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Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

ABSTRACT: Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

PROVIDER: PRJNA479482 | ENA |

REPOSITORIES: ENA

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Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming.

Project description:Pluripotent stem cells hold great investigative potential for developmental biology and regenerative medicine. Recent studies suggest that long noncoding RNAs (lncRNAs) may function as key regulators of the maintenance and the lineage differentiation of stem cells. However, the underlying mechanisms by which lncRNAs affect the reprogramming process of somatic cells into pluripotent cells remain largely unknown. Using fibroblasts and induced pluripotent stem cells (iPSCs) at different stages of reprogramming, we performed RNA transcriptome sequencing (RNA-Seq) to identify lncRNAs that are differentially-expressed in association with pluripotency. An RNA reverse transcription-associated trap sequencing (RAT-seq) approach was then utilized to generate a database to map the regulatory element network for lncRNA candidates. Integration of these datasets can facilitate the identification of functional lncRNAs that are associated with reprogramming. Identification of lncRNAs that regulate pluripotency may lead to new strategies for enhancing iPSC induction in regenerative medicine.

| S-EPMC6244186 | biostudies-literature

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Project description:RNA transcriptome sequencing (RNA-Seq) and RNA reverse transcription-associated trap sequencing (RAT-Seq) were usded to map long noncoding RNA (lncRNAs) in reprogramming of fibroblasts into pluripotency

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Project description:The ability of RNAs to form specific contacts with other macromolecules provides an important mechanism for subcellular compartmentalization. We developed a suite of hybridization-proximity (HyPro) labeling technologies for unbiased discovery of proteins (HyPro-MS) and transcripts (HyPro-seq) associated with RNAs of interest in genetically unperturbed cells. To generate the HyPro-MS dataset reported here, fixed and permeabilized HeLa cells were hybridized with digoxigenin-labeled oligonucleotide probes against noncoding RNAs 45S, NEAT1 or PNCTR and proteins co-localizing with these RNAs were biotinylated in situ using a custom-engineered HyPro enzyme containing a digoxigenin-binding domain. Biotinylated proteins were then captured on streptavidin beads and analyzed by LC-MS/MS.

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