N.A. Kolchanov and V.G. Levitsky

N.A. Kolchanov and V.G. Levitsky

Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia

[email protected] [email protected]

NUCLEOSOME FORMATION SITES: CODING, ORGANIZATION AND

FUNCTION

Kolchanov N.A., IC&G, BGRS 2000

1

NUCLEOSOME POSITIONING CODE: COMMON FEATURES


5’ 3’

160 - 240 bp

2

A nucleosome is schematically considered as an octameric histone core, with one and a half circuits of 146 bp double helix DNA coiled around this core. Nucleosomes are distributed along genome DNA in average distance of about 160-240 bp.

Basic modules of the GeneExpress systemhttp://wwwmgs/mgs/systems/geneexpress/


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http://wwwmgs.bionet.nsc.ru/mgs/systems/nucleosom/Levitsky V.G., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S.,

Kolchanov N.A., Nucleosomal DNA property database. Bioinformatics, 1999, 15, 582-592.


4

NUCLEOSOME RECOGNITION FUNCTION BASED ON THE DISCRIMINANT ANALYSIS OF DINUCLEOTIDE

FREQUENCIES

1. Nucleosome sites 2. Random sequences1) CAACTGCCAC {

)1(,1 jf } 1) TGCACAGCCC {

)2(,1 jf }

………………… ………………….N) CAGTGGTTAA { )1(

,jNf } N) GTGGCCTCAA { )2(,jNf }

Two samples of DNA sequences:

]}[**)](*)({[*1)( )1()2(1,

)1()2(2

1

112 kkkjjjj

N

k

N

jffSfff

Rf

=

+1, f = )1(f ,

-1, f = )2(f .


fj - frequency of a definite dinucleotide in the k-th region of a nucleosome site, whereк = [j/16] +1. K is the number of regions , into which a nucleosome site is partitioned

-60 -40 -20 0 +20 +40 +60

5’ 3’

k=1 KPartitions of a nucleosome site into blocks

5

8 8 10 31 11 8 11 318 8 10 8 8


5a

)(,jiS = *

1

1

N)}(*){( )()(

,)(

1

)(,

jjni

N

nin ffff

][S = ][ )1(S + ][ )2(S

United covariation matrix

The average frequencies for two samples1)(

if = N n

inf1

)(,*

, =1, 2

Covariations

DISTRIBUTIONS OF RECOGNITION FUNCTION VALUES, BASED ON DINUCLEOTIDE FREQUENCIES,

FOR NUCLEOSOME SITES AND RANDOM SEQUENCES

0

0.05

0.1

0.15

0.2

0.25

-2.44 -1.84 -1.25 -0.65 -0.05 0.55 1.14 1.74 2.34 2.94

Recognition function value

Probability


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SITESRANDOM

FALSE POSITIVES AND FALSE NEGATIVES UNDER NUCLEOSOME SITE RECOGNITION BASED

ON DINUCLEOTIDE FREQUENCIES


0%

5%

10%

15%

20%

25%

30%

0% 5% 10% 15% 20% 25% 30%

Falsepositive

rate

Falsenegative

rate

7

INTERFACE OF NUCLEOSOME SITE RECOGNITION PROGRAM


http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/

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RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES IN HUMAN


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150-0.2

0

0.2

0.4

0.6

0.8

-150 -100 -50 0 50 100Position relative by splicing center site, bp

Recognitionfunction

value Exon Intron

Donor sites Acceptor sites

0

0.2

0.4

0.6

0.8

1

1.2

-150 -100 -50 0 50 100 150

Recognitionfunction

value ExonIntron

Position relative by splicing center site, bp

...

RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES IN RODENTS


10

.

0

0.2

0.4

0.6

0.8

1

-150 -100 -50 0 50 100 150

Recognitionfunction

value Exon Intron


0

0.2

0.4

0.6

0.8

1

1.2

-150 -100 -50 0 50 100 150

Recognitionfunction

value ExonIntron


Acceptor sitesDonor sites

...

RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES INDrosophila melanogaster


11

1

-0.6

-0.4

-0.2

00.2

0.4

0.6

0.8

-150 -100 -50 0 50 100 150


-0.6-0.4

-0.20

0.2

0.40.6

0.81

-150 -100 -50 0 50 100 150Position relative by splicing center site, bp

Acceptor sitesDonor sitesRecognition

functionvalue Exon Intron

Recognitionfunction

value ExonIntron...

The eukaryotic genes exon-intron structure can be determined by the nucleosomal organisation of the chromatin and related characteristics of gene expression regulation. (Solovyev V.V., Kolchanov N.A. , 1985, Dokl

Akad Nauk SSSR, 284, 232-237 )

INSERTION OF INTRON INTO THE GENE CODING REGION ALLOWS AN EFFICIENT NUCLEOSOME

FORMATION SITE TO BE INSTALLED


Nucleosomeformationpotential

Nucleosomeformationpotential

Insertion of intron

Gene coding region

intronexon 1 exon 2

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Nucleosomal site


RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES IN THE 5' SPACER

REGION OF THE CHICKEN -GLOBIN GENE

13

Transcription start

HSS HSS HSS

Recognitionfunction

value

43210

-1-2-3-4-5

Position, bp10000 4000 6000 7000 8000

5

2000 3000 5000 9000 10000


14RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES IN ADH GENE OF

Drosophila melanogaster

Transcription starts

Position, bp

Recognitionfunction

value

50004500 5500 6000 6500 7000

43210

-1-2-3-4-5

Genes: S-adenosylhomocysteinhydrolase and a part of the Abd-B gene (with two alternative transcription starts)


RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES FOR BITHORAX COMPLEX

FRAGMENT IN Drosophila melanogaster

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Position, bp

Transcription starts

432

10

-1-2-3

-4

-550000 10000 15000 20000 25000 30000

Recognitionfunction

value

RECOGNITION FUNCTION PROFILE FOR PROMOTER REGION OF HUMAN GENES


-0.4

-0.2

0

0.2

0.4

0.6

0.8

1

-600 -500 -400 -300 -200 -100 0 100 200 300 400 500 600

Position, bp

Recognitionfunctionvalue Transcription start

16


DISTRIBUTION OF RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES OF PROMOTERS OF HUMAN GENES WITH DIFFERENTEXPRESSION PATTERNS

17

0%

2%

4%

6%

8%

10%

12%

14%

-4 -3 -2 -1 0 1 2 3 4

-4 -3 -2 -1 0 1 2 3 40%

2%

4%

6%

8%

10%

12%

14% M= +0.7

0%

2%

4%

6%

8%

10%

12%

14%

-4 -3 -2 -1 0 1 2 3 4

M= -0.7

M= -1.5

promotors of house keeping genes

promotors of widly expressed genes

promotors of Tissue-specific genes

NucleosomalSite

Tissue-specific genes "Housekeeping" genes


RECOGNITION FUNCTION PROFILE FOR NUCLEOSOMAL SITES OF HUMAN GENES

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primary transcript primary transcript

primary transcriptprimary transcript

Transcription start

Transcription start

Transcription start

Transcription start

delta-globin gene

prealbumin gene

ubiquitin gene

chromosomal protein HMG 17 gene

19SCHEME OF INITIATIATION COMLEX ASSEMBLING AND FUNCTIONING


(Nikolov and Burley, 1997)

SCHEMATIC REPRESENTATION OF MMTV PROMOTER DNA WRAPPED AROUND THE HISTONE OCTAMER WITH THE

APPROXIMATE LOCATION OF GLUCOCORTICOID RECEPTORS AND TRANSCRIPTION FACTORS NF-1 AND OTF-1

20


[Mathias Truss et. al. ,The EMBO Jornal vol. 14 no.8 pp. 1737-1751, 1995 ]

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NUCLEOSOME ORGANIZATION OF HSP27 GENE IN D.melanogaster

Nucleosome

Quivy J.P., Backer P.B. The architecture of the heat-inducible Drosophila hsp27 promoter in nuclei J.Molec.Biol.V. 256. 1996 P. 249-263, 96174473


RECOGNITION FUNCTION PROFILE FOR NUCLEOSOME SITES OF THE HUMAN HYDROXIMETHYLBILANSYNTHETASE

GENE (AC M95623)

-5-4-3-2-1012345

0 2000 4000 6000 8000 10000

TSS 1, housekeeping expression TSS 2, tissue-specific expression

mRNA 1mRNA 2

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-

0,10

0,20

0,30

0,40

0,50

0,60

0,70

32,6 33,2 33,8 34,4 35,0 35,6 36,2 36,8 37,4 38,0 38,6 39,2twist, degree

prob

abili

ty, p

TATA

Random sequences

Nucleosomebinding sites

HISTOGRAMS OF TWIST ANGLE MEAN VALUES FOR INVERTEBRATE TATA-BOXES, RANDOM

SEQUENCES, AND NUCLEOSOME BINDING SITES


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-0.4

-0.2

0

0.2

0.4

0.6

0.8

-300 -200 -100 0 100 200 300

Position, bp

Recognition function value

insertion site

RECOGNITION FUNCTION PROFILE OF NUCLEOSOME SITES OF MOBILE ELEMENT

P1 IN Drosophila melanogaster


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Coordinate frame Tip ( ) Inclination( )

Opening () Propeller twist( ) Buckle()

Twist( ) Roll( ) Tilt()

LOCAL CONFORMATIONAL PARAMETERS OF DNA DOUBLE HELIX


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MI P0000001MN ConformationalMD B-DNA ML dinucleotide stepPN TwistPM Calculated by Sklenar, PM and averaged by PonomarenkoPV TwistCalcPU Degree


DISCRIPTION OF THE DINUCLEOTIDE DEPENDENT HELICAL TWIST ANGLE VALUE IN THE KNOWLEDGE BASE

Twist ()

DINUCLEOTIDE AA 38.90 AT 33.81 AG 32.15 AC 31.12 ** TA 33.28 TT 38.90 TG 41.41 * TC 41.31 GA 41.31 GT 31.12 ** GG 34.96 GC 38.50 CA 41.41 * CT 32.15 CG 32.91 CC 34.96//

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MI P0000016MN ConformationalMD DNA/protein-complexML dinucleotide stepPN TiltPM Averaged for X-raysPV TiltComplPU Degree


DISCRIPTION OF THE DINUCLEOTIDE DEPENDENT TILT ANGLE VALUE IN THE

KNOWLEDGE BASE DINUCLEOTIDE AA 1.9 * AT 0.0 AG 1.3 AC 0.3 TA 0.0 TT 1.9 * TG 0.3 TC 1.7 GA 1.7 GT -0.1 ** GG 1.0 GC 0.0 CA 0.3 CT 1.3 CG 0.0 CC 1.0//

Tilt ( )

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SCHEME LOCATION OF THE REGION, DIFFERING BY DNA BENDING, AT THE

SURFACE OF HISTONE OCTAMER


28

Profile for the Melting temperature of nuclosome DNA,window size is 7 bp

67.5

68

68.5

69

69.5

70

70.5

71

-100 -90 -80 -70 -60 -50 -40 -30 -20 -10 0 10 20 30 40 50 60 70 80 90 100

Position relatively the site center (diads), bp

Meltingtemperature,degrees

PROFILE FOR NUCLEOSOME SITEKolchanov N.A., IC&G, BGRS 2000

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Twist,degrees

Inclination,degrees

Position,bp

Position,bp

a)

b)

Inclination

Twist


GRADIENTS FOR NUCLEOSOME SITE 30

a)

b)

Position,bp

Position,bp

Rise,angstrom

Rise

Tip

Tip,degrees

fn - the partial recognizing procedure for sites of the given type:IF f n(S)>0, THEN the S =(s a...s i...s b) is the recognized site;

the recognition values fn(S) are normalized as:

sites)(for ;1)(1

N

n

nn

NSitef

sequences) random(for ;1)(1

N

n

nn

NRandf

Then the mean recognition procedure is defined as follows

N

n

abnabN

NSfSF

1,)()(

IF {F N(S)>0}, THEN {S is the site }.

Site

f1 f2f3 ... fN

FN

CALCULATION OF THE MEAN RECOGNITION SCORE


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0

0,1

0,2

0,3

-4,1 -2,1 -0,1 1,85 3,84recognition score

prob

abili

ty, p

32DISCRIMINANTION ABILITY OF THE NUCLEOSOME SITE RECOGNITION SCORE BASED ON THE CONFORMATIONAL AND

PHYSICAL/CHEMICAL PROPERTIES

The elements (or the signals) of nucleosomal code are dinucleotides (oligonucleotides) determining local conformational (physicochemical) nucleosome site features, necessary for interaction with core histones

Nucleosomal code is point-wise: only particular groups of positions are used for coding genetic messages on local conformational DNA features, significant for interaction of nucleosome sites with core histone. Besides, these groups located in a definite (unfixed) distance.



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Nucleosomal code is extremely degenerated: very differing DNA sequences that interact with histone octamer are recognized

Nucleosomal code is point-wise: it provides the possibility of overlapping with the other types of codes



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Nucleosomal code is extremely excessive: there exists a huge variety of the context-dependable conformational and physicochemical signals that could be used for the coding of DNA sequences packaged into a nucleosome

Positioning of the core octamer at the definite DNA site is performed on the base of specific subset of signals located in particular set of positions


Signal is not used for coding formation of the partucular nucleosome formation due to constraints imposed by other codes

Signal involved in the codingof the partucular nucleosome formation

Site 1 Site 2


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ACNOWLEDGEMENT 36

The authors are grateful to

Dr. M.P. Ponomarenko, Dr. O.A. Podkolodnaya,J.V. Ponomarenko

for participance and help in work

N.A. Kolchanov and V.G. Levitsky

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