How was TSS and TTS identified?

The transcription start site and transcription termination site of each transcript was identified by enriching the primary transcripts and based on the SEnd-seq, a high-throughput and unbiased method that simultaneously maps transcription start and termination sites with single-nucleotide resolution (Ju et al., 2019).

How was PS identified?

RppH processing positions were identified by combining the methods of SEnd-seq (Ju, X.W., 2019) and PABLO (Celesnik, H., 2007). The PS of RNases were identified based on the methods of SEnd-seq (Ju, X.W., 2019) and ISCP (Le Rhun, 2017). Moreover, The PS of unknown enzymes identified by dRNA-seq in several species.

How many species are included in this database?

Currently, the ProSRPSite includes the processing sites (PS) of kinds of enzymes on the genome-wide scale from more than 20 species, such as Escherichia coli, Rhodobacter sphaeroides, Salmonella enterica and Streptococcus pyogenes (Chao et al., 2017; Lecrivain et al., 2018; Broglia et al., 2020; Le Rhun et al., 2017; Spanka et al., 2022). The TTS and TTS of E.coli also has been uploaded in our database (Ju et al., 2019).

What are the applications of this database?

These data are valuable for precisely determining the processing positions for kind of enzyme from more than 20 species, precisely determining the 5ʹ and 3ʹ boundary of genes, and knowing the processing sites (PS) of kinds of enzymes on the genome-wide scale, such as RNase E, PNPase and RppH. These data also are beneficial to understand how the different enzymes cooperating to regulate the expression of multiple genes on a polycistron.

How to use JBrowse to visualize ProSRPSite data?

The JBrowse genome browser will bring users to a page where all sites can be viewed alongside the gene annotations.

Moving

Move the view by clicking and dragging in the track area, or by clicking or in the navigation bar, or by pressing the left and right arrow keys. Center the view at a point by clicking on either the track scale bar or overview bar, or by shift-clicking in the track area.

Zooming

Zoom in and out by clicking or in the navigation bar, or by pressing the up and down arrow keys while holding down "shift ". Select a region and zoom to it ("rubber-band " zoom) by clicking and dragging in the overview or track scale bar, or shift-clicking and dragging in the track area.

Showing Tracks

Turn a track on by dragging its track label from the "Available Tracks " area into the genome area, or double-clicking it. Turn a track off by dragging its track label from the genome area back into the "Available Tracks " area.

References

Broglia, L., Lecrivain, A. L., Renault, T. T., Hahnke, K., Ahmed-Begrich, R., Le Rhun, A., and Charpentier, E.: An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3'-to-5' exoRNases and RNase Y, Nat Commun, 11, 1587, 10.1038/s41467-020-15387-6, 2020.

Chao, Y., Li, L., Girodat, D., Forstner, K. U., Said, N., Corcoran, C., Smiga, M., Papenfort, K., Reinhardt, R., Wieden, H. J., Luisi, B. F., and Vogel, J.: In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways, Mol Cell, 65, 39-51, 10.1016/j.molcel.2016.11.002, 2017.

Ju, X., Li, D., and Liu, S.: Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria, Nat Microbiol, 4, 1907-1918, 10.1038/s41564-019-0500-z, 2019.

Le Rhun, A., Lecrivain, A. L., Reimegard, J., Proux-Wera, E., Broglia, L., Della Beffa, C., and Charpentier, E.: Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes, Nucleic Acids Res, 45, 2329-2340, 10.1093/nar/gkw1316, 2017.

Lecrivain, A. L., Le Rhun, A., Renault, T. T., Ahmed-Begrich, R., Hahnke, K., and Charpentier, E.: In vivo 3'-to-5' exoribonuclease targetomes of Streptococcus pyogenes, Proc Natl Acad Sci U S A, 115, 11814-11819, 10.1073/pnas.1809663115, 2018.

Le Rhun, A. et al. Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes. Nucleic Acids Res 45, 2329-2340 (2017).

Lecrivain, A.L. et al. In vivo 3'-to-5' exoribonuclease targetomes of Streptococcus pyogenes. Proc Natl Acad Sci U S A 115, 11814-11819 (2018).

Broglia, L. et al. An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3'-to-5' exoRNases and RNase Y. Nat Commun 11, 1587 (2020).

Chao, Y. et al. In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Mol Cell 65, 39-51 (2017).

Altuvia, Y. et al. In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. Nucleic Acids Res 46, 10380-10394 (2018).

Spanka, D.T., Reuscher, C.M. & Klug, G. Impact of PNPase on the transcriptome of Rhodobacter sphaeroides and its cooperation with RNase III and RNase E. BMC Genomics 22, 106 (2022).

Khemici, V., Prados, J., Linder, P. & Redder, P. Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation. PLoS Genet 11, e1005577 (2015).

DeLoughery, A., Lalanne, J.B., Losick, R. & Li, G.W. Maturation of polycistronic mRNAs by the endoribonuclease RNase Y and its associated Y-complex in Bacillus subtilis. Proc Natl Acad Sci U S A 115, E5585-E5594 (2018).