Y. L. Yang et al. / HEALTH 1 (2009) 24-30 29
SciRes Copyright © 2009 HEALTH
Then we calculate the base content of A, C, G, T and
GC in the studied sequences (see Table 1). For BC200
RNAs and BC200-alpha RNAs the results are 33%-35%,
28%-29%, 24%-25%, 13%-14%, and 52%-53%, respec-
tively. This fact indicates that there is no obvious dispar-
ity on base content in the two types studied sequences.
That is to say, the base content in the two types BC200
RNA’s sequences is almost equal.
Adequately, we map and compare the Z-curves of
snoRNAs, microRNAs, We can see the z-curves of one
type ncRNA (miRNA) are very similar (see Figure 7).
The same conditions occur in the sequences of snoRNA
(see Figure 8). And the base content is almost equal in
the same type ncRNA sequences.
4. CONCLUSIONS
Based on the above compare and analysis, a initial con-
clusion is drawn that all kinds of Z-curves (i.e.
,, and curves) is almost
same and the content of A, C, G and T base in these
sequences is almost equal, respectively. Furthermore,
there are some differences between the curves coming
from different types, such as BC200 RNA and
BC200-alpha RNA. The fact proves that the Z curves of
ncRNA sequences are related not only with functions but
also with types.
nxnnynnz nnz n
/
On the other hand, <0 means strong H-bond bases
(G/C) are in excess of weak H-bond bases (A/T), it in-
dicates that this type of ncRNA is a stable structure and
not mutated easily.
n
z
On top of this, the curves for the studied se-
quences show a global maximum at the position of about
120bp (BC200 RNA) or 190bp (BC200-alpha RNA).
Furthermore, the almost same in each base content in the
two types ncRNA sequences indicate that base content is
related with their functions or playing roles. Furthermore,
about all curves of BC200 RNA sequence,
<0. Unfortunately, we don’t know the biological sig-
nification about the above results. So many works will
be done in our future research.
nz n
/
nz n
n
z
We do more tests for other type ncRNAs to test the
conclusion. By mapping and comparing the Z-curves of
snoRNAs, microRNAs, we can know that other type
ncRNAs, also have the same statistical character as the
BC200 RNA, both in sample of the z-curves and base
content in the sequences.
5. ACKNOWLEDGMENT
This work was supported by Chinese National Key Fundamental Re-
search Project (Grant No. 90403120) and Shandong Fundamental
Research Project (Grant No. Y2005D12). We are grateful to Key Lab
for Biophysics in Universities of Shandong for help with us. We also
thank our colleagues for advice and for sharing protocols.
REFERENCES
[1] R. Hershberg, S. Altuvia, and H. Margalit, (2003) A
survey of small RNA-encoding genes in Escherichia coli,
Nucleic Acids Res., 31, 1813-1820.
[2] V. T. Nguyen, T. Kiss, A. A. Michels, and O. Bensaude,
(2001) 7SK small nuclear RNA binds to and inhibits the
activity of CDK9/cyclin T complexes, Nature, 414,
322-325.
[3] Z. Yang, Q. Zhu, K. Luo, and Q. Zhou, (2001) The 7SK
small nuclear RNA inhibits the CDK9/cyclin T1 kinase
to control transcription, Nature, 414, 317-322.
[4] S. R. Eddy, (2001) Non-coding RNA genes and the
modern RNA world, Nature Rev. Genet., 2, 919-929.
[5] T. Wu, J. Wang, C. N. Liu, Y. Zhang, B. C. Shi, X. P.
Zhu, Z. H. Zhang, G. Skogerbo, L. Chen, H. C. Lu, Y.
Zhao, and R. S. Chen, (2006) NP Inter: The non-coding
RNAs and protein related biomacromolecules interaction
database, Nucleic Acids Res., 34, D150-D152.
[6] J. R. Neilson, G. X. Zheng, C. B. Burge, and P. A. Sharp,
(2007) Dynamic regulation of miRNA expression in
ordered stages of cellular development, Genes & Dev.,
21, 578–589.
[7] G. Storz, (2002) An expanding universe of noncoding
RNAs, Science, 296, 1260-1263.
[8] T. Zhang, Z. H. Zhang, L. J. Ling, B. C. Shi, and R. S.
Chen, (2004) Conservation analysis of small RNA genes
in Escherichia coli, Bioinformatics, 20, 599-603.
[9] G. Casadesus, M. A. Smith, S. Basu, J. Hua, D. E.
Capobianco, S. L. Siedlak, X. Zhu, and G. Perry, (2007)
Increased isoprostane and prostaglandin are prominent in
neurons in Alzheimer disease, Mol Neurodegener, 2(2).
[10] K. E. Webster, J. R. Merory, and J. E. Wittwer, (2006)
Gait variability in community dwelling adults with
Alzheimer disease, Alzheimer Dis Assoc Disord., 20(1),
37-40.
[11] R. Zhang and C. T. Zhang, (1994) Z curves, an intuitive
tool for visualizing and analyzing DNA sequences, J.
Biomol. Struc. Dyn., 767-782.
[12] C. T. Zhang, R. Zhang, and H. Y. Ou, (2003) The z curve
database: A graphic representation of genome sequences,
Bioinformatics, 19, 593-599.
[13] F. B. Guo, H. Y. Ou, and C. T. Zhang, (2003) ZCURVE:
A new system for recognizing protein-coding genes in
bacterial and archaeal genomes., Nucleic Acids Res., 31,
1780-1789.
[14] J. H. Wang, B. Q. Wang, and L. S. Zhang, (2004)
Theoretical Study on the Z Curve, J. Biomol., 19(2),
129-135.
[15] C. N. Liu, B. Y. Bai, G. Skogerbo, L. Cai, W. Deng, Y.
Zhang, D. B. Bu, Y. Zhao, and R. S. Chen, (2005)
NONECODE: An integrated knowledge database of
non-coding RNAs, Nucleic Acids Res, 33, D112-D115.