PhasiHunter: a Robust Phased SiRNA Regulatory Cascade Mining Tool Based on Multiple Reference Sequences

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2023 Nov 11

PMID 37950456

Authors

Zerong Feng

Jiejie Feng

BaoYi Zhang

Yuhan Fei

Hongsheng Zhang

Ji Huang

Affiliations

Soon will be listed here.

Abstract

Summary: In recent years, phased small interfering RNA has been found to play crucial roles in many biological processes in plants. However, efficiently predicting phasiRNA regulatory cascades with computational methods is still challenging. Here, we introduce PhasiHunter, a phasiRNA regulatory network prediction tool that has several distinctive features compared to existing tools: (i) PhasiHunter employs two major phasiRNA prediction algorithms, namely phase score and hypergeometric distribution-based methods, to ensure the integrity and accuracy of prediction; (ii) PhasiHunter can identify phasiRNAs and their regulatory networks based on multiple reference sequences and the predicted results can be automatically integrated; (iii) PhasiHunter can efficiently identify the phasiRNAs generated through alternative splicing events; and (iv) the excellent data structure and parallel computing architecture allow PhasiHunter to predict phasiRNAs and their regulatory pathways with high efficiency.

Availability And Implementation: PhasiHunter is an open-source tool that is available at https://github.com/HuangLab-CBI/PhasiHunter.

References

Fei Y, Feng J, Wang R, Zhang B, Zhang H, Huang J . PhasiRNAnalyzer: an integrated analyser for plant phased siRNAs. RNA Biol. 2021; 18(11):1622-1629. PMC: 8594884. DOI: 10.1080/15476286.2021.1879543. View

Gebert D, Hewel C, Rosenkranz D . unitas: the universal tool for annotation of small RNAs. BMC Genomics. 2017; 18(1):644. PMC: 5567656. DOI: 10.1186/s12864-017-4031-9. View

Tsuji J, Weng Z . DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. PLoS One. 2016; 11(10):e0164228. PMC: 5063419. DOI: 10.1371/journal.pone.0164228. View

Liu Y, Teng C, Xia R, Meyers B . PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction. Plant Cell. 2020; 32(10):3059-3080. PMC: 7534485. DOI: 10.1105/tpc.20.00335. View

Ma X, Liu C, Gu L, Mo B, Cao X, Chen X . TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants. Bioinformatics. 2017; 34(9):1574-1576. PMC: 6248703. DOI: 10.1093/bioinformatics/btx797. View

Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View

Cock P, Antao T, Chang J, Chapman B, Cox C, Dalke A . Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009; 25(11):1422-3. PMC: 2682512. DOI: 10.1093/bioinformatics/btp163. View

Chen H, Li Y, Wu S . Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. Proc Natl Acad Sci U S A. 2007; 104(9):3318-23. PMC: 1805617. DOI: 10.1073/pnas.0611119104. View

Zhai J, Zhang H, Arikit S, Huang K, Nan G, Walbot V . Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc Natl Acad Sci U S A. 2015; 112(10):3146-51. PMC: 4364226. DOI: 10.1073/pnas.1418918112. View

10.

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

11.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios F, Del Risco H . SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res. 2018; 28(3):396-411. PMC: 5848618. DOI: 10.1101/gr.222976.117. View

12.

Guo Q, Qu X, Jin W . PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades. Bioinformatics. 2014; 31(2):284-6. DOI: 10.1093/bioinformatics/btu628. View

13.

Pearson W, Lipman D . Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988; 85(8):2444-8. PMC: 280013. DOI: 10.1073/pnas.85.8.2444. View

14.

Zhan J, Meyers B . Plant Small RNAs: Their Biogenesis, Regulatory Roles, and Functions. Annu Rev Plant Biol. 2023; 74:21-51. DOI: 10.1146/annurev-arplant-070122-035226. View

15.

Deng P, Muhammad S, Cao M, Wu L . Biogenesis and regulatory hierarchy of phased small interfering RNAs in plants. Plant Biotechnol J. 2018; 16(5):965-975. PMC: 5902766. DOI: 10.1111/pbi.12882. View

16.

Axtell M . A method to discover phased siRNA loci. Methods Mol Biol. 2009; 592:59-70. DOI: 10.1007/978-1-60327-005-2_5. View

17.

Shen W, Le S, Li Y, Hu F . SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS One. 2016; 11(10):e0163962. PMC: 5051824. DOI: 10.1371/journal.pone.0163962. View

18.

Dai X, Zhuang Z, Zhao P . psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018; 46(W1):W49-W54. PMC: 6030838. DOI: 10.1093/nar/gky316. View