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Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA-counterpart in terminal hematopoiesis

ABSTRACT: Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA-counterpart in terminal hematopoiesis

PROVIDER: PRJNA669808 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12833400.fastq.gz	Fastqsanger.gz
	SRR12833401.fastq.gz	Fastqsanger.gz
	SRR12833402.fastq.gz	Fastqsanger.gz
	SRR12833403.fastq.gz	Fastqsanger.gz
	SRR12833404.fastq.gz	Fastqsanger.gz

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Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA counterpart in terminal hematopoiesis.

Project description:Each day, about 1012 erythrocytes and platelets are released into the bloodstream. This substantial output from hematopoietic stem cells is tightly regulated by transcriptional and epigenetic factors. Whether and how circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not known. We recently reported that erythrocytes and platelets contain the highest levels and numbers of circRNAs among hematopoietic cells. Here, we provide the first detailed analysis of circRNA expression during erythroid and megakaryoid differentiation. CircRNA expression not only significantly increased upon enucleation, but also had limited overlap between progenitor cells and mature cells, suggesting that circRNA expression stems from regulated processes rather than resulting from mere accumulation. To study circRNA function in hematopoiesis, we first compared the expression levels of circRNAs with the translation efficiency of their mRNA counterpart. We found that only one out of 2531 (0.04%) circRNAs associated with mRNA-translation regulation. Furthermore, irrespective of thousands of identified putative open reading frames, deep ribosome-footprinting sequencing, and mass spectrometry analysis provided little evidence for translation of endogenously expressed circRNAs. In conclusion, circRNAs alter their expression profile during terminal hematopoietic differentiation, yet their contribution to regulate cellular processes remains enigmatic.

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Circular RNAs exhibit limited evidence for translation, or translation regulation of the mRNA-counterpart in terminal hematopoiesis

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

2021-03-04 | GSE159579 | GEO

Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [Ribo-seq]

Project description:Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [Ribo-seq]

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Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [RNA-seq]

Project description:Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [RNA-seq]

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Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [Ribo-seq]

Project description:Erythrocytes and platelets have high production rates, with 1012 cells released daily into the blood stream. This output from bone-marrow residing hematopoietic stem cells is tightly regulated by transcription factors and epigenetic modifications. Whether and how non-coding RNAs such as circular RNAs (circRNAs) contribute to the differentiation and/or identity of hematopoietic cells is to date not well understood. We recently published a circRNA expression map of hematopoietic cells, which showed that erythrocytes and platelets contain the highest levels and numbers of circRNAs. Whether and how circRNA expression alters during differentiation of erythrocytes and platelet precursors is however not known. Therefore, we here provide the first detailed and comprehensive analysis of circRNA expression during red blood cell and megakaryocyte differentiation. CircRNA expression significantly increased during erythroid precursor differentiation into red blood cells, and in differentiating megakaryocytes, in particular upon enucleation. Many functions have been attributed to circRNAs. To dissect their possible function in hematopoietic differentiation, we first focused on translation regulation. We compared circRNA and mRNA expression to ribosomal foot printing data, and found that only 20 (2.6%) circRNAs associated with translation regulation of their mRNA counterparts. We also identified thousands of putative open reading frames in circRNAs, suggesting that circRNAs may also encode proteins. However, deep ribosome-footprinting sequencing data and in-depth mass spectrometry data analysis provided little evidence for translation of endogenously expressed circRNAs in erythroblasts, megakaryocytes and platelets. In conclusion, circRNAs in platelets and red blood cells are highly abundant and alter their expression profile during differentiation, yet their contribution to regulate cellular processes remains enigmatic.

2021-03-04 | GSE159578 | GEO

Abundant Circular RNA expression in terminal erythropoiesis and megakaryopoiesis shows limited evidence for translation or circRNA-mediated translation regulation [RNA-seq]

2021-03-04 | GSE159577 | GEO

Translation in amino acid-poor environments is limited by tRNAGln charging

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