PulseTD: RNA Life Cycle Dynamics Analysis Based on Pulse Model of 4sU-seq Time Course Sequencing Data

Overview

Journal PeerJ

Specialties Biology
Environmental Health
General Medicine

Date 2020 Jul 28

PMID 32714656

Authors

Xin Wang

Siyu He

Jian Li

Jun Wang

Chengyi Wang

Mingwei Wang

Danni He

Xingfeng Lv

Qiuyan Zhong

Hongjiu Wang

Zhenzhen Wang

Affiliations

Soon will be listed here.

Abstract

The life cycle of intracellular RNA mainly involves transcriptional production, splicing maturation and degradation processes. Their dynamic changes are termed as RNA life cycle dynamics (RLCD). It is still challenging for the accurate and robust identification of RLCD under unknow the functional form of RLCD. By using the pulse model, we developed an R package named pulseTD to identify RLCD by integrating 4sU-seq and RNA-seq data, and it provides flexible functions to capture continuous changes in RCLD rates. More importantly, it also can predict the trend of RNA transcription and expression changes in future time points. The pulseTD shows better accuracy and robustness than some other methods, and it is available on the GitHub repository (https://github.com/bioWzz/pulseTD_0.2.0).

References

La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V . RNA velocity of single cells. Nature. 2018; 560(7719):494-498. PMC: 6130801. DOI: 10.1038/s41586-018-0414-6. View

Zeisel A, Kostler W, Molotski N, Tsai J, Krauthgamer R, Jacob-Hirsch J . Coupled pre-mRNA and mRNA dynamics unveil operational strategies underlying transcriptional responses to stimuli. Mol Syst Biol. 2011; 7:529. PMC: 3202801. DOI: 10.1038/msb.2011.62. View

Sabo A, Kress T, Pelizzola M, de Pretis S, Gorski M, Tesi A . Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis. Nature. 2014; 511(7510):488-492. PMC: 4110711. DOI: 10.1038/nature13537. View

Thapar R, Denmon A . Signaling pathways that control mRNA turnover. Cell Signal. 2013; 25(8):1699-710. PMC: 3703460. DOI: 10.1016/j.cellsig.2013.03.026. View

Melvin W, Milne H, Slater A, Allen H, Keir H . Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. Eur J Biochem. 1978; 92(2):373-9. DOI: 10.1111/j.1432-1033.1978.tb12756.x. View

Uvarovskii A, Dieterich C . pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments. Bioinformatics. 2017; 33(20):3305-3307. DOI: 10.1093/bioinformatics/btx368. View

Chechik G, Koller D . Timing of gene expression responses to environmental changes. J Comput Biol. 2009; 16(2):279-90. DOI: 10.1089/cmb.2008.13TT. View

Schwalb B, Schulz D, Sun M, Zacher B, Dumcke S, Martin D . Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA). Bioinformatics. 2012; 28(6):884-5. DOI: 10.1093/bioinformatics/bts052. View

Moore M, Proudfoot N . Pre-mRNA processing reaches back to transcription and ahead to translation. Cell. 2009; 136(4):688-700. DOI: 10.1016/j.cell.2009.02.001. View

10.

Rabani M, Levin J, Fan L, Adiconis X, Raychowdhury R, Garber M . Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nat Biotechnol. 2011; 29(5):436-42. PMC: 3114636. DOI: 10.1038/nbt.1861. View

11.

Lopez-Maury L, Marguerat S, Bahler J . Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet. 2008; 9(8):583-93. DOI: 10.1038/nrg2398. View

12.

de Pretis S, Kress T, Morelli M, Melloni G, Riva L, Amati B . INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments. Bioinformatics. 2015; 31(17):2829-35. DOI: 10.1093/bioinformatics/btv288. View

13.

Sun M, Schwalb B, Schulz D, Pirkl N, Etzold S, Lariviere L . Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res. 2012; 22(7):1350-9. PMC: 3396375. DOI: 10.1101/gr.130161.111. View

14.

Friedel C, Dolken L, Ruzsics Z, Koszinowski U, Zimmer R . Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res. 2009; 37(17):e115. PMC: 2761256. DOI: 10.1093/nar/gkp542. View

15.

Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo D, Pauli A . High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell. 2014; 159(7):1698-710. PMC: 4272607. DOI: 10.1016/j.cell.2014.11.015. View

16.

Rutkowski A, Erhard F, LHernault A, Bonfert T, Schilhabel M, Crump C . Widespread disruption of host transcription termination in HSV-1 infection. Nat Commun. 2015; 6:7126. PMC: 4441252. DOI: 10.1038/ncomms8126. View

17.

Garibaldi A, Carranza F, Hertel K . Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine. Methods Mol Biol. 2017; 1648:169-176. PMC: 5783291. DOI: 10.1007/978-1-4939-7204-3_13. View