Data for "Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress"

Ryota Yamagami; Philip Bevilacqua

Data for "Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress"

This is the raw data used in the tRNA Structure-seq paper.

Paper abstract: RNA structure plays roles in myriad cellular events including transcription, translation, and RNA processing. Genome-wide analyses of RNA secondary structure in vivo by chemical probing have revealed critical structural features of mRNAs and long ncRNAs. Here, we examine the in vivo secondary structure of a small RNA class, tRNAs. Study of tRNA structure is challenging because tRNAs are heavily modified and strongly structured. We introduce “tRNA structure-seq,” a new workflow that accurately determines in vivo secondary structures of tRNA. The workflow combines dimethyl sulfate (DMS) probing, ultra-processive RT, and mutational profiling (MaP), which provides mutations opposite DMS and natural modifications thereby allowing multiple modifications to be identified in a single read. We applied tRNA structure-seq to E. coli under control and stress conditions. A leading folding algorithm predicts E. coli tRNA structures with only ∼80% average accuracy from sequence alone. Strikingly, tRNA structure-seq, by providing experimental restraints, improves structure prediction under in vivo conditions to ∼95% accuracy, with more than 14 tRNAs predicted completely correctly. tRNA structure-seq also quantifies the relative levels of tRNAs and their natural modifications at single nucleotide resolution, as validated by LC-MS/MS. Our application of tRNA structure-seq yields insights into tRNA structure in living cells, revealing that it is not immutable but has dynamics, with partial unfolding of secondary and tertiary tRNA structure under heat stress that is correlated with a loss of tRNA abundance. This method is applicable to other small RNAs, including those with natural modifications and highly structured regions.

Citation

Yamagami, Ryota; Bevilacqua, Philip (2022). Data for "Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress" [Data set]. Scholarsphere.

Files

Fig1.zip

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Fig2.zip

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Fig3.zip

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Fig5.zip

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Lib10_S10_R1_001.fastq.gz

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SFig11.zip

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SFig12_mutational_profiling_to_measure_modification.zip

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SFig13_MS2_validation.zip

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SFig14_MS2_validation.zip

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SFig15_Bio_replicate_correl.zip

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SFig16_compare_mutational_profiling_with_LC-MSMS_data.zip

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SFig17_count_codons_in_E_coli_BW25113.zip

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SFig1.zip

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SFig2.zip

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SFig7.zip

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SFig8.zip

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SFig9.zip

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tRNA_seq_1_S1_R1_001.fastq.gz

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tRNA_seq_2_S2_R1_001.fastq.gz

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tRNA_seq_5_S5_R1_001.fastq.gz

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tRNA_seq_6_S6_R1_001.fastq.gz

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tRNA_seq_7_S7_R1_001.fastq.gz

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tRNA_seq_9_S9_R1_001.fastq.gz

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Z_README.rtf

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Metadata

Work Title	Data for "Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress"
Access	Open Access
Creators	Ryota Yamagami Philip Bevilacqua
License	CC BY 4.0 (Attribution)
Work Type	Dataset
Publication Date	2022
Related URLs	https://doi.org/10.1073/pnas.2201237119
Deposited	March 16, 2022

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Version 1
published

Created

March 16, 2022 02:51 by rxy33
Added Creator Ryota Yamagami

March 16, 2022 02:53 by rxy33
Added Creator Philip Bevilacqua

March 16, 2022 02:53 by rxy33
Added tRNA_seq_1_S1_R1_001.fastq.gz

March 16, 2022 03:10 by rxy33
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Added Lib42_S42_R1_001.fastq.gz

March 16, 2022 03:10 by rxy33
Updated Publication Date, License Show Changes

March 16, 2022 03:11 by rxy33
Publication Date
- 2022
License
- https://creativecommons.org/licenses/by/4.0/
Added Code_Fig1b.R

March 29, 2022 10:11 by rxy33
Added Figure1.eps

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Deleted Figure1.eps

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Added SFig12_mutational_profiling_to_measure_modification.zip

March 29, 2022 10:18 by rxy33
Added SFig13_MS2_validation.zip

March 29, 2022 10:18 by rxy33
Added SFig14_MS2_validation.zip

March 29, 2022 10:18 by rxy33
Added SFig15_Bio_replicate_correl.zip

March 29, 2022 10:18 by rxy33
Added SFig16_compare_mutational_profiling_with_LC-MSMS_data.zip

March 29, 2022 10:18 by rxy33
Added SFig17_count_codons_in_E_coli_BW25113.zip

March 29, 2022 10:18 by rxy33
Added Z_README.rtf

March 29, 2022 10:18 by rxy33
Published

April 03, 2022 22:22 by rxy33
Updated

April 04, 2024 10:21 by [unknown user]

Version 2
published

Created

May 01, 2022 20:43 by rxy33
Deleted Fig2.zip

May 01, 2022 20:47 by rxy33
Added Fig2.zip

May 01, 2022 20:47 by rxy33
Published

May 01, 2022 20:52 by rxy33
Updated Work Title, Description, Related URLs Show Changes

February 27, 2024 15:27 by avs5190
Work Title
- ~~Data for tRNA Structure-seq paper~~
- Data for "Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress"
Description
- ~~This is the raw data used in the tRNA Structure-seq paper.~~
- This is the raw data used in the tRNA Structure-seq paper.
- Paper abstract: RNA structure plays roles in myriad cellular events including transcription, translation, and RNA processing. Genome-wide analyses of RNA secondary structure in vivo by chemical probing have revealed critical structural features of mRNAs and long ncRNAs. Here, we examine the in vivo secondary structure of a small RNA class, tRNAs. Study of tRNA structure is challenging because tRNAs are heavily modified and strongly structured. We introduce “tRNA structure-seq,” a new workflow that accurately determines in vivo secondary structures of tRNA. The workflow combines dimethyl sulfate (DMS) probing, ultra-processive RT, and mutational profiling (MaP), which provides mutations opposite DMS and natural modifications thereby allowing multiple modifications to be identified in a single read. We applied tRNA structure-seq to E. coli under control and stress conditions. A leading folding algorithm predicts E. coli tRNA structures with only ∼80% average accuracy from sequence alone. Strikingly, tRNA structure-seq, by providing experimental restraints, improves structure prediction under in vivo conditions to ∼95% accuracy, with more than 14 tRNAs predicted completely correctly. tRNA structure-seq also quantifies the relative levels of tRNAs and their natural modifications at single nucleotide resolution, as validated by LC-MS/MS. Our application of tRNA structure-seq yields insights into tRNA structure in living cells, revealing that it is not immutable but has dynamics, with partial unfolding of secondary and tertiary tRNA structure under heat stress that is correlated with a loss of tRNA abundance. This method is applicable to other small RNAs, including those with natural modifications and highly structured regions.
Related URLs
- https://doi.org/10.1073/pnas.2201237119
Updated

April 04, 2024 10:21 by [unknown user]

Data for "Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress"

Citation

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Version 2 published

Version 1
published

Version 2
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