Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA385478 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5508030.fastq.gz | Fastqsanger.gz | |||
| SRR5508027.fastq.gz | Fastqsanger.gz | |||
| SRR5508028.fastq.gz | Fastqsanger.gz | |||
| SRR5508029.fastq.gz | Fastqsanger.gz |
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Project description:Analysis of gene expression by RNA-seq upon siRNA mediated knockdown of scaffold attachment factor A (SAF-A) versus control siRNA in RPE1 cells at 24 hour and 48 hour time points post transfection reveals SAF-A loss does not impact on gene transcription
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Project description:Nuclear chromosomes transcribe far more RNA than required to code for protein. Here we investigate whether non-coding RNA broadly contributes to cytological-scale chromosome territory architecture. We develop a procedure that depletes soluble proteins, chromatin and most nuclear RNA from the nucleus, but does not delocalize XIST, a known architectural RNA, from an insoluble chromosome “scaffold.” RNA-seq analysis reveals most RNA in the nuclear scaffold is repeat-rich, non-coding, and predominantly derived from introns of nascent transcripts. This repeat-rich (C0T-1) RNA inversely correlates with chromatin compaction in normal and experimentally manipulated nuclei, demonstrating RNA physically antagonizes a propensity for chromatin to condense. C0T-1 hnRNA co-distributes on euchromatin with several known scaffold proteins including scaffold attachment factor A (SAF-A). We further show that RNA is required for SAF-A to interact with chromatin and to form structurally embedded scaffold-attachment regions (SARs) in the nuclear genome. Collectively, results indicate nascent transcripts serve a dynamic structural role in the open architecture of active chromosome territories
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Project description:α-satellite RNA has been shown to interact with specific sets of RNA-binding proteins. By forming complexes with centromere proteins CENPA, CENPB, and CENPC, α-satellite RNA demonstrated its essential role in maintaining functional human centromeres. Also, α-satellite RNA has been reported to interact with SUV39H1, which is the histone methyltransferase that is responsible for H3K9me3. Together with the findings in mice and some other eukaryotes that RNA components are required for the recruitment of heterochromatin proteins and the maintenance of pericentric heterochromatin, it has long been suspected that α-satellite RNA might also be involved in the heterochromatin formation and recruitment of HP1 in human cells. In this study, we identified Scaffold Attachment Factor-A (SAF-A) as a novel α-satellite RNA binding protein. SAF-A, also known as hnRNPU, the most abundant member in the hnRNP complex, was initially identified as the major component of the nuclear scaffold. It binds to the nuclear scaffold in AT-rich regions through its DNA-binding domain. In recent years, several studies have suggested that SAF-A may play a more fundamental and general role in nuclear organization in interphase. Depletion of SAF-A will lead to pronounced chromatin condensation of gene-rich regions and global changes in 3D genome architecture.
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Project description:α-satellite RNA has been shown to interact with specific sets of RNA-binding proteins. By forming complexes with centromere proteins CENPA, CENPB, and CENPC, α-satellite RNA demonstrated its essential role in maintaining functional human centromeres. Also, α-satellite RNA has been reported to interact with SUV39H1, which is the histone methyltransferase that is responsible for H3K9me3. Together with the findings in mice and some other eukaryotes that RNA components are required for the recruitment of heterochromatin proteins and the maintenance of pericentric heterochromatin, it has long been suspected that α-satellite RNA might also be involved in the heterochromatin formation and recruitment of HP1 in human cells. In this study, we identified Scaffold Attachment Factor-A (SAF-A) as a novel α-satellite RNA binding protein. SAF-A, also known as hnRNPU, the most abundant member in the hnRNP complex, was initially identified as the major component of the nuclear scaffold. It binds to the nuclear scaffold in AT-rich regions through its DNA-binding domain. In recent years, several studies have suggested that SAF-A may play a more fundamental and general role in nuclear organization in interphase. Depletion of SAF-A will lead to pronounced chromatin condensation of gene-rich regions and global changes in 3D genome architecture.
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Project description:The impact of depleting SAF-A (HNRNPU) on the genome-wide replication timing program in human hTERT-RPE1 cells was assessed by a single-cell replication timing analysis.
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Project description:The human cell nucleus is comprised of proteins, chromatin and RNA, yet how they interact to form supramolecular structures and drive key biological processes remains unknown. Conflicting models have proposed either a fluid-like or solid-like nature for the intranuclear microenvironment. To reconcile this discrepancy, we investigated the 3D structure and properties of the nuclear interior using experiments and computer simulations. We reveal a novel mechanism where newly synthesized RNA interacts with SAF-A (scaffold attachment factor A, or HNRNPU), forming interconnected microgels degraded by the exonuclease XRN2, leading to dynamic cycles of gelation and fluidization. This emergent microgel network depends on transcription, and is disrupted by SAF- A depletion. It also decreases protein mobility and regulates chromatin compaction by modulating microphase separation, thereby opening transcriptionally active regions. This tunable intranuclear network exhibits scale-dependent fluid- and solid-like features, that we suggest may regulate transcription by controlling access to regulatory proteins and polymerases.
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Project description:RNA components seem to be required for the localization of SAF-A on chromatin. A SAF-A/RNA mesh model has been proposed and supported by super-resolved images, in which SAF-A forms a homogeneous mesh together with nuclear scaffolding RNA species to regulate chromatin structure. As an evolutionarily conserved RNA-binding protein, SAF-A has been reported to interact with a wide variety of RNAs in different cell types. Particularly, a recent study points out that repetitive non-coding sequences of pre-mRNAs and lncRNAs can serve as scaffold RNAs to counter chromatin compaction and maintain chromosome territory architecture together with SAF-A. At this moment, most studies have demonstrated the role of SAF-A/RNA in regulating interphase chromatin structure, and very few works have covered the role of SAF-A/RNA in mitosis. A recent study showed that SAF-A, together with most of its interacting RNAs, needs to be evicted from the condensing chromosomes during mitosis. This brings out an open question of how the SAF-A/RNA scaffold is disassembled and rebuilt when the cell enters and exits mitosis. Here, we showed that α-satellite RNA is dynamically expressed and stays associated with the centromeric chromatin throughout the mitotic cell cycle. Specific interactions between α-satellite RNA and SAF-A were observed both in vitro and in vivo. Depletion of either α-satellite RNA or SAF-A would lead to chromosome missegregation phenotypes during mitosis. More importantly, interfering with α-satellite RNA showed an evident effect on the chromatin relocalization of SAF-A, and further LAP2 upon mitosis exit. Therefore, we proposed that α-satellite RNA may act as a foundation stone for recruiting SAF-A scaffold upon mitosis exit.
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Project description:Scaffold Attachment Factor B (SAFB) is a conserved RNA Binding Protein (RBP) that is essential for early mammalian development. However, the RNAs that associate with SAFB in mouse embryonic stem cells have not been characterized. Here, we addressed this unknown using RNA-seq and SAFB RNA immunoprecipitation followed by RNA-seq (RIP-seq) in wild-type mouse embryonic stem cells (ESCs) and in ESCs in which SAFB and SAFB2 were knocked out. The transcript most enriched in SAFB association was the lncRNA Malat1, which contains a series of purine-rich motifs in its 5 end. Beyond Malat1, SAFB predominantly associated with introns of protein-coding genes also through purine-rich motifs. Knockout of SAFB/2 led to down- and upregulation of genes in multiple biological pathways. The nascent transcripts of many downregulated genes associated with high levels of SAFB in wild-type cells, implying that SAFB binding promotes the expression of these genes. Reintroduction of SAFB into double-knockout cells restored gene expression towards wild-type levels, an effect that was again observable at the level of nascent transcripts. Proteomic analyses indicate an enrichment of nuclear speckle-associated, SR proteins in FLAG-tagged SAFB immunoprecipitated samples. Comparison to immunoprecipitates made from FLAG-tagging of another nuclear-enriched RNA-binding protein called HNRNPU (also known as SAF-A) identified both similarities and differences. Perhaps most notably, we observed a stronger enrichment for speckle-associated proteins in SAFB immunoprecipitations and a strong enrichment for paraspeckle-associated proteins in HNRNPU immunoprecipitations. Our findings suggest that among other potential functions in mouse embryonic stem cells, SAFB directly promotes the expression of a subset of genes through its ability to bind purine regions in nascent RNA.
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