Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Li, Jianqin ^a   Wu, Bin ^a   Xu, Jiang ^a   Liu, Chang ^a  

^a INSTITUTE OF MEDICINAL PLANT DEVELOPMENT   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450; LIGNIN; LONG INTERGENIC NON CODING RNA; TRITERPENOID; UNCLASSIFIED DRUG; UNTRANSLATED RNA; FUNGAL PROTEIN; FUNGAL RNA; LONG UNTRANSLATED RNA; TRITERPENE;

3' UNTRANSLATED REGION; APC GENE; ARTICLE; BASIDIOMYCETES; BIOSYNTHESIS; CAZY GENE; CONTROLLED STUDY; CYP450 GENE; DEVELOPMENTAL STAGE; FUNGAL GENE; FUNGAL GENOME; GANODERMA LUCIDUM; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; MATBGENE; NONHUMAN; PROCESS DEVELOPMENT; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA SEQUENCE; SIGNAL TRANSDUCTION; BIOLOGY; CHROMOSOME; CHROMOSOME MAP; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MYCELIUM; PHYSIOLOGY; POLYMERASE CHAIN REACTION; PROCEDURES; SEQUENCE ANALYSIS;

CHROMOSOME MAPPING; CHROMOSOMES, FUNGAL; COMPUTATIONAL BIOLOGY; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; LIGNIN; MYCELIUM; POLYMERASE CHAIN REACTION; REISHI; RNA, FUNGAL; RNA, LONG NONCODING; SEQUENCE ANALYSIS, RNA; TRANSCRIPTION, GENETIC; TRITERPENES;

EID: 84903315355     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0099442     Document Type: Article

References (75)

1. Sanodiya BS, Thakur GS, Baghel RK, Prasad GB, Bisen PS (2009) Ganoderma lucidum: a potent pharmacological macrofungus. Curr Pharm Biotechnol 10: 717-742.
2. Boh B, Berovic M, Zhang J, Zhi-Bin L (2007) Ganoderma lucidum and its pharmaceutically active compounds. Biotechnol Annu Rev 13: 265-301. (Pubitemid 47387127)
3. Chen S, Xu J, Liu C, Zhu Y, Nelson DR, et al. (2012) Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nature Communications 3: 913.
4. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
5. Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, et al. (2008) Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods 5: 629-635. (Pubitemid 351911868)
6. Costa FF (2010) Non-coding RNAs: Meet thy masters. Bioessays 32: 599-608.
7. Liu J, Jung C, Xu J, Wang H, Deng S, et al. (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24: 4333-4345.
8. Bumgarner SL, Dowell RD, Grisafi P, Gifford DK, Fink GR (2009) Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A 106: 18321-18326.
9. Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
10. Szell M, Bata-Csorgo Z, Kemeny L (2008) The enigmatic world of mRNA-like ncRNAs: their role in human evolution and in human diseases. Semin Cancer Biol 18: 141-148.
11. Wilusz JE, Sunwoo H, Spector DL (2009) Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 23: 1494-1504.
12. Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes & Development 25: 29-40.
13. Martens JA, Laprade L, Winston F (2004) Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429: 571-574. (Pubitemid 38737662)
14. Houseley J, Rubbi L, Grunstein M, Tollervey D, Vogelauer M (2008) A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster. Molecular cell 32: 685-695.
15. Pinskaya M, Gourvennec S, Morillon A (2009) H3 lysine 4 di-and tri-methylation deposited by cryptic transcription attenuates promoter activation. The EMBO Journal 28: 1697-1707.
16. Thiebaut M, Colin J, Neil H, Jacquier A, Séraphin B, et al. (2008) Futile Cycle of Transcription Initiation and Termination Modulates the Response to Nucleotide Shortage in S. cerevisiae. Molecular cell 31: 671-682.
17. Kaushik K, Leonard VE, Shamsudheen K, Lalwani MK, Jalali S, et al. (2013) Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish. PLoS One 8: e83616.
18. Ponjavic J, Oliver PL, Lunter G, Ponting CP (2009) Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet 5: e1000617.
19. Sun J, Lin Y, Wu J (2013) Long Non-Coding RNA Expression Profiling of Mouse Testis during Postnatal Development. PLoS One 8: e75750.
20. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136: 629-641.
21. Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, et al. (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19: 57-69.
22. Hirsch J, Lefort V, Vankersschaver M, Boualem A, Lucas A, et al. (2006) Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol 140: 1192-1204. (Pubitemid 43956207)
23. Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, et al. (2009) Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci USA 106: 2453-2458.
24. MacIntosh GC, Wilkerson C, Green PJ (2001) Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol 127: 765-776. (Pubitemid 33119060)
25. Rymarquis LA, Kastenmayer JP, Huttenhofer AG, Green PJ (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci 13: 329-334.
26. Wen J, Parker BJ, Weiller GF (2007) In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In Silico Biol 7: 485-505. (Pubitemid 351217192)
27. Wu B, Li Y, Yan H, Ma Y, Luo H, et al. (2012) Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC genomics 13: 15.
28. Xin M, Wang Y, Yao Y, Song N, Hu Z, et al. (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC plant biology 11: 61.
29. Burleigh SH, Harrison MJ (1997) A novel gene whose expression in Medicago truncatula roots is suppressed in response to colonization by vesicular-arbuscular mycorrhizal (VAM) fungi and to phosphate nutrition. Plant Mol Biol 34: 199-208. (Pubitemid 27266157)
30. Burleigh SH, Harrison MJ (1999) The down-regulation of Mt4-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots. Plant Physiol 119: 241-248. (Pubitemid 29384601)
31. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, PugaMI, et al. (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39: 1033-1037. (Pubitemid 47185180)
32. Liu C, Muchhal US, Raghothama KG (1997) Differential expression of TPS11, a phosphate starvation-induced gene in tomato. Plant Mol Biol 33: 867-874. (Pubitemid 27165124)
33. Martin AC, del Pozo JC, Iglesias J, Rubio V, Solano R, et al. (2000) Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. Plant J 24: 559-567. (Pubitemid 32041918)
34. Shin H, Shin HS, Chen R, Harrison MJ (2006) Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation. Plant J 45: 712-726. (Pubitemid 43373690)
35. Dinger ME, Pang KC, Mercer TR, Mattick JS (2008) Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol 4: e1000176.
36. Sugiyama R, Kazama Y, Miyazawa Y, Matsunaga S, Kawano S (2003) CCLS96.1, a member of a multicopy gene family, may encode a non-coding RNA preferentially transcribed in reproductive organs of Silene latifolia. DNA Res 10: 213-220.
37. Teramoto H, Toyama T, Takeba G, Tsuji H (1996) Noncoding RNA for CR20, a cytokinin-repressed gene of cucumber. Plant Mol Biol 32: 797-808. (Pubitemid 27016995)
38. Crespi MD, Jurkevitch E, Poiret M, d'Aubenton-Carafa Y, Petrovics G, et al. (1994) enod40, a gene expressed during nodule organogenesis, codes for a non-translatable RNA involved in plant growth. EMBO J 13: 5099-5112. (Pubitemid 24341091)
39. Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331: 76-79.
40. Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462: 799-802.
41. De Santa F, Barozzi I, Mietton F, Ghisletti S, Polletti S, et al. (2010) A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol 8: e1000384.
42. Natoli G, Andrau JC (2012) Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet 46: 1-19.
43. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143: 46-58.
44. Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, et al. (2010) Widespread transcription at neuronal activity-regulated enhancers. Nature 465: 182-187.
45. Li W, Notani D, Ma Q, Tanasa B, Nunez E, et al. (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature 498: 516-520.
46. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, et al. (2013) Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature 494: 497-501.
47. Kung JT, Colognori D, Lee JT (2013) Long Noncoding RNAs: Past, Present, and Future. Genetics 193: 651-669.
48. Heard E (2005) Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr Opin Genet Dev 15: 482-489.
49. Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev 21: 11-42. (Pubitemid 46089704)
50. Feng J, Bi C, Clark BS, Mady R, Shah P, et al. (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20: 1470-1484. (Pubitemid 43830654)
51. Wang X, Arai S, Song X, Reichart D, Du K, et al. (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454: 126-130. (Pubitemid 351934270)
52. Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, et al. (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8: 39.
53. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7: 562-578.
54. International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
55. Rymarquis LA, Kastenmayer JP, Huttenhofer AG, Green PJ (2008) Diamonds in the rough: mRNA-like non-coding RNAs. Trends Plant Sci 13: 329-334.
56. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, et al. (2007) RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316: 1484-1488. (Pubitemid 46906616)
57. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-157.
58. Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, et al. (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35: W345-349.
59. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261. (Pubitemid 38081651)
60. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic acids research 28: 27-30. (Pubitemid 30047706)
61. Park J, Jang S, Kim S, Kong S, Choi J, et al. (2008) FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics 24: 1024-1025. (Pubitemid 351448042)
62. Young RS, Marques AC, Tibbit C, Haerty W, Bassett AR, et al. (2012) Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol 4: 427-442.
63. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, et al. (2012) The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome research 22: 1775-1789.
64. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, et al. (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature biotechnology 28: 503-510.
65. Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331: 76-79.
66. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106: 11667-11672.
67. Xin M, Wang Y, Yao Y, Song N, Hu Z, et al. (2011) Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol 11: 61.
68. Jiang N, Yang Y, Janbon G, Pan J, Zhu X (2012) Identification and functional demonstration of miRNAs in the fungus Cryptococcus neoformans. PLoS One 7: e52734.
69. Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, et al. (2008) Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 456: 130-134.
70. Bertani S, Sauer S, Bolotin E, Sauer F (2011) The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol Cell 43: 1040-1046.
71. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, et al. (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472: 120-124.
72. Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 25: 29-40.
73. Maenner S, Blaud M, Fouillen L, Savoye A, Marchand V, et al. (2010) 2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS biology 8: e1000276.
74. Wang D, Garcia-Bassets I, Benner C, Li W, Su X, et al. (2011) Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474: 390-394.
75. Pollier J, Moses T, González-Guzmán M, De Geyter N, Lippens S, et al. (2013) The protein quality control system manages plant defence compound synthesis. Nature 504: 148-152.