Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA385478 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
2017-06-01 | GSE98541 | GEO
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
2021-07-06 | GSE124979 | GEO
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.
2021-12-15 | E-MTAB-10234 | biostudies-arrayexpress
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.
2023-07-20 | PXD038103 | Pride
Project description:The nuclear matrix associated hnRNP U/SAF-A protein has been implicated in diverse pathways from transcriptional regulation to telomere length control to X inactivation, but the precise mechanism underlying each of these processes has remained elusive. Here, we report hnRNP U as a regulator of SMN2 splicing from a custom RNAi screen. Genome-wide analysis by CLIP-seq reveals that hnRNP U binds virtually to all classes of regulatory non-coding RNAs, including all snRNAs required for splicing of both major and minor classes of introns, leading to the discovery that hnRNP U regulates U2 snRNP maturation and Cajal body morphology in the nucleus. Global analysis of hnRNP U-dependent splicing by RNA-seq coupled with bioinformatic analysis of associated splicing signals suggests a general rule for splice site selection through modulating the core splicing machinery. These findings exemplify hnRNP U/SAF-A as a potent regulator of nuclear ribonucleoprotein particles in diverse gene expression pathways. Examination of hnRNP U regulated splicing in Hela cells with CLIP-seq (two biological replicates) and paired-end RNA-seq (control and hnRNP U knockdown)
2012-02-16 | E-GEOD-34491 | biostudies-arrayexpress
Project description:Single-cell replication timing analysis of hTERT-RPE1 cells depleted for SAF-A protein
| PRJEB43704 | ENA
Project description:RNA sequencing analysis after MK5 knockdown in LATS1/2-null RPE1 cells
| PRJNA573472 | ENA
Project description:RNA-seq in human RPE1-hTERT cells
| PRJNA609332 | ENA
Project description:The nuclear scaffold, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we mapped 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate from HeLa cells across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites recovered mapped predominately near expressed genes and localized near transcription start sites and the ends of genes.
2011-03-23 | GSE26477 | GEO
Project description:Gene expression was profiled in unperturbed RPE1-hTERT cells by RNA-seq.
2020-02-29 | GSE146121 | GEO