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Product NameCatalog NoDescriptionFormatPrice
Human ncRNA Promoter Microarray AS-nP-H 27, 248 LncRNA promoter regions 4*180K
Mouse ncRNA Promoter Microarray AS-nP-M 18,552 LncRNA promoter regions 4*180K

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)

Arraystar Human 4x180 K ncRNA Promoter Microarrays are specifically designed for the unbias identification of epigenetic modifications and transcription factor (TF) binding sites within 27, 248 LncRNA promoter regions by using 60-mer tiling probes at approximately 230 bp spacing. In addition, our Human ncRNA Promoter Array can also interrogate 622 miRNA promoters. Further, probes for positive, negative are included to facilitate experimental performance assessment. 

Arraystar Mouse 4x180 K ncRNA Promoter Microarrays are specifically designed for the unbias identification of epigenetic modifications and transcription factor (TF) binding sites within 18,552 LncRNA promoter regions by using 60-mer tiling probes at approximately 165 bp spacing. In addition, our Mouse ncRNA Promoter Array can also interrogate 346 miRNA promoters. Further, probes for positive, negative are included to facilitate experimental performance assessment. 

References
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.

Arraystar Human ncRNA Promoter Microarray

• Includes the same comprehensive and updated repertoire of LncRNAs present on the Arraystar Human LncRNA microarray V4.0.

• Provides coverage of promoter regions for all annotated LncRNAs, as well as 622 microRNA promoters.

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

• Generates an integrated regulation map of all LncRNAs, when combined with data from our Arraystar Human LncRNA Array V4.0 service.

Arraystar Mouse ncRNA Promoter Microarray

• Includes the same comprehensive and updated repertoire of LncRNAs present on the Arraystar Mouse LncRNA microarray V3.0.

• Provides coverage of promoter regions for all annotated LncRNAs, as well as 346 microRNA promoters.

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

• Generates an integrated regulation map of all LncRNAs, when combined with data from our Arraystar Mouse LncRNA Array V3.0 service.

Total number of probes:         180 K

Probe length:                             60 mer

Median Probe Spacing:            230 bp

Genome build:                               hg19

High-throughput tiling regions:

Term Tiling regions Number Source
LncRNAs LncRNA promoter regions from 2.2 kb upstream of TSS to 500 bp downstream of TSS 25,743 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 3,870 Cabili et al., 2011
miRNAs Possible miRNA promoter regions (50 kb upstream to mature miRNA) 622 miRBase 19.0

Total number of probes:         180 K

Probe length:                             60 mer

Median Probe Spacing:            165 bp

Genome build:                               MM9

High-throughput tiling regions:

Term Tiling regions Number Source
LncRNAs LncRNA promoter regions from 2.2 kb upstream of TSS to 500 bp downstream of TSS 24,447 RefSeq, UCSC Knowngene, Ensembl, RNAdb 2.0, NRED
LincRNAs from other literatures LncRNA promoter regions from 2.2 kb upstream of TSS to 500 bp downstream of TSS 477 Cabili et al., 2011
miRNAs Possible miRNA promoter regions (host gene's promoter or from -50 kb to miRNA) 346 miRBase 19.0