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Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

ABSTRACT: Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

PROVIDER: PRJNA543791 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9090701.fastq.gz	Fastqsanger.gz
	SRR9090702.fastq.gz	Fastqsanger.gz
	SRR9090703.fastq.gz	Fastqsanger.gz
	SRR9090704.fastq.gz	Fastqsanger.gz
	SRR9090705.fastq.gz	Fastqsanger.gz

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Transcriptome-wide maps of STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

Project description:We report the application of enhanced cross-linking immunoprecipitation (eCLIP) sequencing technology for high-throughput profiling of STRAP-RNA interactions in mouse embryos (E9.5) or embryoid body (EB) cells. Based on the eCLIP-seq data, we computationally identified a transcriptome-wide set of high-confidence peaks (over ten thousands) and most of STRAP-peaks distributed in the murine genome by defining certain exons and introns as well as their intersection. STRAP eCLIP signals in embryos were dramatically enriched at exon/intron and intron/exon borders. Numerous STRAP peaks are significantly enriched on the genes with critical roles in early organ development. Finally, we show two examples of STRAP-RNA binding that link to its regulated genes at the alternative splicing level. Together, we uncover the position- and context- dependent effects of STRAP on splicing regulation during mouse embryonic stem cells lineage commitment. Our studies provide a very useful platform to decipher STRAP’s role in the many steps in RNA biogenesis for future studies.

2020-09-16 | GSE131472 | GEO

STRAP-dependent alternative splicing events STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

Project description:STRAP-dependent alternative splicing events STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

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Next generation sequencing facilitates quantitative analysis of STRAP-dependent alternative splicing events

Project description:We report the application of next generation sequencing for evaluating alternative splicing (AS) events on lineage-committed WT and Strap-KO embryoid body (EB) cells. We also analyzed AS during mouse embryo development using RNA-seq data. Of all STRAP-regulated AS, exon-skipping events were the most frequent ones with significant changes in 49% (240 out of 489) cases. Retained introns were also overrepresented (20%, 97 out of 489) as compared to other types of AS STRAP appears to function in promoting both exon inclusion and skipping at different exons. GO function revealed STRAP-regulated AS events involve in protein catabolism, molecular binding and cell motility. More specifically, they included neuronal migration and development. Together, these analyses uncovered the previous unknown role of STRAP involved in the substantial transcriptional diversity at the exon level in certain development stage. Our study also represents the first detailed analysis of AS events in the mouse early organogenesis with biologic replicates, generated by RNA-seq technology.

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STRAP-dependent alternative splicing events; STRAP-RNA interactions in mouse early embryo and lineage-committed cells.

Project description:This SuperSeries is composed of the SubSeries listed below.

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Project description:Genome-wide maps of chromatin state (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3) in pluripotent and lineage-committed cells We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Histone H3 or H4 tri-methylation ChIP-Seq in singlicate from murine embryonic stem (ES) cells, ES-derived neural precursor cells, and embryonic fibroblasts.

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Project description:Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

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Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

Project description:Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

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Genome-wide maps of chromatin state in pre-osteoblastic and lineage-committed cells.

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