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Homo sapiens

ABSTRACT: RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships (RNA-seq)

PROVIDER: PRJNA284147 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2028250.fastq.gz	Fastqsanger.gz
	SRR2028251.fastq.gz	Fastqsanger.gz
	SRR2028252.fastq.gz	Fastqsanger.gz
	SRR2028253.fastq.gz	Fastqsanger.gz
	SRR2028254.fastq.gz	Fastqsanger.gz

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RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Project description:RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

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Project description:RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships RDIP-seq)

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RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships (RNA-seq)

Project description:Mapping of RNA:DNA hybrids in human cells reveals a number of characteristics of these non-canonical nucleic acid structures. A directional sequencing approach reveals the RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to the stability of these structures. The RNA:DNA hybrids are enriched at loci with decreased DNA methylation and increased DNase hypersensitivity, and within larger domains with characteristics of heterochromatin formation. Studies of chromatin at RNA:DNA hybrids shows the presence of the ILF2 and ILF3 transcription factors, supporting a model of certain transcription factors binding preferentially to the RNA:DNA conformation. Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting a model of RNA generating these structures in trans. The results of the study indicate heterogeneous functions of these genomic elements and new insights into their formation and stability in vivo.

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RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships RDIP-seq)

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RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships (RNA-seq)

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Project description:The biotin labeled DNA:RNA hybrids with or without RNA m5C modification were incubated with lysates of 293 cells treated with H2O2, and were pulled down by Streptavidin. The proteins pulled down by the empty beads control, unmodified or m5C-modified hybrids were analyzed by mass spectrometry

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human HEK293T S9.6 Mass spectrometry

Project description:We are interested in proteins which could preferentially interact with DNA: RNA hybrids upon DNA damage. To achieve that, we treated HEK293T with 10 Gy IR, followed by 20 min recovery. We applied S9.6 antibody, which could recognize DNA: RNA hybrids structure, to isolate their interactome upon either normal conditions or DNA damage conditions, after which those proteins sample were sent for mass spec analysis, and proteins specifically interacting with DNA: RNA hybrids were then screened and analysed.

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Human SKI component SKIV2L regulates telomeric DNA-RNA hybrids and prevents telomere fragility

Project description:Super killer (SKI) complex is a well-known cytoplasmic 3′ to 5′ mRNA decay complex that functions with the exosome to degrade excessive and aberrant mRNAs. Recently, SKIV2L, the 3′ to 5′ RNA helicase of the human SKI (hSKI) complex has been implicated with the extraction of mRNA at stalled ribosomes, tackling aberrant translation. Here, we show that SKIV2L and TTC37 of the hSKI complex are present within the nucleus, localise on chromatin and at some telomeres during the G2 cell cycle phase. In cells, SKIV2L prevents telomere replication stress shown as fragile telomeres and increases the stability of telomere DNA-RNA hybrids in G2 of the cell cycle whereas its absence decreases the amount of those structures. We further demonstrate that purified hSKI complex binds telomeric DNA and RNA substrates in vitro. Moreover, SKIV2L association with telomeres is dependent on DNA-RNA hybrids but its helicase activity is dispensable for its telomeric function. Taken together, our results provide a nuclear function for SKIV2L of the hSKI complex in overcoming replication stress at telomeres mediated by its recruitment to DNA-RNA hybrid structures in G2 and thus maintaining telomere stability.

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Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in host immune evasion by antigenic variation

Project description:RNA-DNA hybrids are widespread epigenetic features of genomes that provide a growing range of activities in transcription, chromatin and DNA replication and repair. Understanding of these diverse functions has been advanced by characterising the proteins that interact with the hybrids, with all such studies revealing hundreds of potential interactors. However, all interaction analyses to date have focused on mammalian cells, and so it is unclear if a similar spectrum of RNA-DNA hybrid interactors found in other eukaryotes, thus limiting our understanding of the conserved and lineage-specific activities linked to these genetic structures. The African trypanosome is a compelling organism in which to address these questions. As a divergent single-cell eukaryotic parasite of the Discoba grouping, Trypanosoma brucei displays substantial divergence in several aspects of core biology from its mammalian host and, unusually for a protist, has well-developed tools for molecular genetic analysis. For these reasons, we used DNA-RNA hybrid immunoprecipitation coupled with mass spectrometry to reveal 602 putative interactors in T. brucei mammal- or insect vector-infective stage cells. We show that the approach selects for a subset of the parasite proteome and reveals a range of predicted RNA-DNA hybrid associated activities, some overlapping with similar studies in mammals. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, impact on T. brucei nuclear RNA-DNA hybrid and DNA damage levels. Moreover, loss of each affects the operation of the crucial parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA-DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as many conserved with mammals, and so likely fundamental to eukaryotic genome function.

2024-01-26 | PXD042146 | Pride

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