Mapping the genome landscape using tiling array technology.
With the availability of complete genome sequences for a growing number of organisms, high-throughput methods for gene annotation and analysis of genome dynamics are needed. The application of whole-genome tiling microarrays for studies of global gene expression is providing a more unbiased view of the transcriptional activity within genomes. For example, this approach has led to the identification and isolation of many novel non-protein-coding RNAs (ncRNAs), which have been suggested to comprise a major component of the transcriptome that have novel functions involved in epigenetic regulation of the genome. Additionally, tiling arrays have been recently applied to the study of histone modifications and methylation of cytosine bases (DNA methylation). Surprisingly, recent studies combining the analysis of gene expression (transcriptome) and DNA methylation (methylome) using whole-genome tiling arrays revealed that DNA methylation regulates the expression levels of many ncRNAs. Further capture and integration of additional types of genome-wide data sets will help to illuminate additional hidden features of the dynamic genomic landscape that are regulated by both genetic and epigenetic pathways in plants.
Yazaki
Junshi
J
The Salk Institute for Biological Studies, Plant Molecular and Cellular, Laboratory 10010 North Torrey Pines Road La Jolla, CA 92037, USA.
Gregory
Brian D
BD
Ecker
Joseph R
JR
D019175:DNA Methylation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010944:Plants / Q000235:genetics*
Science. 2007 Apr 20;316(5823):398-9
17446388
Science. 2005 Sep 2;309(5740):1559-63
16141072
Genetics. 1999 Sep;153(1):401-13
10471722
Proc Natl Acad Sci U S A. 1985 May;82(9):2560-4
3857599
Cold Spring Harb Symp Quant Biol. 2006;71:111-6
17381286
Nature. 2004 Sep 16;431(7006):364-70
15372044
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):14156-61
11698668
Science. 2007 Jun 8;316(5830):1497-502
17540862
Proc Natl Acad Sci U S A. 1997 Nov 25;94(24):13057-62
9371799
Genome Biol. 2003;4(10):R66
14519201
PLoS Genet. 2006 Jun 2;2(6):e83
16741558
PLoS Genet. 2006 Oct 13;2(10):e171
17040132
Genome Res. 2007 Jun;17(6):898-909
17568005
Development. 2004 Nov;131(21):5263-76
15456723
Mol Cell. 2000 Oct;6(4):791-802
11090618
Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8334-9
8710871
Science. 1995 Oct 20;270(5235):467-70
7569999
Nature. 2001 May 10;411(6834):212-4
11346800
Trends Genet. 2006 Jan;22(1):1-5
16290135
Cell. 2005 Dec 29;123(7):1279-91
16377568
Curr Opin Genet Dev. 2007 Apr;17(2):139-44
17317145
Proc Natl Acad Sci U S A. 2005 Mar 22;102(12):4453-8
15755812
Proc Natl Acad Sci U S A. 1993 May 15;90(10):4557-61
8506299
Cold Spring Harb Symp Quant Biol. 2004;69:355-61
16117668
Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62
17626786
Nature. 2006 May 18;441(7091):349-53
16625203
Nature. 2001 Feb 15;409(6822):922-7
11237012
Cell. 1995 Dec 1;83(5):725-34
8521489
Cell. 2006 Sep 22;126(6):1189-201
16949657
Genome Biol. 2005;6(4):R30
15833117
Cell. 2006 Apr 21;125(2):315-26
16630819
Cell. 2007 May 18;129(4):823-37
17512414
Science. 2002 May 3;296(5569):916-9
11988577
Science. 2005 Sep 2;309(5740):1529-30
16141064
Genomics. 2004 Mar;83(3):349-60
14986705
Genes Dev. 2002 Jan 15;16(2):171-82
11799061
EMBO J. 2006 Aug 9;25(15):3565-75
16874305
Curr Biol. 2007 Jan 9;17(1):54-9
17208187
Cell. 2006 Apr 21;125(2):301-13
16630818
Proc Natl Acad Sci U S A. 1996 Oct 1;93(20):10614-9
8855227
Bioessays. 2004 Aug;26(8):833-43
15273986
Science. 2003 Dec 19;302(5653):2141-4
14684825
Nat Genet. 2006 Jun;38(6):626-35
16645617
Chromosome Res. 2005;13(3):299-308
15868423
Nat Rev Genet. 2005 May;6(5):351-60
15861207
PLoS Biol. 2007 May;5(5):e129
17439305
Mol Cell Biol. 1988 Nov;8(11):4608-15
2850465
Proc Natl Acad Sci U S A. 2007 Apr 17;104(16):6752-7
17409185
Genome Biol. 2006;7(5):R38
16684369
Nature. 2004 Jun 3;429(6991):571-4
15175754
Development. 2006 Dec;133(24):4925-31
17108001
Curr Opin Cell Biol. 2003 Jun;15(3):281-9
12787769
Science. 2002 May 3;296(5569):907-10
11988574
Nat Genet. 2006 Jan;38(1):124-9
16369532
Science. 2007 Jun 8;316(5830):1484-8
17510325
Science. 2003 Oct 31;302(5646):842-6
14593172
Nat Genet. 2004 Mar;36(3):299-303
14981516
Genome Res. 2004 Feb;14(2):287-95
14762065
BMC Genomics. 2005;6:104
16083503
Nat Rev Genet. 2004 Jul;5(7):532-44
15211355
Genomics. 2005 Jan;85(1):1-15
15607417
Nat Genet. 2007 Jan;39(1):61-9
17128275
Biochim Biophys Acta. 2007 May-Jun;1769(5-6):276-86
17341434
Cell. 2002 Jul 12;110(1):33-42
12150995
Genome Biol. 2004;5(3):210
15005803
Science. 1997 Aug 22;277(5329):1100-3
9262479
Curr Opin Plant Biol. 2005 Oct;8(5):553-61
16043386
Genes Dev. 2001 Mar 1;15(5):591-602
11238379
Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3633-8
17360694
Plant Cell. 2000 Mar;12(3):357-69
10715322
Annu Rev Genomics Hum Genet. 2004;5:443-77
15485356
Curr Biol. 2005 Jan 26;15(2):154-9
15668172
Plant J. 2006 Jul;47(1):152-62
16824183
Cell. 2007 Feb 23;128(4):763-76
17320512
Science. 2005 Sep 2;309(5740):1564-6
16141073
Nature. 2003 Aug 28;424(6952):1078-83
12944972