Spatiotemporal role of the lncRNA Evx1as in embryonic patterning
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ABSTRACT:
PROVIDER: PRJNA412253 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6078630_1.fastq.gz | Fastqsanger.gz | |||
| SRR6078630_2.fastq.gz | Fastqsanger.gz | |||
| SRR6078640_1.fastq.gz | Fastqsanger.gz | |||
| SRR6078640_2.fastq.gz | Fastqsanger.gz | |||
| SRR6078650_1.fastq.gz | Fastqsanger.gz |
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Project description:We performed spatial transcriptome analysis on cryosections of gastrulating embryos from E6.5 to E7.5 by low-input RNA sequencing (Geo-seq). Careful spatial transcriptomic analysis revealed that the lncRNA Evx1as plays a transient spatiotemporal role in regulating embryonic patterning during gastrulation, yet is dispensable for overall development and survival. Altogether, these results suggest that many lncRNAs are generally dispensable for normal development and survival, but may be selectively required in a particular context in vivo.
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Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.
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