Long non-coding RNAs (LncRNAs) are transcripts greater than 200 nucleotides in length with no protein-coding capacity. In mammals, there are tens of thousands of LncRNAs transcribed specifically in different tissues and developmental stages. The tissue-specific expression patterns of LncRNAs in development and the distinct subcellular location of LncRNAs strongly suggest that their expression is under precise control (Amaral and Mattick, 2008; Dinger et al., 2008; Mercer et al., 2008). However, it remains largely unknown how LncRNAs are regulated at the level of their transcription. There is evidence that epigenetic modifications, including DNA methylation, histone modifications, and chromatin remodeling, contribute to the cell type-specific expression patterns of LncRNAs. Recent work suggests that LncRNA promoters are subject to purifying selection (Ponjavic et al., 2007), are on average more conserved than promoters of protein-coding genes (Carninci et al., 2005), and are associated with transcription factors and regulated chromatin marks (Cawley et al., 2004; Kim et al., 2005; Boyer et al., 2006; Huarte et al., 2010; Lujambio et al., 2010; Mohammad et al., 2010; Wu et al., 2010)

 

The first-generation Arraystar Human LncRNA Promoter Microarray was the first commercially-available microarray for profiling epigenetic modifications at the promoter regions of Long non-coding RNA (LncRNA) genes. The newly-released Arraystar Human 1M LncRNA Promoter Microarray V2.0 is designed for the identification of epigenetic modifications and transcription factor (TF) binding sites within LncRNA promoter regions. In addition, our LncRNA Promoter Array V2.0 can interrogate other biologically significant genomic regions, including mRNA promoters, miRNA promoters, bivalent domains, CpG islands and CpG island shores. The Arraystar Human LncRNA Promoter Microarray V2.0 uses 60-mer tiling probes at 112 bp spacing, for unbiased discovery of epigenetic modifications and TF binding sites. Further, probes for positive, negative and non-CpG control regions are included, to facilitate experimental performance assessment.

 

•   Includes the same comprehensive and updated repertoire of LncRNAs present on the Arraystar Human LncRNA microarray V3.0, in a simple and convenient, single-array format.

•   Provides coverage of promoter regions for all annotated LncRNAs and protein-coding genes, as well as other features, such as CpG islands, CpG island shores, H3K4-K27 bivalent domains, potential microRNA promoters, and many others.       

•   Uses long (60 mer) oligonucleotide probes, delivering results with unparalleled sensitivity and specificity.

•   Provides detailed annotation for each genomic feature, along with our comprehensive subgroup analysis, to satisfy all of your research needs.

•   Generates an integrated regulation map of all LncRNAs and protein-coding genes, when combined with data from our Arraystar Human LncRNA Array V3.0 service.

More information describing the tiled genomic features 

Total number of probes:         1 M

Probe length:                            60 mer

Median Probe Spacing:            112 bp

Genome build:                             hg19

 

Term	Tiling regions	Number	Source
LncRNA	LncRNA promoter regions from 2.2 kb upstream of TSS to 500 bp downstream of TSS	23,073	RefSeq, UCSC Knowngene, Gencode v13, RNAdb 2.0, NRED
LincRNAs identified by Cabili et al.	LncRNA promoter regions from 2.2 kb upstream of TSS to 500 bp downstream of TSS	5728	Cabili et al., 2011
Ultraconserved Regions (UCRs)	UCRs + 10 kb flanking each end	481	Bejerano et al., 2004; Calin et al., 2007
HOX clusters	HOXA, HOXB, HOXC and HOXD clusters and their 5' and 3' 30 kb flanking regions	4	Rinn et al., 2007
mRNA	Possible mRNA promoter regions from 2.2 kb upstream of TSS to 500 bp downstream of TSS	26,109	NCBI RefSeq
miRNA	Possible miRNA promoter regions (15 kb upstream to mature miRNA)	1,595	miRBase 19.0
Bivalent domains	K4-K27 bivalent domain regions	5,273	Bernstein et al., 2006; Pan et al., 2007; Zhao et al., 2007
CpG islands and shores	CpG island regions and 2 kb regions flanking CpG islands	15,156	UCSC

1.  Amaral, P.P., and Mattick, J.S. (2008). Noncoding RNA in development. Mamm Genome 19, 454-492.

2.  Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S., and Haussler, D. (2004). Ultraconserved elements in the human genome. Science 304, 1321-1325.

3.  Bernstein, B.E., Mikkelsen, T.S., Xie, X., Kamal, M., Huebert, D.J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006). A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326.

4.  Boyer, L.A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L.A., Lee, T.I., Levine, S.S., Wernig, M., Tajonar, A., Ray, M.K., et al. (2006). Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349-353.

5.  Calin, G.A., Liu, C.G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E.J., Wojcik, S.E., et al. (2007). Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12, 215-229.

6.  Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., et al. (2005). The transcriptional landscape of the mammalian genome. Science 309, 1559-1563.

7.  Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. (2004). Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509.

8.  Dinger, M.E., Amaral, P.P., Mercer, T.R., Pang, K.C., Bruce, S.J., Gardiner, B.B., Askarian-Amiri, M.E., Ru, K., Solda, G., Simons, C., et al. (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18, 1433-1445.

9.  Guttman, M., Amit, I., Garber, M., French, C., Lin, M.F., Feldser, D., Huarte, M., Zuk, O., Carey, B.W., Cassady, J.P., et al. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227.

10.  Huarte, M., Guttman, M., Feldser, D., Garber, M., Koziol, M.J., Kenzelmann-Broz, D., Khalil, A.M., Zuk, O., Amit, I., Rabani, M., et al. (2010). A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409-419.

11.  Khalil, A.M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B.E., van Oudenaarden, 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.

12.  Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., and Ren, B. (2005). A high-resolution map of active promoters in the human genome. Nature 436, 876-880.

13.  Lujambio, A., Portela, A., Liz, J., Melo, S.A., Rossi, S., Spizzo, R., Croce, C.M., Calin, G.A., and Esteller, M. (2010). CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 29, 6390-6401.

14.  Mercer, T.R., Dinger, M.E., Sunkin, S.M., Mehler, M.F., and Mattick, J.S. (2008). Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105, 716-721.

15.  Mohammad, F., Mondal, T., Guseva, N., Pandey, G.K., and Kanduri, C. (2010). Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 137, 2493-2499.

16.  Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G.A., Stewart, R., and Thomson, J.A. (2007). Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1, 299-312.

17.  Ponjavic, J., Ponting, C.P., and Lunter, G. (2007). Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res 17, 556-565.

18.  Rinn, J.L., Kertesz, M., Wang, J.K., Squazzo, S.L., Xu, X., Brugmann, S.A., Goodnough, L.H., Helms, J.A., Farnham, P.J., Segal, E., et al. (2007). Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323.

19.  Wu, S.C., Kallin, E.M., and Zhang, Y. (2010). Role of H3K27 methylation in the regulation of lncRNA expression. Cell Res 20, 1109-1116.

20.   Zhao, X.D., Han, X., Chew, J.L., Liu, J., Chiu, K.P., Choo, A., Orlov, Y.L., Sung, W.K., Shahab, A., Kuznetsov, V.A., et al. (2007). Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell 1, 286-298.