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The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites

ABSTRACT: The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites

PROVIDER: PRJNA637293 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11924304.fastq.gz	Fastqsanger.gz
	SRR11924305.fastq.gz	Fastqsanger.gz
	SRR11924307.fastq.gz	Fastqsanger.gz
	SRR11924308.fastq.gz	Fastqsanger.gz
	SRR11924310.fastq.gz	Fastqsanger.gz

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The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2'-<i>O</i>-Me sites.

Project description:During zebrafish development, an early type of rRNA is gradually replaced by a late type that is substantially different in sequence. We applied RiboMeth-seq to rRNA from developmental stages for profiling of 2'-O-Me, to learn if changes in methylation pattern were a component of the shift. We compiled a catalog of 2'-O-Me sites and cognate box C/D guide RNAs comprising 98 high-confidence sites, including 10 sites that were not known from other vertebrates, one of which was specific to late-type rRNA. We identified a subset of sites that changed in methylation status during development and found that some of these could be explained by availability of their cognate SNORDs. Sites that changed during development were enriched in the novel sites revealed in zebrafish. We propose that the early type of rRNA is a specialized form and that its structure and ribose methylation pattern may be an adaptation to features of development, including translation of specific maternal mRNAs.

| S-EPMC7668251 | biostudies-literature

Delayed leaf greening involves a major shift in expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

Project description:Delayed leaf greening involves a major shift in expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

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The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2’-O-Me sites

Project description:A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns during Zebrafish (Danio rerio) development

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Project description:This SuperSeries is composed of the following subset Series: GSE13653: Affinity purification of ribosomes and associated RNAs from stress-treated cells GSE13654: Affinity purification of ribosomes and associated RNAs using tagged Rpl16a and Rpl16b Refer to individual Series

2010-06-25 | E-GEOD-13682 | biostudies-arrayexpress

Delayed leaf greening involves a major shift in expression of cytosolic and mitochondrial ribosomes to plastid ribosomes in the highly phosphorus-use-efficient Hakea prostrata (Proteaceae)

Project description:Hakea prostrata (Proteaceae) maintains a high photosynthetic rate at low leaf phosphorus and exhibits delayed leaf greening, a convergent adaptation found in many plant families where investment in photosynthetic machinery is delayed until after the leaf structure is built, saving on nutrient investment. To identify the dynamics of gene expression underlying delayed greening, we made a de novo transcriptome assembly for H. prostrata using roots and leaves from hydroponically grown plants, and leaves from five morphologically distinct stages of leaf development from wild plants. Abundance of unique transcripts was compared among the developing leaf stages to identify differentially expressed genes, which were separated into groups based on co-expression patterns. In general, transcripts encoding functions associated with leaf structure decreased in abundance across leaf development, with this concomitant with the decline in foliar P and N concentrations. An enrichment of differentially expressed genes associated with photosynthetic function increased in abundance at or after leaf expansion and much later in development than in species that do not have delayed greening. The abundance of transcripts encoding cytoplasmic and mitochondrial ribosomal subunits generally declined across leaf development, whilst transcripts encoding chloroplast ribosomal subunits increased. Taken together, these results indicate a clear shift in protein synthesis apparatus, moving from a leaf developmental stage and into the photosynthetically-active stage.

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The ASC-1 complex promotes translation initiation of the scanning ribosomes

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