Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

UID: 10617

Author(s): Das, Mom*, Zattas, Dimitrios*, Lima, Christopher D.* * MSK affiliated

Publisher(s): Memorial Sloan Kettering Cancer Center

Core Facilities: Structural Biology

Description: Summary from the GEO: "Abstract: Quality control requires discrimination between functional and aberrant species to selectively target substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation and helicase-dependent 3′ to 5′ degradation by the RNA exosome. Using reconstitution biochemistry we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to selectively target and degrade an unmodified tRNA while leaving native tRNA intact. Inactivation of the distributive exoribonuclease activity of Rrp6 results in loss of substrate discrimination, leading to degradation of all RNAs. These data suggest that the activities of the Mtr4 helicase and Rrp6 exoribonuclease endow the TRAMP-RNA exosome complex with the ability to protect stable RNA while degrading defective RNA species."

Overall Design from the GEO: "Comparison of global RNA analysis of yeast strains containing either wild-type (WT) or exoribonuclease inactive Rrp6 (Rrp6 exo-) or lacking Rrp6 completely (rrp6Δ). Two biological replicates of each sample are included."

Subject of Study

Subject(s)

Access via GEO
Plain Text and TDF Data of expression profiling by high throughput sequencing
Accession #: GSE160368

Access via SRA
RNA Sequence reads for 6 samples
Accession #: SRP289703

Access via BioProject
Additional information about overall initiative.
Accession #: PRJNA673126
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Das M, Zattas D, Zinder J, et al. Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome. Proceedings of the National Academy of Sciences of the United States of America. 2021; 118(14):e2024846118.
Data Type: Genomic
Equipment Used: Illumina HiSeq 4000
High throughput gene sequencing system
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): Plain Text, TAR, TDF
Data Tool(s): RNA Seq
Dataset Size: 280 MB (TAR of TDF), 333.5 KB (TXT)

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