Replication associated strand asymmetries Replication associated strand asymmetries

in mammalian genomesin mammalian genomes

In silico In silico detection of replication originsdetection of replication origins

Maxime HuvetMarie TouchonYves d'Aubenton-CarafaClaude Thermes

(CGM, Gif sur Yvette)(CGM, Gif sur Yvette)

Samuel NicolayBenjamin AuditEdward Brodie of Brodie Alain Arneodo

(ENS-Lyon)(ENS-Lyon)

Supports: CNRS, ACI IMPBio, ANR

Long genome sequence fragments tend to show on the same strand: fA = fT and fG = fC

« SECOND PARITY RULE »  

00,20,40,60,81

1,21,4

0 0,2 0,4 0,6 0,8 1 1,2 1,40

20

40

60

80

0 20 40 60 80

A (M

b)

T (Mb) T (Mb)

A (M

b)

0

20

40

60

80

0 20 40 60 80C (Mb)

00,20,40,60,81

1,21,4

0 0,2 0,4 0,6 0,8 1 1,2 1,4

C (Mb)

G (M

b)

G (M

b)

Bacteria/Archaebacteria Human chromosomes

AA

TT

GG

CC

at equilibrium

Second Parity rule (PR2): f fAA = = ffTT and and ffGG = = ffC C (at large scales)

(Chargaff, 1962; Sueoka, Lobry, 1995)

Same mutation/repair processes on the 2 DNA strands

Same values of complementary sustitution rates

LARGE SCALE PROPERTIES OF GENOMIC MUTATIONS

REPLICATION : asymmetry of mutation/repair processes between leading and lagging strands

replication

origin

lagging strand

leading strand

5’

3’

What mechanisms cause composition asymmetries ?

EUBACTERIA: G > C and T > A in the leading strand

nG – nC

nG + nC

SGC = > 0nT – n A

nT + n A

STA = > 0

3’

5’

Composition asymmetry in procaryotes

nG – nC

nG + nC

1 kb windows

SSGC GC ==

x 106 pb

SS GC

GC

G > CG < C5’5’ 3’3’

Bacillus subtilisBacillus subtilis

leading strandleading strandlagging strand

ORIORI

TERTERTERTER

RNA POLYMERASE

5’

3’

3’

3’

5’

5’

non-transcribedstrand

transcribed strand

TRANSCRIPTION : asymmetry of mutation/repair processes between transcribed and non-transcribed strands

What mechanisms cause composition asymmetries ?

nG – nC

nG + nC

SGC = > 0nT – n A

nT + n A

STA = > 0

EUBACTERIA: G > C and T > A on the non-transcribed strand

Skew profiles associated to transcription and replication in Eubacteria

transcriptional skew profile

5’

3’

5’ 3’5’

3’

(+)(-)

S

transcribedstrand

non-transcribedstrand5’ 3’

0

replicative skew profile

3’3’

ORIORI

5’5’

5’ 3’

5’ 3’

S

leadingstrand

laggingstrand

0

superposition of replication and transcription

5’ leadingstrand 3’

S

ORIORI

laggingstrand

0

S = STA + SGC

S

Bacillus subtilis

Mbp

genes (strand +) genes (strand -) intergenic regions

STRAND ASYMMETRIES IN EUKARYOTES ?

1. Strand asymmetries associated to transcription

in the human genome

Strand asymmetries associated to transcription in human genes

Introns (126 000)

≈ 12 000 genes(no exons, no repeats)

Downward jumps (3’)Upward jumps (5’)

nT – n A

nT + n A

STA =

nG – nC

nG + nC

SGC =

∆S = STA + SGC ~ 7%

Mean skew associated to transcription

Intergenic sequences Intergenic sequences

-40 -20 0 20 40-40 -20 0 20 40

66

44

22

00

-2-2

88

-40 -20 0 20 40-40 -20 0 20 40

66

44

22

00

-2-2

88

-40 -20 0 20 40-40 -20 0 20 40

66

44

22

00

-2-2

88

-40 -20 0 20 40-40 -20 0 20 40

66

44

22

00

-2-2

88

(kb)(kb)

5’5’ 3’3’

5’5’ 3’3’

STA

SGC

2. Strand asymmetries associated to replication

in the human genome

Skew profiles around human replication origins

genes (strand +) genes (strand -) intergenic regions

Superimposition of replication and transcription biases

S

genes (strand +) genes (strand -) intergenic regions

ORI

5'

3'

ORI

S 0

Transcription : ∆S ~ ± 7%

Replication : ∆S ~ + 14%

Conservation of skew profiles in mammalian genomes

human

mouse

rat

dog

Conservation of replication origins in mammalian genomes

3. In silico detection of replication origins

in the human genome

Detection of upward jumps associated to replication

Main problem :

• necessity to avoid the jumps due only to transcription

Scale of analysis :

• larger than typical size of genes

• smaller than typical size of replicons necessity of multi-scale analysis

5'

3'ORI

S 0ORI ORI

100 kb 1 Mb

Genes

Mean size : 30 kb

w

=20

0 kb

w =

100

kb w

=50

kb

w =

10 k

b

S S

der

ivat

ive

S de

rivat

ive

S S

numerous jumps

high precision

few jumps

low precision

w

first derivative

Multi scale jump detection using the wavelet transform

Multi scale jump detection using the wavelet transform

Signal smoothenedat large scale (200 kb) Identification of transitions

position of transitions (1 kb)

Histograms of jump amplitude

upward

downward

%

Asymmetry of the human genome

x (Mb)x (Mb)

« Factory roof » skew profiles

MCM4 TOP1SS

x (kbx (kb))SS

« Factory roofs » around experimentally determined replication origins

Conservation of potential origins in mammalian genomes

human

mouse

dog

Replication terminaison sites : distributed between fixed adjacent origins

Model of eucaryotic replicon

OO OOTT

Eucaryote Procaryote

OO TT

Ori 1 Ori 2 Ori 1 Ori 2 Ori 1 Ori 2at each cycle: after several cycles: after N cycles:

S

759 « factory roofs spanning »

~ 40% of the human genome

factory roofwavelets

Detection of factory roofs using the wavelet transform

ASYMMETRY OF HUMAN GENOME

factory roofs = 40 %

factory roofs < 1 %

transcriptional skew profile

5’

3’5’ 3’

5’

3’

(+)(-)S

transcribedstrand

non-transcribedstrand5’ 3’

0

replicative skew profile

superposition of transcription and replication

33’’

ORORII

55’’

5’

3’

5’ 3’

ORIORI

S 0

ORIORI

33’’

ORORII

55’’

5’

3’

EUCARYOTIC REPLICON MODEL

Comparison with replication timing data

Woodfine et al., Cell Cycle (2005)

early

late

oriori

Position on human chromosome 6 (Mbp)

Replication

timing

GENE ORGANISATION IN HUMAN CHROMOSOMES

Organisation of transcription around predicted replication origins

Co-orientation of transcription and replication

S

ORIORI ORIORI

Open chromatin

Replication origins are situated at the center

of open chromatin regions

GenomicDNA

Model of mammalian chromatin organization

Conclusions

• Existence of replication-coupled strand asymmetries in human genome

• Replication origins correspond to large transitions of skew profiles

• These transitions are conserved in mammalian genomes

• Detection of more than one thousand putative origins active in germ-line cells

• « Factory roof » profiles : regularly distributed termination sites

• Essential rome of replication in organisation of gene order and expression