RNA Structure in Genomic Sequence:

Supplementary information for:
De novo prediction of structured RNAs from genomic sequences

Jan Gorodkin, Ivo L. Hofacker, Elfar Torarinsson, Zizhen Yao, Jakob H. Havgaard, Walter L. Ruzzo


The main methods described in the paper were also applied in other studies and here are some examples.

Exploiting sequence based multiple alignments for ncRNA screens

RNAz has also been used for genomic screens in for example: Arabidopsis thaliana [Song et al., 2009], Nematodes [Missal et al., 2006], Drosophilids [Rose et al., 2007], Teleost fishes [Rose et al., 2008], Urochordates [Missal et al., 2005], yeast [Steigele et al., 2007], porcine EST sequences [Seemann et al., 2007], as well as various bacteria. EvoFold also was applied to screen Drosophila melanogaster [Stark et al., 2007].

Screen by pairwise local structural alignments

Foldalign has been used to search structural RNA motifs in prokaryotes, amoeba, and humans [Bidnenko et al., 2009,Ahmed et al., 2006,Vyas et al., 2009] and it has further been used to investigate structures of potential ncRNAs in bacteria and for phylogenetic analysis of beetles [Sridhar et al., 2009,Angelini and Jockusch, 2008].

Employing local multiple structural alignments

CMfinder was also recently applied to screen for ncRNAs in prokaryotes [Yao et al., 2007,Weinberg et al., 2007]. Besides re-discovering majority of the known ncRNAs in prokaryotes [Yao et al., 2007], the CMfinder-based pipeline found 22 novel ncRNA motifs [Weinberg et al., 2007], including SAM-IV [Weinberg et al., 2008], S-adenosylhomocysteine [Wang et al., 2008], preQ1 [Meyer et al., 2008], molybdenum cofactor [Regulski et al., 2008] and cyclic di-GMP [Sudarsan et al., 2008] riboswitches, subsequently validated experimentally.


Follow the links to the UCSC genome browser


Ahmed et al., 2006
Ahmed, A., Beech, P., Lay, S., Gilson, P., and Fisher, P. (2006).
Import-associated translational inhibition: novel in vivo evidence for cotranslational protein import into Dictyostelium discoideum mitochondria.
Eukaryot Cell., 5(8):1314-27.

Angelini and Jockusch, 2008
Angelini, D. and Jockusch, E. (2008).
Relationships among pest flour beetles of the genus Tribolium (Tenebrionidae) inferred from multiple molecular markers.
Mol Phylogenet Evol., 46(1):127-41.

Bidnenko et al., 2009
Bidnenko, E., Chopin, A., Ehrlich, S., and Chopin, M. (2009).
Activation of mRNA translation by phage protein and low temperature: the case of Lactococcus lactis abortive infection system AbiD1.
BMC Mol Biol., 10:4.

Meyer et al., 2008
Meyer, M. M., Roth, A., Chervin, S. M., Garcia, G. A., and Breaker, R. R. (2008).
Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria.
RNA, 14:685-695.

Missal et al., 2005
Missal, K., Rose, D., and Stadler, P. F. (2005).
Non-coding RNAs in ciona intestinalis.
Bioinformatics, 21 Suppl 2:ii77-8.

Missal et al., 2006
Missal, K., Zhu, X., Rose, D., Deng, W., Skogerbø, G., Chen, R., and Stadler, P. F. (2006).
Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae.
J Exp Zoolog B Mol Dev Evol, 306(4):379-92.

Regulski et al., 2008
Regulski, E. E., Moy, R. H., Weinberg, Z., Barrick, J. E., Yao, Z., Ruzzo, W. L., and Breaker, R. R. (2008).
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
Mol. Microbiol., 68:918-932.

Rose et al., 2007
Rose, D., Hackermüller, J., Washietl, S., Reiche, K., Hertel, J., Findeiss, S., Stadler, P. F., and Prohaska, S. J. (2007).
Computational RNomics of drosophilids.
BMC Genomics, 8:406.

Rose et al., 2008
Rose, D., Jöris, J., Hackermüller, J., Reiche, K., Li, Q., and Stadler, P. F. (2008).
Duplicated RNA genes in teleost fish genomes.
J Bioinform Comput Biol, 6(6):1157-75.

Seemann et al., 2007
Seemann, S. E., Gilchrist, M. J., Hofacker, I. L., Stadler, P. F., and Gorodkin, J. (2007).
Detection of RNA structures in porcine EST data and related mammals.
BMC Genomics, 8:316.

Song et al., 2009
Song, D., Yang, Y., Yu, B., Zheng, B., Deng, Z., Lu, B. L., Chen, X., and Jiang, T. (2009).
Computational prediction of novel non-coding RNAs in arabidopsis thaliana.
BMC Bioinformatics, 10 Suppl 1:S36.

Sridhar et al., 2009
Sridhar, J., Sekar, K., and Rafi, Z. (2009).
CsrA interacting small RNAs in Haemophilus spp genomes: a theoretical analysis.
Arch Microbiol., 191(5):451-9.

Stark et al., 2007
Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Hodges, E., Hinrichs, A. S., Caspi, A., Paten, B., Park, S. W., Han, M. V., Maeder, M. L., Polansky, B. J., Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M. W., Park, Y., Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J., Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M., and Kellis, M. (2007).
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.
Nature, 450:219-232.

Steigele et al., 2007
Steigele, S., Huber, W., Stocsits, C., Stadler, P. F., and Nieselt, K. (2007).
Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions.
BMC Biol, 5:25.

Sudarsan et al., 2008
Sudarsan, N., Lee, E. R., Weinberg, Z., Moy, R. H., Kim, J. N., Link, K. H., and Breaker, R. R. (2008).
Riboswitches in eubacteria sense the second messenger cyclic di-GMP.
Science, 321:411-413.

Vyas et al., 2009
Vyas, K., Chaudhuri, S., Leaman, D., Komar, A., Musiyenko, A., Barik, S., and Mazumder, B. (2009).
Genome-wide polysome profiling reveals an inflammation-responsive posttranscriptional operon in gamma interferon-activated monocytes.
Mol Cell Biol., 29(2):458-70.

Wang et al., 2008
Wang, J. X., Lee, E. R., Morales, D. R., Lim, J., and Breaker, R. R. (2008).
Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling.
Mol. Cell, 29:691-702.

Weinberg et al., 2007
Weinberg, Z., Barrick, J., Yao, Z., Roth, A., Kim, J., Gore, J., Wang, J., Lee, E., Block, K., Sudarsan, N., Neph, S., Tompa, M., Ruzzo, W., and Breaker, R. (2007).
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
Nucl. Acids Res., 35:4809-4819.

Weinberg et al., 2008
Weinberg, Z., Regulski, E. E., Hammond, M. C., Barrick, J. E., Yao, Z., Ruzzo, W. L., and Breaker, R. R. (2008).
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
RNA, 14:822-828.

Yao et al., 2007
Yao, Z., Barrick, J., Weinberg, Z., Neph, S., Breaker, R., Tompa, M., and Ruzzo, W. (2007).
A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes.
PLoS Comput. Biol., 3:e126.