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Marker genes of Biscogniauxia sp. strain SG25

ABSTRACT: - Biscogniauxia sp. strain SG25 internal transcribed spacer (ITS) region, contains ITS1, 5.8S rRNA gene, ITS2 complete nrDNA sequence - >Biscogniauxia sp. strain SG25 large subunit (LSU), contains 28S rRNA gene partial sequence, complete D1/D2 region nrDNA sequence

PROVIDER: PRJEB32032 | ENA |

REPOSITORIES: ENA

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Marker genes of Daldinia sp. strain SG1

Project description:- Daldinia sp. strain SG1 internal transcribed spacer (ITS) region, contains ITS1, 5.8S rRNA gene, ITS2 complete nrDNA sequence - Daldinia sp. strain SG1 large subunit (LSU), contains 28S rRNA gene partial sequence, complete D1/D2 region nrDNA sequence

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Marker genes of Didymosphaeriaceae, cf. Tremateia sp. strain SG8c

Project description:- Didymosphaeriaceae, cf. Tremateia sp. strain SG8c internal transcribed spacer (ITS) region, contains ITS1, 5.8S rRNA gene, ITS2 complete nrDNA sequence - Didymosphaeriaceae, cf. Tremateia sp. strain SG8c large subunit (LSU), contains 28S rRNA gene partial sequence, complete D1/D2 region nrDNA sequence

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Purpureocillium lilacinum strain T26B internal transcribed spacer (ITS) region

Project description:Purpureocillium lilacinum strain T26B internal transcribed spacer (ITS) region, contains ITS1, 5.8S rRNA gene, ITS2 complete nrDNA sequence

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Xylaria cubensis strain TS7 internal transcribed spacer (ITS) region

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Structural transitions during yeast large ribosomal subunit maturation analyzed by tethered nuclease structure probing

Project description:Yeast large ribosomal subunit (LSU) precursors are subject to substantial changes in protein composition during their maturation due to coordinated transient interactions with a large number of ribosome biogenesis factors and due to the assembly of ribosomal proteins. These compositional changes go along with stepwise processing of LSU rRNA precursors and with specific rRNA folding events, as revealed by recent cryo-electron microscopy analyses of late nuclear and cytoplasmic LSU precursors. Here we aimed to analyze changes in the spatial rRNA surrounding of selected ribosomal proteins during yeast LSU maturation. For this we combined a recently developed tethered tertiary structure probing approach with both targeted and high-throughput readout strategies. Several structural features of late LSU precursors were faithfully detected by this procedure. In addition, the obtained data let us suggest that early rRNA precursor processing events are accompanied by a global transition from a flexible to a spatially restricted rRNA conformation. For intermediate LSU precursors, a number of structural hallmarks could be addressed which include the fold of the internal transcribed spacer between 5.8S rRNA and 25S rRNA, the orientation of the central protuberance and the spatial organization of the interface between LSU rRNA domains I and III.

2017-04-01 | GSE97276 | GEO

Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX) for deciphering the region-specific interactome of 45S rRNA

Project description:We used Targeted RNase H-mediated Extraction of crosslinked RBPs (TREX)to assess the endogenous region-specific binding partners of 45S rRNA in human HCT116 cells. We performed TREX experiments against the full-length 45S, as well as each individual region (5'ETS. 18S, ITS1, 5.8S, ITS2, 28S, and 3'ETS). Extracted proteins from RNase H digested and control cells (4 or 5 replicate per region per condition) were compared, using label-free (LFQ) Quantitative proteomics.

2023-12-27 | PXD044659 | Pride

Exonuclease Requirements for Mammalian Ribosomal RNA Biogenesis and Surveillance

Project description:Ribosomal RNAs (rRNAs) biogenesis are multistep processes requiring the activity of several nuclear and cytoplasmic exonucleases. The exact processing steps for mammalian 5.8S rRNA remains obscure. Here, using loss-of-function approaches in mouse embryonic stem cells and deep sequencing of rRNA intermediates, we investigate at nucleotide resolution the requirements of exonucleases known to be involved in 5.8S maturation, and explore the role of the Perlman syndrome-associated 3’-5’ exonuclease Dis3l2 in rRNA processing. We expand the repertoire of Dis3l2 targets to three 5.8S, 5S, and 28S rRNAs. We uncover a novel cytoplasmic intermediate that we name ‘7SB’ rRNA that is generated through sequential processing by distinct exosome complexes. 7SB rRNA can be oligouridylated by TUT4/7 and subsequently processed by Dis3l2 and Eri1. Moreover, exosome depletion triggers Dis3l2-mediated decay (DMD) as a surveillance pathway for rRNAs. Our data identify previously unknown 5.8S rRNA processing steps and provide nucleotide level insight into the exonuclease requirements for mammalian rRNA processing.

2019-04-13 | GSE129734 | GEO

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Project description:rDNA Region (ITS And rRNA genes for SSU rRNA, ITS1, 5.8S rRNA, ITS2, LSU rRNA (partial)

| PRJEB51811 | ENA

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Project description:rDNA Region (ITS And rRNA genes for SSU rRNA, ITS1, 5.8S rRNA, ITS2, LSU rRNA (partial)

| PRJEB51814 | ENA

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Project description:We have recently found that the human methyltransferase ZCCHC4 is responsible for introducing the single m6A modification in 28S rRNA. The project is aimed at further elucidating the functional consequences of such methylation. To this end, protein mass spectrometry is utilized to identify proteins that bind preferentially to the methylated or unmethylated form of the m6A containing hairpin sequence in 28S rRNA. Specifically, this is done by incubating a HeLa cell extract with an methylated or unmethylated RNA oligonucleotide containing a biotin affinity tag, which is used to pull-down the RNA with associated proteins.

2019-11-22 | PXD013354 | Pride

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