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Nuclear fractionation reveals chromatin-enriched RNA binding proteins and transcriptional regulatory activity of QKI5 during monocytic differentiation

ABSTRACT: Nuclear fractionation reveals chromatin-enriched RNA binding proteins and transcriptional regulatory activity of QKI5 during monocytic differentiation

PROVIDER: PRJNA679956 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13103101_1.fastq.gz	Fastqsanger.gz
	SRR13103101_2.fastq.gz	Fastqsanger.gz
	SRR13103102_1.fastq.gz	Fastqsanger.gz
	SRR13103102_2.fastq.gz	Fastqsanger.gz
	SRR13103103_1.fastq.gz	Fastqsanger.gz

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Nuclear fractionation reveals chromatin-enriched RNA binding proteins and transcriptional regulatory activity of QKI5 during monocytic differentiation

Project description:Background: Cellular RNA binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are not well-characterized and remain undefined in hematopoietic cells. Results: We first provide a full view of RBPs' distribution pattern in the nucleus and screen for chromatin-enriched RBPs (Che-RBPs) in different human cells. Subsequently, by generating ChIP-seq, CLIP-seq and RNA-seq datasets and conducting combined analysis, the transcriptional regulatory potential of certain hematopoietic Che-RBPs are predicted. From this analysis, quaking (QKI5) emerges as a potential transcriptional activator during monocytic differentiation. QKI5 is over-represented in gene promoter regions, independent of RNA or transcription factors. Furthermore, DNA-bound QKI5 activates the transcription of several critical monocytic differentiation-associated genes, including CXCL2, IL16 and PTPN6. Finally, we show that the differentiation promoting activity of QKI5 is largely dependent on CXCL2, irrespective of its RNA binding capacity. Conclusions: Our study indicates that Che-RBPs are versatile factors that orchestrate gene expression in different cellular contexts, and identifies QKI5, a classic RBP regulating RNA processing, as a novel transcriptional activator during monocytic differentiation.

2021-09-09 | GSE161943 | GEO

A global screening identifies chromatin-enriched RNA-binding proteins and the transcriptional regulatory activity of QKI5 during monocytic differentiation

Project description:Background: Cellular RNA binding proteins (RBPs) have multiple roles in post-transcriptional control, and some have been shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs have not been well-characterized and remain undefined in hematopoietic cells. Results: We first provided a full view of RBPs’ distribution pattern in nucleus and screened for chromatin-enriched RBPs (Che-RBPs) in different human cells. Subsequently, by generating ChIP-seq, CLIP-seq and RNA-seq datasets and conducting combined analysis, the transcriptional regulatory potential of certain hematopoietic Che-RBPs were predicted and from which quaking (QKI5) emerged as a potential transcriptional activator during monocytic differentiation. QKI5 was over-represented in gene promoter regions, independent of RNA or transcription factors. Furthermore, promoter-occupied QKI5 activated the transcription of several critical monocytic differentiation-associated genes, including CXCL2, IL16 and PTPN6. Finally, we showed that the differentiation-promoting activity of QKI5 is largely dependent on CXCL2, irrespective of its RNA-binding capacity. Conclusions: Our study indicates that Che-RBPs are versatile factors that orchestrate gene expression in different cellular contexts, and identifies QKI5, a classic RBP regulating RNA processing, as a novel transcriptional activator during monocytic differentiation.

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