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Homo sapiens

ABSTRACT: PAR-CLIP-seq reveals RNAs directly interacting with CTCF in human transformed cell line U2OS

PROVIDER: PRJNA232376 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1056280.fastq.gz	Fastqsanger.gz
	SRR1056281.fastq.gz	Fastqsanger.gz
	SRR1056282.fastq.gz	Fastqsanger.gz

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PAR-CLIP-seq reveals RNAs directly interacting with CTCF in human transformed cell line U2OS

Project description:This experiment sought to determine the genome-wide interactome of CTCF in human cells. PAR-CLIP seq for CTCF was performed in U2OS cells in 2 biological replicates

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Project description:The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear MOV10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the R package wavClusteR, is generally applicable to any substitution-based inference problem in genomics. The data comprises one MOV10 PAR-CLIP data file and one nuclear RNA-seq file

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