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Mapping targets for small nucleolar RNAs in yeast

ABSTRACT: Mapping targets for small nucleolar RNAs in yeast

PROVIDER: PRJNA472155 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7186980.fastq.gz	Fastqsanger.gz
	SRR7186990.fastq.gz	Fastqsanger.gz
	SRR7186981.fastq.gz	Fastqsanger.gz
	SRR7186991.fastq.gz	Fastqsanger.gz
	SRR7186982.fastq.gz	Fastqsanger.gz

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Mapping targets for small nucleolar RNAs in yeast.

Project description:Mapping targets for small nucleolar RNAs in yeast.

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Mapping targets for small nucleolar RNAs in human cells

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Mapping targets for small nucleolar RNAs in yeast

Project description:We report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH).

2018-08-17 | GSE114680 | GEO

Mapping targets for small nucleolar RNAs in yeast.

Project description:Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here we report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions.

| S-EPMC6171561 | biostudies-literature

Mapping targets for small nucleolar RNAs in human cells [RNA-seq]

Project description:Mapping targets for small nucleolar RNAs in human cells [RNA-seq]

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Mapping targets for small nucleolar RNAs in human cells [CLASH/FLASH]

Project description:Mapping targets for small nucleolar RNAs in human cells [CLASH/FLASH]

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Mapping targets for small nucleolar RNAs in yeast.

Project description:We report the effects of depleting U3 and snR4 in yeast BY4741 cells on the abundance of different types of RNA within the cell.

2018-08-17 | GSE118369 | GEO

Small RNAs in budding yeast

Project description:Small RNAs in budding yeast

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Mapping targets for small nucleolar RNAs in human cells [CLASH/FLASH]

Project description:We report the identification of potential novel RNA targets for box C/D snoRNAs in human HEK293 cells, using the approaches of UV crosslinking and sequencing of hybrids (CLASH), and formaldehyde crosslinking and sequencing of hybrids (FLASH).

2021-07-21 | GSE114825 | GEO

Mediator is essential for small nuclear and nucleolar RNA transcription in yeast

Project description:Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein coding RNAs (ncRNAs) including small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA promoters use the same factors as mRNA promoters, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in the transcription of sn/snoRNA genes. We found that the Mediator maps to most sn/snoRNA gene regulatory regions and that rapid depletion of the essential structural subunit Med14 strongly reduces RNAPII and TFIIB occupancy as well as nascent transcription of sn/snoRNA genes. Deletion of Med3 and Med15, subunits of the activator-interacting Mediator tail module, does not affect Mediator recruitment to or RNAPII and TFIIB occupancy of sn/snoRNA genes. Our analyses suggest that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.

2018-10-08 | GSE112721 | GEO

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