Identification of neoblast- And regeneration-specific miRNAs in the planarian Schmidtea mediterranea

RNA

Volumn 19, Issue 10, 2013, Pages 1394-1404

  Sasidharan, Vidyanand ^a   Lu, Yi Chien ^b   Bansal, Dhiru ^a   Dasari, Pranavi ^a   Poduval, Deepak ^a   Seshasayee, Aswin ^a   Resch, Alissa M ^c   Graveley, Brenton R ^c   Palakodeti, Dasaradhi ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

^c UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

MicroRNA; Neoblast; Planaria; Regeneration

Indexed keywords

MICRORNA;

ARTICLE; CELL MIGRATION; CELL SUBPOPULATION; CENTRAL NERVOUS SYSTEM; GANGLION; GENE EXPRESSION REGULATION; GENE REPRESSION; MULTIGENE FAMILY; NEOBLAST; NONHUMAN; PLATYHELMINTH; PRIMORDIUM; PRIORITY JOURNAL; RNA STABILITY; SCHMIDTEA MEDITERRANEA; TISSUE REGENERATION; WOUND HEALING;

MICRORNA; NEOBLAST; PLANARIA; REGENERATION;

ANIMALS; BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; IN SITU HYBRIDIZATION; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANARIANS; REAL-TIME POLYMERASE CHAIN REACTION; REGENERATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; STEM CELLS;

EID: 84884692986     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.038653.113     Document Type: Article

References (40)

1. Aboobaker AA. 2011. Planarian stem cells: A simple paradigmfor regeneration. Trends Cell Biol 21: 304-311.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
3. Bartel DP. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241-247. (Pubitemid 40270816)
5. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, et al. 2005. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
6. de Hoon MJ, Imoto S, Nolan J, Miyano S. 2004. Open source clustering software. Bioinformatics 20: 1453-1454. (Pubitemid 38931415)
7. Eisenhoffer GT, Kang H, Sánchez Alvarado A. 2008. Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell 3: 327-339.
8. Friedländer MR, Adamidi C, Han T, Lebedeva S, Isenbarger TA, Hirst M, Marra M, Nusbaum C, Lee WL, Jenkin JC, et al. 2009. High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci 106: 11546-1151.
9. Friedländer MR, Mackowiak SD, Li N, Chen W, Rajewsky N. 2012. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40: 37-52.
10. González-Estévez C, Arseni V, Thambyrajah RS, Felix DA, Aboobaker AA. 2009. Diverse miRNA spatial expression patterns suggest important roles in homeostasis and regeneration in planarians. Int J Dev Biol 53: 493-505.
11. Hayashi T, Asami M, Higuchi S, Shibata N, Agata K. 2006. Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting. Dev Growth Differ 48: 371-380. (Pubitemid 44035795)
12. Kim YK, Yu J, Han TS, Park SY, Namkoong B, Kim DH, Hur K, Yoo MW, Lee HJ, Yang HK, et al. 2009. Functional links between clustered microRNAs: Suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer. Nucleic Acids Res 37: 1672-1681.
13. King RS, Newmark PA. 2012. The cell biology of regeneration. J Cell Biol 196: 553-562.
14. King RS, Newmark PA. 2013. In situ hybridization protocol for enhanced detection of gene expression in the planarian Schmidtea mediterranea. BMC Dev Biol 12: 13-18.
15. Kuhn S, Johnson SL, Furness DN, Chen J, Ingham N, Hilton JM, Steffes G, Lewis MA, Zampini V, Hackney CM, et al. 2011. miR-96 regulates the progression of differentiation in mammalian cochlear inner and outer hair cells. Proc Natl Acad Sci 108: 2355-2360.
16. Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, et al. 2012. A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals. Stem Cells 30: 1734-1745.
17. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
18. Li YQ, Zeng A, Han XS, Wang C, Li G, Zhang ZC, Wang JY, Qin YW, Jing Q. 2011. Argonaute-2 regulates the proliferation of adult stem cells in planarian. Cell Res 21: 1750-1754.
19. Lobo D, Beane WS, Levin M. 2012. Modeling planarian regeneration: A primer for reverse-engineering the worm. PLoS Comput Biol 8: e1002481.
20. Lu YC, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW, Graveley BR. 2009. Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea. RNA 15: 1483-1491.
21. Marco A, Hooks KB, Griffiths-Jones S. 2012. Evolution and function of the extended miR-2 microRNA family. RNA Biology 9: 1-7.
22. Onal P, Grün D, Adamidi C, Rybak A, Solana J, Mastrobuoni G, Wang Y, Rahn HP, Chen W, Kempa S, et al. 2012. Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells. EMBO J 31: 2755-2769.
23. Palakodeti D, Smielewska M, Graveley BR. 2006. MicroRNAs from the planarian Schmidtea mediterranea: A model system for stem cell biology. RNA 12: 1640-1649. (Pubitemid 44316029)
24. Palakodeti D, Smielewska M, Lu YC, Yeo GW, Graveley BR. 2008. The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians. RNA 14: 1174-1186. (Pubitemid 351717497)
25. Pearson BJ, Eisenhoffer GT, Gurley KA, Rink JC, Miller DE, Sánchez Alvarado A. 2009. Formaldehyde-based whole-mount in situ hybridization method for planarians. Dev Dyn 238: 443-450.
26. Qin YF, Fang HM, Tian QN, Bao ZX, Lu P, Zhao JM, Mai J, Zhu ZY, Shu LL, Zhao L, et al. 2011. Transcriptome profiling and digital gene expression by deep-sequencing in normal/regenerative tissues of planarian Dugesia japonica . Genomics 97: 364-371.
27. Reddien PW. 2011. Constitutive gene expression and the specification of tissue identity in adult planarian biology. Trends Genet 27: 277-285.
28. Resch AM, Palakodeti D, Lu YC, Horowitz M, Graveley BR. 2012. Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea. PLoS One 7: e34447.
29. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
30. Rouhana L, Shibata N, Nishimura O, Agata K. 2010. Different requirements for conserved post-transcriptional regulators in planarian regeneration and stem cell maintenance. Dev Biol 341: 429-443.
31. Ryazansky SS, Gvozdev VA, Berezikov E. 2011. Evidence for post-transcriptional regulation of clustered microRNAs in Drosophila. BMC Genomics 12: 371.
32. Saldanha AJ. 2004. Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248. (Pubitemid 39619217)
33. Solana J, Kao D, Mihaylova Y, Jaber-Hijazi F, Malla S, Wilson R, Aboobaker A. 2012. Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol 13: R19.
34. Tian QN, Bao ZX, Lu P, Qin YF, Chen SJ, Liang F, Mai J, Zhao JM, Zhu ZY, Zhang YZ, et al. 2012. Differential expression of microRNA patterns in planarian normal and regenerative tissues. Mol Biol Rep 39: 2653-2658.
35. Wagner DE, Wang IE, Reddien PW. 2011. Clonogenic neoblasts are pluripotent adult stem cells that underlie planarian regeneration. Science 13: 811-816.
36. Wenemoser D, Reddien PW. 2010. Planarian regeneration involves distinct stem cell responses to wounds and tissue absence. Dev Biol 344: 979-991.
37. Wenemoser D, Lapan SW, Wilkinson AW, Bell GW, Reddien PW. 2012. A molecular wound response program associated with regeneration initiation in planarians. Genes Dev 26: 988-1002.
38. Weng R, Cohen SM. 2012. Drosophila miR-124 regulates neuroblast proliferation through its target anachronism. Development 139: 1427-1434.
39. Xu J, Wong C. 2008. A computational screen for mouse signaling pathways targeted by microRNA clusters. RNA 14: 1276-1283. (Pubitemid 351872185)
40. Xu Z, Chen M, Ren Z, Zhang N, Xu H, Liu X, Tian G, Song L, Yang H. 2013. Deep sequencing identifies regulated small RNAs in Dugesia japonica. Mol Biol Rep 40: 4075-4081. Technology