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  4. Vol 8, Issue 1, 2024

A review of computational model-based prediction of lncRNA subcellular localization

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DOI: 10.23977/acss.2024.080105 | Downloads: 25 | Views: 263

Author(s)

Rongneng Sun 1, Qingsong Guo 1, Xiaofen Yuan 1

Affiliation(s)

1 Yunnan Normal University, Kunming, China

Corresponding Author

Qingsong Guo

ABSTRACT

Long non-coding RNAs (lncRNA) play pivotal roles in diverse cellular processes, and the determination of lncRNA subcellular localization serves as crucial information for elucidating their functional roles. However, conventional biochemical experimental methodologies employed for identifying lncRNA subcellular localization exhibit inherent complexities, challenges in reproducibility, and substantial costs. In the contemporary era of burgeoning bioinformatics, computational models for predicting the subcellular localization of biomolecules offer a viable alternative. Notably, these computational approaches boast high efficiency and relatively lower costs, presenting a substantial reduction in time and human resource expenditure compared to traditional experimental protocols. This comprehensive review encapsulates the latest strides in leveraging computational models for the prediction of lncRNA subcellular localization, offering novel avenues for a profound comprehension of lncRNA functionality and their intricate involvement in cellular processes.

KEYWORDS

Long non-coding RNAs (lncRNA), subcellular localization, database, computational model

CITE THIS PAPER

Rongneng Sun, Qingsong Guo, Xiaofen Yuan, A review of computational model-based prediction of lncRNA subcellular localization. Advances in Computer, Signals and Systems (2024) Vol. 8: 46-51. DOI: http://dx.doi.org/10.23977/acss.2024.080105.

REFERENCES

[1] Taft, R.J.; Pang, K.C.; Mercer, T.R.; Dinger, M.E.; Mattick, J.S. Non-coding RNAs: Regulators of disease.J. Pathol. 2010, 220, 126- 139.[PubMed]
[2] Martin KC, Ephrussi A. mRNA localization: gene expression in the spatial dimension[J]. Cell. 2009 Feb 20;136(4):719-30. 
[3] Hu L, Hou D, Huang D, et al. Long-stranded non-coding RNAs and epigenetic regulation[J]. Genomics and Applied Biology, 2016,35(012):3319-3324.
[4] Gupta, R. A., Shah, N., Wang, K.C., Kim, J., Horlings, H. M., & Wong, D.J.: Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010, 464(7291):1071.
[5] Rashid F,Shah A,Shan G. Long Non-coding RNAs in the Cytoplasm[J].Genomics Proteomics & Bioinformatics, 2016,14(2):73-80.
[6] Chen Y G, Satpathy A T, Chang H Y. Generegulation in the immune system by longnoncoding RNAs[J]. Nature immunology, 2017, 18(9): 962-972.
[7] Chen M T,Lin H S,Shen C,et al. PU.1-Regulated LongNoncoding RNA lnc-MC Controls Human Monocyte/ Macrophage Differentiation through Interaction with MicroRNA 199a-5p[J].Molecular & Cellular Biology,2015,35(18):3212-3224.
[8] Tay Y, Kats L, Salmena L, et al. Coding-independent regulation of the tumour suppressor PTEN by competing endogenous mRNAs[J]. Cell, 2011, 147(2): 344-357.
[9] Yao R W, Wang Y, Chen L L. Cellular functions of long noncoding RNAs[J]. Nature cell biology, 2019, 21(5):542-551.
[10] Chen L L. Linking long noncoding RNA localization and function[J]. Trends in biochemical sciences, 2016, 41(9): 761-772.
[11] Wen X, Gao L, Guo X, et al. lncSLdb: aresource for long non-coding RNA subcellular localization[J]. Database, 2018.
[12] Zhang T,Tan P,Wang L,et al. RNALocate:a resource for RNA subcellular localizations[J].Nucleic acids research,2017,45(D1):D135-D138.
[13] Mas-Ponte D, Carlevaro-Fita J,Palumbo E,et al.LncATLAS database for subcellular localization of long noncoding RNAs [J]. Rna, 2017, 23(7):1080- 1087.
[14] Wen X, Gao L, Guo X, Li X, Huang X, Wang Y, Xu H, He R, Jia C, Liang F. lncSLdb: a resource for long non-coding RNA subcellular localization[J]. Database (Oxford). 2018 Jan 1;2018:1-6.
[15] Amaral P P,Clark M B,Gascoigne D K,et al.lncRNAdb:a reference database for long noncoding RNAs[J].Nucleic acids research,2011,39(suppl_1). D146-D151.
[16] Volders P J,Anckaert J,Verheggen K,et al.LNCipedia 5:towards a reference set of human long non-coding RNAs[J].Nucleic acids research,2019,47( D1):D135-D139.
[17] Geer L Y, Marchler-Bauer A, Geer R C, et al. The NCBI biosystems database[J]. Nucleic acids research, 2010,
38(suppl_1): D492-D496.
[18] Su Z D, Huang Y, Zhang Z Y,et al. iLoc-LncRNA:predict the subcellular location of LncRNAs by incorporeating octamer composition into general PseKNC [J]. Bioinformatics, 2018, 34(24):4196-4204.
[19] Ahmad A, Lin H, Shatabda S. Locate-R: Subcellular localization of long non-coding RNAs using nucleotide compositions [J]. Genomics, 2020, 112(3): 2583-2589.
[20] Yang X-F, Zhou Y-K, Zhang L, et al. Predicting LncRNA Subcellular Localization Using Unbalanced Pseudo-k Nucleotide Composition[J]. Current Bioinformatics. 2020; 15(6).
[21] Y. Fan, M. Chen and Q. Zhu. lncLocPred: Predicting LncRNA Subcellular Localization Using Multiple Sequence Feature Information[J]. IEEE Access, vol. 2020; 8(124702-124711).
[22] Yan D X,CHEN Yingli. Subcellular multi-localization prediction of long-chain non-coding RNAs based on sequence information[J]. Journal of Inner Mongolia University (Natural Science Edition),2022,53(01):38-47.
[23] Sun X H. Research on multi-feature fusion algorithm for long-stranded non-coding RNA subcellular localization prediction problem [D]. Jilin University, 2022.
[24] Cao Z, Pan X, Yang Y, et al. The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier[J]. Bioinformatics, 2018, 34(13): 2185-2194.
[25] GUDENAS B L,WANG L. Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features [J] Scientific Reports, 2018, 8(1):1- 10.
[26] Lin Y, Pan X. Hong-Bin Shen. lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning[J]. Bioinformatics. 2021; 37(16):2308-2316.
[27] Zhu X P. A subcellular localization method of lncRNA based on unbalanced data distribution framework [D]. Jilin University, 2022.
[28] Li M, Zhao B Y, Yin R, et al. GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation, Briefings in Bioinformatics, Volume 24, Issue 1, January 2023, bbac565.
[29] Cai J Z, Wang T.,Deng, X. et al. GM-lncLoc: LncRNAs subcellular localization prediction based on graph neural network with meta-learning. MC Genomics 24, 52 (2023).
[30] Zeng M, Wu Y F, Li Y M, et al. LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism, Bioinformatics, Volume 39, Issue 12, December 2023, btad752.

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