How do Replication and Transcription Change Genomes?
description
Transcript of How do Replication and Transcription Change Genomes?
![Page 1: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/1.jpg)
How do Replication and Transcription Change Genomes?
Andrey Grigoriev
Director, Center for Computational and Integrative Biology Rutgers University
![Page 2: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/2.jpg)
2
What are we going to do?
• Observe effects of fundamental processes
• Estimate their relative contribution
• Link them to genome features
• Analyze nucleotide composition
![Page 3: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/3.jpg)
How do Replication and Transcription Change Genomes?
Well, do they?
![Page 4: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/4.jpg)
4
Replication and Transcription
• textbook view
faithful reproduction machinery
• basis for selection
parental DNA fitness advantages
![Page 5: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/5.jpg)
5
Replication and Transcription
• paradox
both systematically change genomes
which they faithfully reproduce
• and they leave traces
![Page 6: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/6.jpg)
6
What is in the sequence?
• The usual – coding, regulatory regions, exons, introns,
RNAs, etc.
• Biases in nucleotide composition– Traces of organism‘s „lifestyle“– Links to genome features
![Page 7: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/7.jpg)
7
Counting nucleotides: GC Skew
sw = ([G]-[C])/([G]+[C])
• Short sequence interval (window) w
• Relative excess of G vs C [-1;1]
• Plot vs % of genome position [0;100]
![Page 8: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/8.jpg)
8
0 20 40 60 80 100
0 20 40 60 80 100
position, % genome length
Simian virus 40
Haemophilis influenzae
![Page 9: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/9.jpg)
9
Cumulative Skew Diagrams
sw = ([G]-[C])/([G]+[C])
S = W sw w/L
For W adjacent windows of size w << L
S is an integral of skew function
![Page 10: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/10.jpg)
10
0 20 40 60 80 100
0 20 40 60 80 100
position, % genome length
Simian virus 40
replication origin (ori)
replication terminus (ter)
![Page 11: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/11.jpg)
11
0 20 40 60 80 100
0 20 40 60 80 100
position, % genome length
Haemophilis influenzae
replication origin (ori)
replication terminus (ter)
![Page 12: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/12.jpg)
12
Genome of Escherichia coli
position, % genome length
0 20 40 60 80 100
Terminus
Origin
![Page 13: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/13.jpg)
13
Genome of Bacillus subtilis
0 20 40 60 80 100
position, % genome length
![Page 14: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/14.jpg)
14
Genome of Borellia burgdorferi
position, % genome length
0 20 40 60 80 100
![Page 15: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/15.jpg)
15
Cumulative Skew Diagrams
• Now widely used to predict ori and ter in novel and less studied microbial genomes
• Predictions confirmed experimentally
• Constant skews over half-genomes
• oriter G>C terori G<C
• Strand properties change at ori and ter
![Page 16: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/16.jpg)
16
Causes: Selection vs. Mutation
• Properties of encoded proteins
• Regulatory sequences
• Most pronounced in 3rd codon position
• Suggests mutation, not selection pressure
![Page 17: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/17.jpg)
17
DNA single-stranded, not protected
continuous DNA synthesis
discontinuous DNA synthesismRNA synthesis
template DNA
Transcription Replication
![Page 18: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/18.jpg)
18
Most Consistent Explanation
• spontaneous deamination of C or 5-MetC
– by far the most frequent mutation (rates raise over 100-fold when DNA is single-stranded)
– fixing the mutated base during the next round of replication
– depletion of cytosines vs guanines
![Page 19: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/19.jpg)
19
Cytosine Deamination
Cytosine
Uracil
Thymine
![Page 20: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/20.jpg)
20
Replication
• Leading strand exposed in replication bubble, generation after generation
• Unusual replication models consistent with the single-strand hypothesis– adenovirus– mitochondria
![Page 21: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/21.jpg)
21
0 20 40 60 80 100
Series1Poly. (Series1)
position, % genome length
Adenovirus Replicationorigins
![Page 22: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/22.jpg)
22
Replication or Transcription
• Leading-lagging switch at ori and ter
• Consistent with replication models
• Transcription often colinear with replication
• Direction often changes at ori and ter
![Page 23: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/23.jpg)
23
0 20 40 60 80 100
position, % genome length
Replication vs. Transcription
HPV-16
![Page 24: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/24.jpg)
24
Replication vs. Transcription
• Comparable contribution to skew
• [G]=900, [C]=690 in the same direction
additive effect on skew
• [G]=758, [C]=773 in the opposite direction
cancel each other out
![Page 25: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/25.jpg)
25
Genome of Bacillus subtilis
0 20 40 60 80 100
position, % genome length
![Page 26: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/26.jpg)
26
Diagrams „jagged“
• Sequence constraints – amino acid composition, regulatory sequences,
etc.
• Sequence inversions – swaps strands and change the skew to its
opposite between the borders of the inversion
• Horizontal transfer between species
![Page 27: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/27.jpg)
27
5‘ 3‘
A B C D A C B D
3‘5‘
Inversion
![Page 28: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/28.jpg)
28
Rearrangements in two sequenced strains of Helicobacter pylori
Colored areas under the curve correspond to inversions and translocations
cagPAI – pathogenicity island (likely horizontal transfer)
![Page 29: How do Replication and Transcription Change Genomes?](https://reader036.fdocuments.in/reader036/viewer/2022062410/56815931550346895dc667bb/html5/thumbnails/29.jpg)
29
Conclusions
• Analyze nucleotide composition
• Observe effects of fundamental processes
• Link them to genome features
• Estimate their relative contribution
• Start asking own questions