-02-24 | E-GEOD-36049 | biostudies-arrayexpress

A molecular mechanism for compartmentalization and silencing of chromatin domains at the nuclear lamina [ChIP-seq]

Project description:A large fraction of the mammalian genome is organized into inactive chromosomal domains associated with the nuclear lamina. Using genomic repositioning assays we show that Lamina associated domains (LADs), spanning the developmentally regulated IgH and Cyp3a loci, contain transportable DNA regions that associate chromatin with the nuclear lamina and repress gene activity in fibroblasts. We characterized DNA regions within LADs that are functionally capable of positioning chromatin domains at the inner nuclear membrane (INM) lamina. We mapped and characterized the IgH and other LADs in murine fibroblasts. We show that these murine LADs have a unique chromatin structure with discrete boundaries. We demonstrate DNA regions within LADs that are capable of directing the association of chromatin domains with the INM-lamina as well as the silencing of a co-integrated reporter gene.

2012-02-24 | E-GEOD-36048 | biostudies-arrayexpress

Genome-wide maps of nuclear lamina interactions in HeLa cells identified using MethylAdenine IDentification (MadID).

Project description:Mapping of lamina-associated domains using MadID experiment. A methyltransferase (M.EcoGII) targeted to the nuclear envelope is able to add methyl groups to adenine residues (m6A) on chromatin in contact to the nuclear periphery. A m6A-specific immunoprecipitation is performed on isolated genomic DNA, followed by Ilumina deep sequencing to identify contact sites.

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