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Caenorhabditis elegans

ABSTRACT: Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RIP-Seq)

PROVIDER: PRJNA265848 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1635360.fastq.gz	Fastqsanger.gz
	SRR1635361.fastq.gz	Fastqsanger.gz
	SRR1635362.fastq.gz	Fastqsanger.gz
	SRR1635363.fastq.gz	Fastqsanger.gz
	SRR1635354.fastq.gz	Fastqsanger.gz

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RNA m6A methylome of Caenorhabditis elegans

Project description:One of the most abundant RNA modifications is N6-methyladenosine (m6A). RNA from all forms of life, including viruses, contain m6A. This modification has been detected in many types of RNAs, such as mRNA, ribosomal RNA, long non-coding RNAs, small nuclear RNAs and microRNAs. Diverse set of proteins have been characterized to methylate, demethylate and specifically bind to this modification in different organisms. C. elegans is a unique model organism with abundant m6A modification, although its genome does not code for orthologs of the well characterized m6A methyltransferase METTL3/METTL14 complex or the demethylases FTO or ALKBH5. Furthermore, orthologs of the YTH family m6A reader proteins seem to be absent from the worm genome as well. To gain insights into how this modification is installed in this organism, we set out to identify enzymes that contribute to the abundant level of m6A in C. elegans. We designed a targeted RNAi screen by which the expression of 22 candidate putative RNA methyltransferase genes are knocked down. We measured global RNA methylation level by HPLC-MS/MS analysis after two generations of RNAi-mediated knock down. The knock down of two candidate methyltransferases resulted in a decrease in global m6A level in total RNA. The first methyltransferase, F33A8.4, is an ortholog of the human ZCCHC4 gene. The second methyltransferase, C38D4.9, is an ortholog of the human METTL5 gene. In order to determine if ZCCHC4 or METTL5 are involved in the deposition of m6A at the mRNA level, m6A-RIP-seq experiments were performed in mRNA derived from WT (N2), ZCCHC4 KO, METTL5 KO and ZCCHC4/METTL5 dKO C. elegans embryos.

2021-04-06 | GSE148786 | GEO

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (ribosome)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status.

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