This data freeze accompanies 5PSeq Explorer and it contains 775 5PSeq datasets compiled from 18 published studies interrogating various aspects of biology at the interface of mRNA decay and translation, including both genetic and environmental perturbations. To enable comparability across conditions and cross-species we processed all data uniformly (see Methods). The generated database consists of: (1) metadata, (2) raw processed counts files of amino acid, codon, frame preferences, metagene counts around start and termination sites, additional count files as documented on the Fivepseq package output documentation, and (3) RNA composition.For Eukaryotes, the collection consists of 378 yeast samples (Ascomycota phylum) with an overrepresentation for Saccharomyces cerevisiae (n= 340). For bacteria, we provide 397 samples across Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota and Verrucomicrobiota phyla with an overreprepresentation for Bacillus subtilis (n= 67) and Aggregatibacter actinomycetemcomitans (n=59).

This data freeze accompanies 5PSeq Explorer and it contains 775 5PSeq datasets compiled from 18 published studies interrogating various aspects of biology at the interface of mRNA decay and translation, including both genetic and environmental perturbations. To enable comparability across conditions and cross-species we processed all data uniformly (see Methods). The generated database consists of: (1) metadata, (2) raw processed counts files of amino acid, codon, frame preferences, metagene counts around start and termination sites, additional count files as documented on the Fivepseq package output documentation, and (3) RNA composition.For Eukaryotes, the collection consists of 378 yeast samples (Ascomycota phylum) with an overrepresentation for Saccharomyces cerevisiae (n= 340). For bacteria, we provide 397 samples across Actinomycetota, Bacillota, Bacteroides, Bacteroidota, Proteobacteria, Pseudomonadota and Verrucomicrobiota phyla with an overreprepresentation for Bacillus subtilis (n= 67) and Aggregatibacter actinomycetemcomitans (n=59).

Coverage traks for  5´ monophosphorylated mRNA decay intermediates (5´P) in bacterial species from vaginal swabs.Bedgraph files provide information for the 5'P coverage for the forward and reverse strand. Datasets are provided for 8 samples (r1 to r8).

Regulation of mRNA stability is a central process in gene expression. Here, report an atlas of 5´ monophosphorylated mRNA decay intermediates (5´P) in 96 species. We use those data to demonstrate that in species with 5´-3´exonuclease activity, the exoribonuclease RNase J follows the trailing ribosome, producing an in vivo single-nucleotide toeprint of its 5´ position. While in other species, ribosome position alters endonucleolytic cleavage sites. Our work demonstrates the universal connection between RNA decay and translation and paves the way for use of metadegradome sequencing to investigate post-transcriptional regulation of unculturable species present and complex microbial communities.
Data was analyzed using our fivepseq software.  Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa099, https://doi.org/10.1093/nargab/lqaa099

Coverage traks for  5´ monophosphorylated mRNA decay intermediates (5´P) in bacterial species from vaginal swabs.Bedgraph files provide information for the 5'P coverage for the forward and reverse strand. Datasets are provided for 8 samples (r1 to r8).

Regulation of mRNA stability is a central process in gene expression. Here, report an atlas of 5´ monophosphorylated mRNA decay intermediates (5´P) in 96 species. We use those data to demonstrate that in species with 5´-3´exonuclease activity, the exoribonuclease RNase J follows the trailing ribosome, producing an in vivo single-nucleotide toeprint of its 5´ position. While in other species, ribosome position alters endonucleolytic cleavage sites. Our work demonstrates the universal connection between RNA decay and translation and paves the way for use of metadegradome sequencing to investigate post-transcriptional regulation of unculturable species present and complex microbial communities.
Data was analyzed using our fivepseq software.  Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa099, https://doi.org/10.1093/nargab/lqaa099

Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200
Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession numbers GSE114899. Data was analyzed using fivepseq pipeline http://pelechanolab.com/software/fivepseq/
Related manuscript abstract:
Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5’ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.
Raw data:Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession number GSE114899 and GSE151632

Supplementary information for the manuscript: A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae. Olga Rodríguez-Galán, Juan J García-Gómez, Iván V Rosado, Wu Wei, Alfonso Méndez-Godoy, Benjamin Pillet, Alisa Alekseenko, Lars M Steinmetz, Vicent Pelechano, Dieter Kressler, Jesús de la Cruz, Nucleic Acids Research, , gkaa1200, https://doi.org/10.1093/nar/gkaa1200
Here we provide browsable metagene analysis for 5´P mRNA degradation profiles.Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession numbers GSE114899. Data was analyzed using fivepseq pipeline http://pelechanolab.com/software/fivepseq/
Related manuscript abstract:
Proteostasis needs to be tightly controlled to meet the cellular demand for correctly de novo folded proteins and to avoid protein aggregation. While a coupling between translation rate and co-translational folding, likely involving an interplay between the ribosome and its associated chaperones, clearly appears to exist, the underlying mechanisms and the contribution of ribosomal proteins remain to be explored. The ribosomal protein uL3 contains a long internal loop whose tip region is in close proximity to the ribosomal peptidyl transferase center. Intriguingly, the rpl3[W255C] allele, in which the residue making the closest contact to this catalytic site is mutated, affects diverse aspects of ribosome biogenesis and function. Here, we have uncovered, by performing a synthetic lethal screen with this allele, an unexpected link between translation and the folding of nascent proteins by the ribosome-associated Ssb-RAC chaperone system. Our results reveal that uL3 and Ssb-RAC cooperate to prevent 80S ribosomes from piling up within the 5’ region of mRNAs early on during translation elongation. Together, our study provides compelling in vivo evidence for a functional connection between peptide bond formation at the peptidyl transferase center and chaperone-assisted de novo folding of nascent polypeptides at the solvent-side of the peptide exit tunnel.
Raw data:Raw and processed sequencing data are deposited at Gene Expression Omnibus (GEO) with accession number GSE114899 and GSE151632

Supplementary information for manuscript: "Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq" from Lilit Nersisyan, Maria Ropat and Vicent Pelechano (2020)
Dataset updated to fivepseq version1.0b6

5'P mRNA degradome datasets analyzed with fivepseq. (http://pelechanolab.com/software/fivepseq/). Raw Saccharomyces cerevisiae data is available from GEO under accession code GSE91064 and for Arabidopsis thaliana under accessions GSE72505 and GSE77549.

Browsable dataset containing transcript boundaries for the manuscript:
Jingwen Wang, Bingnan Li, Sueli Marques, Lars M Steinmetz, Wu Wei, Vicent Pelechano, TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes, Nucleic Acids Research, Volume 48, Issue 18, 09 October 2020, Page e104, https://doi.org/10.1093/nar/gkaa691
The alignment files contains sequences of K562 cells using TIF-Seq2 method. The sequencing reads were aligned to the human reference genome hg38. Each read pair represents the boundary of an individual transcript. The first reads in pairs are 5' ends, while the second reads in pairs are 3' ends. The alignment files can be loaded into IGV for visualization. You can set up view as pairs in the alignment track.
Source code for the associated manuscript is available from GitHub at https://github.com/jingwen/TIFseq2
Raw data is deposited at GEO with access code GSE140912