Role of plant MicroRNA in cross-species regulatory networks of humans

BMC Systems Biology

Volumn 10, Issue 1, 2016, Pages

  Zhang, Hao ^a,b   Li, Yanpu ^a   Liu, Yuanning ^a,b   Liu, Haiming ^a   Wang, Hongyu ^a   Jin, Wen ^a   Zhang, Yanmei ^a   Zhang, Chao ^c   Xu, Dong ^a,b  

^a JILIN UNIVERSITY   (China)

^b UNIVERSITY OF MISSOURI   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Core module; Cross species regulation; Functional analysis; MiRNA

Indexed keywords

MICRORNA; PLANT RNA;

ANTIBODY SPECIFICITY; ARABIDOPSIS; DIET; GASTROINTESTINAL TRACT; GENE REGULATORY NETWORK; GENETICS; HUMAN; METABOLISM; PHYSIOLOGICAL STRESS; PHYSIOLOGY; TRANSPORT AT THE CELLULAR LEVEL; URINARY TRACT;

ARABIDOPSIS; BIOLOGICAL TRANSPORT; DIET; GASTROINTESTINAL TRACT; GENE REGULATORY NETWORKS; HUMANS; MICRORNAS; ORGAN SPECIFICITY; RNA, PLANT; STRESS, PHYSIOLOGICAL; URINARY TRACT;

EID: 84984856998     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/s12918-016-0292-1     Document Type: Article

References (34)

1. Jiang M, Sang X, Hong Z. Beyond nutrients: food-derived microRNAs provide cross-kingdom regulation. Bioessays. 2012;34(4):280-4.
2. Hughes DT, Sperandio V. Inter-kingdom signalling: communication between bacteria and their hosts. Nat Rev Microbiol. 2008;6(2):111-20.
3. Weiberg A, et al. Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science. 2013;342(6154):118-23.
4. LaMonte G, et al. Translocation of sickle cell erythrocyte microRNAs into Plasmodium falciparum inhibits parasite translation and contributes to malaria resistance. Cell Host Microbe. 2012;12(2):187-99.
5. Gu Y, et al. Lactation-related microRNA expression profiles of porcine breast milk exosomes. PLoS One. 2012;7(8):e43691.
6. Liang H, Zen K, Zhang J, Zhang CY, Chen X. New roles for microRNAs in cross-species communication. RNA Biol. 2013;10(3):367-70.
7. Huang J, et al. Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med. 2007;13(10):1241-7.
8. Zhang L, et al. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res. 2012;22(1):107-26.
9. Zhang Y, et al. Analysis of plant-derived miRNAs in animal small RNA datasets. BMC Genomics. 2012;13(3):177.
10. Liang H, et al. Regulation of mammalian gene expression by exogenous microRNAs. Wiley Interdiscip Rev RNA. 2012;3(5):733-42.
11. Vaucheret H, Chupeau Y. Ingested plant miRNAs regulate gene expression in animals. Cell Res. 2012;22(1):3-5.
12. Grillo G, et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2010;38(38):D75-80.
13. Bushati N, Cohen S. M. microRNA functions. Annu Rev Cell Dev Biol. 2008;23:175-205.
14. Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. Fast and effective prediction of microRNA/target duplexes. RNA. 2004;10(10):1507-17.
15. Garcia-Hernandez M, et al. TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics. 2010;2(6):239-53.
16. Zhang Z, et al. PMRD: plant microRNA database. Nucleic Acids Res. 2010;38:D806-13.
17. Rubio-Somoza I, Weigel D. MicroRNA networks and developmental plasticity in plants. Trends Plant Sci. 2011;16(5):258-64.
18. Zhang B, Pan X, Cobb GP, Anderson TA. Plant microRNA: a small regulatory molecule with big impact. Dev Biol. 2006;289(1):3-16.
19. Li A, Mao L. Evolution of plant microRNA gene families. Cell Res. 2007;17(3):212-8.
20. Montojo J, et al. GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop. Bioinformatics. 2010;26(22):2927-8.
21. Zhang C, et al. Mosaic: making biological sense of complex networks. Bioinformatics. 2012;28(14):1943-4.
22. Zhang C, et al. NOA: a cytoscape plugin for network ontology analysis. Bioinformatics. 2013;29(16):2066-7.
23. da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57.
24. Xiao SJ, Zhang C, Zou Q, Ji ZL. TiSGeD: a database for tissue-specific genes. Bioinformatics. 2010;26(9):1273-5.
25. Thomine S, Lanquar V. Iron transport and signaling in plants. Ann Rev Plant Biol. 2003;54(4):99-131.
26. Vert G, et al. IRT1, an Arabidopsis transporter essential for iron uptake from the soil and for plant growth. Plant Cell. 2002;14(6):1223-33.
27. Thomine S, Wang R, Ward JM, Crawford NM, Schroeder JI. Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proc Natl Acad Sci U S A. 2000;97(9):4991-6.
28. Eide DJ. The molecular biology of metal ion transport in Saccharomyces cerevisiae. Annu Rev Nutr. 1998;18(1):441-69.
29. Segerstrom SC, Miller GE. Psychological stress and the human immune system: a meta-analytic study of 30 years of inquiry. Psychol Bull. 2004;130(4):601-30.
30. Arabidopsis Genome I. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796-815.
31. Riechmann JL, et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000;290(5499):2105-10.
32. Schmid M, et al. A gene expression map of Arabidopsis thaliana development. Nat Genet. 2005;37(5):501-6.
33. Brin S, Page L. The anatomy of a large-scale hypertextual Web search engine. Computer Networks and ISDN Systems. 1998;30(98):107-17.
34. Na D, Son H, Gsponer J. Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity. BMC Genomics. 2014;15(1):1091.