Geometrical study on diseaserelated ncRNAs based on Z-curve method

doi:10.4236/health.2009.11005

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HEALTH, 2009, 1, 24-30

Published Online June 2009 in SciRes. http://www.scirp.org/journal/health

Geometrical study on diseaserelated ncRNAs

based on Z-curve method

Yan-Ling Yang1,2, Ji-Hua Wang1,2

1Key Lab for Biophysics in Universities of Shandong, Jinan, Shandong, P. R. China; 2Physics Department of De Zhou University, De

Zhou, Shandong, P. R. China.

Email: [email protected]

Received 13 April 2009; revised 1 May 2009; accepted 7 May 2009.

ABSTRACT

The Z curve is a very useful method for visual-

izing and analyzing DNA sequences. It is a

three-dimensional space curve that constitutes

a unique representation of a given DNA se-

quence. It becomes more and more important to

study non-coding regions in the recent years.

Using Z curve method, 15 disease-related ncRNAs

and some snoRNAs and miRNAs sequences are

selected from the NONCODE database in this

paper, which relate to Alzheimer Disease. The

corresponding Z curves of the studied ncRNAs,

sequences have been mapped and compared.

The statistical features of the Z curves are ob-

tained. These features indicate that the ncRNAs

sequences playing same roles in the celluar

process have almost the same Z-curves. And

the base content in these sequences is almost

same too.

Keywor ds: non-codingRNA; Alzheimer disease;

snoRNA; miRNA; Z-curve

1. INTRODUCTION

It is widely accepted that Non-coding sequences play

important roles in the process of translation in organisms

ranging from bacteria to mammals [1,2,3]. At the present

time the research on non-coding region and its function

is still a hot field all over the world. Among the re-

searches about non-coding sequences, the study on non-

protein-coding RNAs (ncRNAs) is becoming increas-

ingly important and has been made great progress al-

ready.

Traditionally, most RNA molecules were regarded as

carriers conveying information from the gene to the

translation machinery [4]. However, since the late 1990s,

it has been widely acknowledged that other types of

non-protein-coding RNA molecules are present in or-

ganisms ranging from bacteria to mammals, which affect

a large variety of processes including plasmid replication,

phage development, bacterial virulence, chromosome

structure, DNA transcription, RNA processing and

modification, development control and others [5]. These

observations suggest that the traditional view of the

structure of the genetic reg ‰ ulatory systems in organ-

isms is far from complete. And the considerable number

of non-coding RNAs (ncRNAs) that has been detected in

the past few years was largely unexpected [6].

As new members and classes of ncRNAs being pro-

gressively discovered, the understanding of the impor-

tance of ncRNAs in basic cellular processes is ever in-

creasing. Although the functions of the many recently

identified ncRNAs remain mostly unknown, increasing

evidence stands in support of the notion that ncRNAs

represent a diverse and important functional output of

most genomes [7].

Furthermore, the understanding of the significance of

ncRNAs as central components of various cellular proc-

esses has risen sharply over the recent years. However,

there are so many unsolved problems in this field and

many of these ncRNAs still have uncharacterized func-

tions.

Some diseases, which have constituted a threat to

human beings, are related to different ncRNAs. Such as

Alzheimer disease, cancers, diabetes, heart diseases, etc.

[8]. Among these diseases, Alzheimer disease has be-

come the fourth-biggest cause of the illness threaten the

old men, s lives, next below the cancers，heart diseases

and cerebrovascular diseases. Alzheimer disease is a

progressive degenerative disorder of the brain character-

ized by a slow, progressive decline in cognitive function

and behavior. As the disease advances, persons with

Alzheimer disease have tough time with daily usage of

things like using the phone, cooking, handling money, or

driving the car. The disease is more common in elder

population. It is estimated that Alzheimer disease affects

15 million people worldwide and approximately 4 mil-

lion Americans [9]. The neuropathologic hallmarks of

the disorder are amyloid-rich senile plaques, neurofibril-

lary tangles, and neuronal degeneration.

It has reported that three genes with autosomal domi-

Y. L. Yang et al. / HEALTH 1 (2009) 24-30 25

nant mutations have been identified that may lead to

Alzheimer symptoms in carriers before they reach age

60. [10]. The clinical features of Alzheimer disease

overlaps with common signs of aging, and other types of

dementia, hence the diagnosis remains difficult.

We make use the ZCURVE method, which is pro-

posed by Professor Zhang Chun-ting, to analysis

ncRNAs related to Alzheimer disease. ZCURVE is a

geometrical approach to study DNA sequences. Based

on the Z curve method, some global and local features of

the sequence can be detected in a perceivable way [11].

In this work, we download 15 Specific ncRNAs

(BC200 RNA) sequences from the NONCODE database,

which relate to Alzheimer disease and come from dif-

ferent organisms. The corresponding Z curves of the

selected sequences have been mapped and shown. By

analyzing and comparing the Z curves, the common

features of them are found and the features may be as a

criterion to study same type of disease-related ncRNAs.

2. MATERIAL AND METHOD

2.1. Material

The NONCODE database is an integrated knowledge

database designed for the analysis of non-coding RNAs

(ncRNAs). Since NONCODE was first released 3 years

ago [15], the number of known ncRNAs has grown rap-

idly, and there is growing recognition that ncRNAs play

important regulatory roles in most organisms. In the up-

dated version of NONCODE (NONCODE v2.0), the

number of collected ncRNAs has reached 206 226, in-

cluding a wide range of microRNAs, Piwi-interacting

RNAs and mRNA- like ncRNAs. The improvements

brought to the database include not only new and up-

dated ncRNA data sets, but also an incorporation of

BLAST alignment search service and access through our

custom UCSC Genome Browser [12].

All ncRNAs in NONCODE were filtered automatically

from GenBank and the literature, and were then later

manually curated. With the exception of rRNAs and

tRNAs, all classes of reported ncRNAs are included. In

addition to containing sequence data, NONCODE provides

a user-friendly interface, a visualization platform and a

convenient search option, allowing efficient recovery of

sequences, regulatory elements in the flanking sequences,

related publications and other information [13,14].

We pick up 15 ncRNA (BC200 RNA) and 20 snoRNA

sequences from this database, which belong to specific

ncRNAs and relate with Alzheimer disease. Ade-

quately,we select miRNA of human, virus and sequences

from miRNA database.All selected sequences can be

directly downloaded from the webpage.

2.2. Method

The Z curve is a unique three-dimensional space curve

representation for a given DNA sequence in the sense

that each can be uniquely reconstructed given the other.

Consider a DNA sequence read from the 5' to the 3'-end

with N bases. Inspect the sequence one base at a time,

beginning from the first base. Let the number of the in-

specting steps is denoted by n, i.e., n =1, 2... N. In the

nth step, count the cumulative numbers of the bases A, C,

G and T, occurring in the subsequence from the first to

the nth base in the DNA sequence inspected. Denoting

the cumulative occurring numbers of the bases A, C, G

and T in the above subsequence by An, Cn, Gn and Tn,

respectively. The Z curve is a three-dimensional space

curve and composed of a series of nodes P0, P1, P2, . . . ,

PN , whose coordinates , and (n = 0, 1,

2, . . . , N, where N is the length of the DNA sequence

being studied) are uniquely determined by the

Z-transform of DNA sequence.













)()(

nnnnn

CGTAz

TGCAy

TCGAx

where, NnNNzyx nnn ,...,2,1,0],,[,, 





. The three

components of the Z curve, i.e., ， and , rep-

resent three independent distributions that completely

describe the DNA sequence being studied. Furthermore,

the three independent components , and

have a clear biological meaning, respectively [11].

It is noted that the Z curve defined above is generally

not smooth at each node. Sometimes, a smooth proce-

dure is needed. The B-spline functions are used to

smooth the Z curve. For more detailed information about

the Z curve defined, please refer to references

[16,17,18].

In summary, the Z curve is the unique representation

for a given DNA sequence in a three-dimensional space

and each can be uniquely reconstructed from the other. It

offers an intuitive and convenient approach to study

DNA sequences geometrically.

3. RESULT AND DISCUSSION

3.1. Figures and Tables

The accession numbers of selected Bc200 RNA sequences

in NONCODE and NCBI database are as follows:

1. n289 (AC090426); 2. n637 (AF020057); 3. n751

(AF067778); 4. n752 (AF067779); 5. n753 (AF067780);

6. n754 (AF067781); 7. n755 (AF067782); 8.n756

(AF067783); 9.n757 (AF067784); 10. n758 (AF067785);

11. n759 (AF067786); 12. n760 (AF067787); 13. n761

(AF067788); 14. n4617 (M17307); 15. n4817 (U01305).

Where, sequence 1, 14 and 15 belong to BC200 RNA

and other sequences belong to BC200-alpha RNA. Their

26 Y. L. Yang et al. / HEALTH 1 (2009) 24-30

cellular roles are regulators, but their sequence length is

different and coming from different organisms, respec-

tively.

and compare them, respectively (see Figures 1-6). From

the obtained pictures, we can see obviously that all cor-

responding curves for BC200-alpha RNA are almost no

disparity, not only having same shapes but also same

tendency (see Figures 1-3). The same condition occurs

in the BC200 RNA sequences (see Figure 4).

Using Z-plotter and Origin7.5 software, corresponding

Z curves of the selected 15 sequences are mapped and

part of typical curves are selected shown in Figures 1-6.

In addition to mapping Z-curves, the base (A, C, G, T

and GC) content of the studied sequences is respectively

calculated based on the Z Curve Theory. The typical

results are shown at Table 1.

However, the corresponding Z curves of BC200 RNA

and BC200-alpha RNA sequences have obvious dispari-

ties (see Figures 5,6). The fact shows the Z curves are

different too, in spite of the studied sequences all related

with one type disease but their functions are different. It

means the shapes and tendency of Z curves is related

with functions of ncRNA sequences.

We also select snoRNAs and microRNAs of human,

Arabidopsis thaliana and virus in NONCODE and miRNA

database, respectively. Then map the corresponding z-

curves based on Z CURVE method and analyze them. In addition, the n



curves for the studied se-

quences show a global maximum at the position of

about 120bp (BC200 RNA) or 190bp (BC200-alpha

RNA).

Results are shown in Figure 7,8.

3.2. Discussion

We pick up part of typical Z curves of studied sequences

050100 150 200

-40

-35

-30

-25

-20

-15

-10

-5

50100 150 200

-35

-30

-25

-20

-15

-10

-5

Figure 1. The Zn-n curves for two BC200 RNA sequences 2 and 10 (coming from orangutan and crab-eating macaque, respec-

tively). The curves are very similar in global and local.

050100 150 200

-50

-40

-30

-20

-10

Figure 2. The Z/

n-n curves for two BC200-alpha RNA sequences 5 and 8(coming from hamadryas baboon and crab-eating

macaque respectively). The curves are same in global and local.

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Y. L. Yang et al. / HEALTH 1 (2009) 24-30 27

-10010 2030 40

-30

-20

-10

-30-20

-10

0102030

Z Axis

Y Axis

xis

Figure 3. The 3D curves for two BC200 RNA sequences 2 and 5 (coming from human and orangutan, respectively). The

curves are same in global and local.

020406080100 120140

-16

-14

-12

-10

-8

-6

-4

-2

020 40 60 80100120140

-14

-12

-10

-8

-6

-4

-2

Figure 4. The Z/

n-n curves for two sequences 1 and 14. The curves are very similar in global and local and all <0.

z

020 40 60 80100120140

-25

-20

-15

-10

-5

050100 150 200

-35

-30

-25

-20

-15

-10

-5

Figure 5. The zn curves for two sequences 1 and 5. The curves are obviously different in local and global, especially in the

end.

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28 Y. L. Yang et al. / HEALTH 1 (2009) 24-30

050100 150 200

-10

020406080100 120 140

-12

-10

-8

-6

-4

-2

Figure 6. The Yn-n curves for two sequences 5 and 1. The curves are very different in global and local.

-20

-10

-20

-10

-20

-10

human-mature-3dz

-20

-10

-20

-10

-5

virus-matur e-3dzz

Figure 7. The Z curves of microRNAs of human, Arabidopsis thaliana and virus. The curves are very similar in global.

Figure 8. The Z/ curves of two snoRNAs n68 and n75.

Table 1. The content of bases of the studied sequences 2, 8,

10 and15.

A C G T G+C

n637 66(33%) 57 (29%) 49 (25%) 28 (14%)53%

n756 71 (34%) 58 (28%) 48 (24%) 27 (13%)52%

n758 69(35%) 56 (28%) 48 (24%) 27 (14%)52%

n4817 66(33%) 57(29%) 49(24%) 28(14%)53%

And then, in the nz n



curves of BC200 RNA and

BC200-alpha RNA sequences, all <0 (see Figure 1)

means strong H-bond bases (G/C) are in excess of weak

H-bond bases (A/T). It indicates that this type of ncRNA

is a stable structure and not mutated easily. At the same

time, about

nz n





curves of BC200 RNA sequences,

all n



< 0 (see Figure 2).

-20

-10

-20

-10

-5

拟南芥

-mature-3dz

Arabidopsis thaliana-mature-3dz

Y. L. Yang et al. / HEALTH 1 (2009) 24-30 29

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.

nxnnynnz nnz 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.

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



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.

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