The molecular basis of lamin- chromatin interactions [SAMMY-Seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1119464 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR29270242.fastq.gz | Fastqsanger.gz | |||
| SRR29270243.fastq.gz | Fastqsanger.gz | |||
| SRR29270248.fastq.gz | Fastqsanger.gz | |||
| SRR29270249.fastq.gz | Fastqsanger.gz |
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Project description:The molecular basis of lamin- chromatin interactions [RNA-Seq]
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Project description:The molecular basis of lamin- chromatin interactions [ChIP-Seq]
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Project description:Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlying the inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation.
2025-05-28 | GSE268924 | GEO
Project description:Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlyingthe inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation.
2025-05-28 | GSE268923 | GEO
Project description:Lamins are the main constituents of the nuclear lamina, a fibrillar layer underlyingthe inner nuclear membrane. The nuclear lamina governs chromatinorganization through lamina-associated domainswithin the densely packed heterochromatin regions. Employing cryo-focused ion beam (cryo-FIB) milling in conjunction withcryo-electron tomography (cryo-ET), we mappedthe concentration of nucleosomesat the lamin-chromatin interface. Depletion of lamin A/C induces nanometer-scale chromatin decompaction, macroscopic-scale alterations in gene expression and chromatin-wide alterations of chromatin properties, revealed by 4f-genome-wide analysis. Cryo-electron microscopy (cryo-EM) structural analysis revealed a specific interaction between nucleosomes and the tail domain of lamin A. A unique motif of lamin A that distinguishes it from other lamin isoforms. These findings illuminatethe dynamic interplay between specific lamins and chromatin, shaping chromatin architecture and epigenetic regulation.
2025-05-28 | GSE268922 | GEO
Project description:Nuclear structure and function are governed by lamins, which are intermediate filaments mostly consisting of alpha-helices. Different lamin assembly models have been proposed based on low resolution or fragmented structures. However, their assembly mechanisms at the molecular level are poorly understood. Here, we present a crystal structure of a long human lamin fragment at 3.2 Å resolution, which visualized the full-length features. The structure presented the anti-parallel arrangement of two coiled-coil dimers, which was important for the assembly process. We further discovered a new interaction between the lamin dimers by using chemical cross-linking and mass analysis. Based on these two interactions we proposed a molecular mechanism of lamin assembly, which agreed well with the recent model representing the native state, and could explain pathological mutations. Our findings provide the structural information to understand molecular mechanisms of assembly of intermediate filaments, and molecular insights into nuclear functions and aging process.
2019-08-26 | PXD013144 | Pride
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:Dynamic interactions of nuclear lamins with chromatin through so-called lamin-associated domains (LADs) contribute to spatial arrangements of the genome. Here, we provide evidence for pre-patterning of differentiation-driven formation of lamin A/C LADs by domains of histone H2B modified by the nutrient sensor O-linked N-acetylglucosamine (H2BGlcNAc), which we term GADs. We demonstrate a two-step process of lamin A/C LAD formation during in vitro adipogenesis, involving (i) a spreading of lamin A/C-chromatin interactions during the transition from progenitor cell proliferation to cell cycle arrest, and (ii) a genome-scale redistribution these interactions through a process of LAD ‘exchange’ within hours of adipogenic induction. Chromatin state modeling reveals that lamin A/C LADs can be found both in active and repressive chromatin contexts which can be influenced by cell differentiation status. De novo formation of adipogenic lamin A/C LADs occurs non-randomly on GADs, consisting of megabase-size intergenic and repressive chromatin domains. Accordingly, while pre-differentiation lamin A/C LADs are gene-rich, post-differentiation LADs harbor repressive features reminiscent of lamin B1 LADs. Moreover, release of lamin A/C from genes directly involved in glycolysis concurs with their transcriptional upregulation after adipogenic induction, and with concordant downstream elevations in H2BGlcNAc levels and O-GlcNAc cycling. Our results unveil an epigenetic pre-patterning of adipogenic LADs by GADs, suggesting a coupling of developmentally regulated lamin A/C-genome interactions to a metabolically sensitive chromatin modification. Examination of LMNA and H2BGlcNAc binding in ASCs across differentiation
2015-09-04 | E-GEOD-63346 | biostudies-arrayexpress
Project description:Molecular basis of Urostyle development
| PRJNA1017454 | ENA
Project description:Lamin A is a nuclear intermediate filament protein critical for nuclear architecture and mechanics and mutated in a wide range of human diseases. Yet little is known about the molecular architecture of lamins and mechanisms of their assembly. Here we use cross-linking SILAC mass spectrometry to determine interactions within lamin dimers and between dimers in higher-order polymers. We find evidence for a compression mechanism where coiled coils in the lamin A rod can slide onto each other to contract rod length, likely driven by a wide range of electrostatic interactions with the flexible linkers between coiled coils. Similar interactions occur with unstructured regions flanking the rod domain during oligomeric assembly. Mutations linked to human disease block these interactions, suggesting that this spring-like contraction can explain in part the dynamic mechanical stretch and flexibility properties of the lamin polymer and other intermediate filament networks.
2019-07-12 | PXD014009 | Pride