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Repriming limits R-loop formation at DNA secondary structures during S phase

ABSTRACT: Repriming limits R-loop formation at DNA secondary structures during S phase

PROVIDER: PRJNA448895 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6949340_1.fastq.gz	Fastqsanger.gz
	SRR6949340_2.fastq.gz	Fastqsanger.gz
	SRR6949350_1.fastq.gz	Fastqsanger.gz
	SRR6949350_2.fastq.gz	Fastqsanger.gz
	SRR6949360_1.fastq.gz	Fastqsanger.gz

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Repriming limits R-loop formation at DNA secondary structures during S phase

Project description:The goal of this study was to compare the qualitative and quantitative differences in the presence of DNA:RNA hybrids (R-loops) between wild type and PrimPol knockout cell lines. Our initial genetic experiments on a reporter locus have showed a link between the formation of R-loop and non-B DNA motifs; we have therefore analysed the correlation between R-loop abundance and of sequences computationaly predicted to form triplex-DNA or G-quadruplex forming sequences, and whether this changes between the two cell lines.

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Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons

Project description:Alternative splicing (AS) generates large amounts of RNA isoforms and dramatically increases the complexities of transcriptomes and proteomes. However, it remains unclear how RNA structures contribute to AS regulation. Here, we systematically search transcriptomes for secondary structures with concealed branch-sites (BSs) in the alternatively spliced introns and predict thousands from six organisms, of which many are evolutionarily conserved. Intriguingly, a highly conserved stem-loop structure with concealed BSs is found in animal SF3B3 genes and colocalizes with a downstream poison exon (PE). Destabilization of this structure allows increased usage of the branch sites and results in enhanced PE inclusion in both human and Drosophila cells, leading to decreased expression of SF3B3. Through an RNAi screen of 28 RNA-binding proteins, we find that this stem-loop structure is sensitive to U2 and U2-associated proteins. Furthermore, we find that SF3B3 also facilitates DNA repair and protects genome stability by enhancing interaction between ERCC6/CSB and arrested RNA polymerase II. Importantly, both Drosophila and human cells with the secondary structure mutated by genome editing exhibit altered DNA repair in vivo. This study provides a novel and common mechanism for AS regulation of PEs and reveals a physiological function of SF3B3 in DNA repair.

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High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

Project description:We have successfully characterized R-loop structures using non-denaturing bisulfite treatment coupled with single-molecule sequencing to reveal that R-loops form defined overlapping molecular clusters around promoter, gene body, and terminal regions of genes. Our results uncovers that R-loop formation is both driven by favorable DNA sequence as well as topological state.

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Project description:In vivo atlas of RNA secondary structures recognized by ADARs

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Project description:By using a novel high-throughput method, named chemical inference of RNA structures (CIRS-seq), that uses dimethyl sulfate (DMS), and N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT) to modify RNA residues in single-stranded conformation within native RNA secondary structures, we investigated the structural features of mouse embryonic stem cell (ESC) transcripts. Our analysis revealed an unexpected higher structuring of the 5' and 3' untranslated regions (UTRs) compared to the coding regions, a reduced structuring at the Kozak sequence and stop codon, and a three-nucleotide periodicity across the coding region of messenger RNAs. We also observed that ncRNAs exhibit a higher degree of structuring with respect to protein coding transcripts. Moreover, we found that the Lin28a binding protein binds selectively to RNA motifs with a strong preference toward a single stranded conformation. Transcritome-wide mapping of RNA secondary structures in mouse embryonic stem cells (mESC)

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