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Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)

ABSTRACT: Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)

PROVIDER: PRJNA751597 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15327108_1.fastq.gz	Fastqsanger.gz
	SRR15327108_2.fastq.gz	Fastqsanger.gz
	SRR15327109_1.fastq.gz	Fastqsanger.gz
	SRR15327109_2.fastq.gz	Fastqsanger.gz
	SRR15327110_1.fastq.gz	Fastqsanger.gz

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Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (Illumina short-read sequencing)

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Dissecting long non-coding RNAs derived from microRNA genes in hematopoiesis (scRNA sequencing)

Project description:Albeit majority of eukaryotic genome can be pervasively transcribed to a diverse population of lncRNAs and various subtypes of lncRNA have been discovered. However, the genome-wide study of miRNA-derived lncRNAs is still lacking. Here, we report that over 800 miRNA gene-originated lncRNAs (molncRNAs) generated from miRNA loci. One of them, molnc-301b from miR-301b and miR-130b, functions as an "RNA decoy" to facilitate dissociation of the chromatin remodeling protein SMARCA5 from chromatin and thereby sequester transcription and mRNA translation. Specifically, molnc-301b attenuates erythropoiesis via mitigating the transcription of erythropoietic and translation-associated genes, such as GATA1 and FOS. In addition, we have established a useful and powerful CRISPR screen platform to characterize the biological functions of molncRNAs at large-scale and single-cell level, and identified 26 functional molncRNAs in hematopoietic cells. Collectively, we focused on miRNA-derived lncRNAs, deciphered their landscape during normal hematopoiesis, and comprehensively evaluated their potential roles.

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Project description:Genome-wide transcription produces a complex population of transcripts and a wide variety of functional lncRNAs occasionally evolve from them. Here, we identify and characterize miRNA gene originated lncRNAs (molncRNAs) by employing Pacific Biosciences long-read sequencing. Combining with RNA-sequencing in differentiating hematopoietic erythrocytes, we construct a global molncRNA landscape during human erythropoiesis. Among them, miR-301b and miR-130b originated lncRNA, molnc-301b, orchestrates erythropoiesis independent of miRNAs. Mechanistically, molnc-301b attenuates the transcription of a series of erythropoietic and translation-associated genes by antagonizing SMARCA5's chromatin binding. Furthermore, molnc-301b perturbs translation of key erythroid mRNAs selectively, as GATA1 and FOS. Our findings identify a novel class of lncRNA and reveal the essential role of molnc-301b in erythroid differentiation. Of note, molnc-301b orchestrates erythropoiesis via jointly controlling the transcription and translation of key erythroid regulators. In addition, we finally establish functional molncRNA screen platform by using large-scale pooled CRISPR-based single-cell RNA-seq, and uncover 36 functional molncRNAs in erythrocytes. These results thus unearth a previously unannotated class of lncRNAs and provide a useful platform for the discovery and functional study of molncRNAs.

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Project description:BACKGROUND: Recent analysis of the mouse transcriptional data has revealed the existence of approximately 34,000 messenger-like non-coding RNAs (ml-ncRNAs). Whereas the functional properties of these ml-ncRNAs are beginning to be unravelled, no functional information is available for the large majority of these transcripts. RESULTS: A few ml-ncRNA have been shown to have genomic loci that overlap with microRNA loci, leading us to suspect that a fraction of ml-ncRNA may encode microRNAs. We therefore developed an algorithm (PriMir) for specifically detecting potential microRNA-encoding transcripts in the entire set of 34,030 mouse full-length ml-ncRNAs. In combination with mouse-rat sequence conservation, this algorithm detected 97 (80 of them were novel) strong miRNA-encoding candidates, and for 52 of these we obtained experimental evidence for the existence of their corresponding mature microRNA by microarray and stem-loop RT-PCR. Sequence analysis of the microRNA-encoding RNAs revealed an internal motif, whose presence correlates strongly (R2 = 0.9, P-value = 2.2 x 10(-16)) with the occurrence of stem-loops with characteristics of known pre-miRNAs, indicating the presence of a larger number microRNA-encoding RNAs (from 300 up to 800) in the ml-ncRNAs population. CONCLUSION: Our work highlights a unique group of ml-ncRNAs and offers clues to their functions.

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