RNA sequencing of HeLa cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE201426 | GEO | 2022/10/11
REPOSITORIES: GEO
Similar Datasets
Project description:Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3b represents a family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3b interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3b and RISC mutants are similarly defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay. Moreover, both Top3b and AGO2 mutants exhibit reduced levels of heterochromatin protein HP1 in pericentric heterochromatin. Furthermore, expression of several genes and transposable elements in heterochromatin is increased in the Top3b mutant. Notably, Top3b mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of transposable elements. Our data suggest that Top3b may act as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing.
2018-09-12 | GSE119777 | GEO
Project description:Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3b represents a family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3b interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3b and RISC mutants are similarly defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay. Moreover, both Top3b and AGO2 mutants exhibit reduced levels of heterochromatin protein HP1 in pericentric heterochromatin. Furthermore, expression of several genes and transposable elements in heterochromatin is increased in the Top3b mutant. Notably, Top3b mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of transposable elements. Our data suggest that Top3b may act as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing.
2018-09-12 | GSE119626 | GEO
Project description:Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3b represents a new family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3b interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3b and RISC mutants are defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay; and this defect is suppressed in their double mutants. Moreover, both Top3b and AGO2 single mutants exhibit reduced heterochromatin protein HP1 in pericentric heterochromatin; and this reduction is also suppressed in their double mutant. Furthermore, expression of several genes and transposable elements (TEs) in heterochromatin is increased in the Top3b mutant. Notably, Top3b mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of TEs. Our data suggest that Top3b acts as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing. Grant title: An RNA topoisomerase complex interacts with Fragile X syndrome protein to promote neurodevelopment and maintain normal life-span. Grant ID: AG000689-08. Source: NIA/NIH
2018-08-29 | GSE119185 | GEO
Project description:Both transcription and replication can take place simultaneously on the same DNA template, potentially leading to transcription-replication conflicts (TRCs) and topological problems. Here we asked which topoisomerase(s) is/are the best candidate(s) for sensing TRC. Genome-wide topoisomerase binding sites were mapped in parallel for all the nuclear topoisomerases (TOP1, TOP2A, TOP2B, TOP3A and TOP3B). To increase the signal to noise ratio (SNR), we used ectopic expression of those topoisomerases in H293 cells followed by a modified CUT&Tag method. Although each topoisomerase showed distinct binding patterns, all topoisomerase binding signals positively correlated with gene transcription. TOP3A binding signals were suppressed by DNA replication inhibition. This was also observed but to a lesser extent for TOP2A and TOP2B. Hence, we propose the involvement of TOP3A in sensing both head-on TRCs (HO-TRCs) and codirectional TRCs (CD-TRCs). In which case, the TOP3A signals appear concentrated within the promoters and first 20 kb regions of the 5’ -end of genes, suggesting the prevalence of TRCs and the recruitment of TOP3A in the 5’-regions of transcribed and replicated genes.
2024-07-31 | GSE269841 | GEO
Project description:DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes - and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast, and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy enables us to reveal the influence primary DNA sequence has upon Top2 cleavage - distinguishing canonical DNA double-strand breaks (DSBs) from a major population of DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.
2019-09-28 | GSE137685 | GEO
Project description:DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.
2019-09-28 | GSE136943 | GEO
Project description:Here we dissect the transcriptional response in S. cerevisiae cells lacking DNA topoisomerases. We use microarray technology coupled with a functional genomics approach and demonstrate intimate connections between topoisomerase dependency, promoter chromatin architecture and gene transcription. Our findings suggest that DNA topoisomerases I and II play a role for transcription initiation. We observe a genome wide reduction in mRNA levels and identify a distinct functional subset of the genome with particular requirements for topoisomerases. These genes are characterized by high transcriptional plasticity, they are chromatin regulated and distinguished by having an enrichment of a nucleosome at a critical position in the promoter region, suggesting that topoisomerases influence transcription initiation by affecting promoter chromatin structure. In further support of a role of topoisomerases for initiation, we demonstrate that genome wide topoisomerase dependency reflects transcriptional activity but not transcriptional length. We exemplify the importance of topoisomerases for initiation of chromatin-regulated genes by showing that the enzymes are essential although redundant for PHO5 induction and are necessary for a step required for promoter nucleosome removal. W303 versus top1Î?, top2ts and top1Î?top2ts. 3 biological replicates for each mutant versus wildtype counterpart amounting to 12 microarrays.
2012-07-31 | E-GEOD-22809 | biostudies-arrayexpress
Project description:DNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo. This data set contains maps of Top2 CCs in the S. cerevisiae genome, generated by CC-seq of BY4741 cells -/+ etoposide (VP16).
2019-09-28 | GSE136675 | GEO
Project description:Expression data from lack of DNA topoisomerase I, DNA topoisomerase II and complete lack of both topoisomerases
2015-09-15 | E-GEOD-22809 | ExpressionAtlas
Project description:Topoisomerases are crucial to solve DNA topological problems, but they have not been linked to RNA metabolism. Here we show that human topoisomerase 3β (Top3β) is an RNA topoisomerase that biochemically and genetically interacts with FMRP, a protein deficient in Fragile X syndrome and known to regulate translation of mRNAs important for neuronal function and autism. Notably, the FMRP-Top3β interaction is abolished by a disease-associated FMRP mutation, and several human genetic studies link Top3β mutation to schizophrenia and intellectual disability. Top3β binds multiple mRNAs encoded by genes with neuronal functions related to schizophrenia and autism. Expression of one such gene, ptk2/FAK, is reduced in neuromuscular junctions of Top3β mutant flies. Synapse formation is defective in Top3β mutant flies and mice, as observed in FMRP mutant animals. Our findings suggest that Top3β acts as an RNA topoisomerase and works with FMRP to promote expression of mRNAs critical for neurodevelopment and mental health.
2013-08-04 | GSE47502 | GEO