![Page 1: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/1.jpg)
Regulatory Genomics
Lecture 1 November 2012
Yitzhak (Tzachi) Pilpel
Lecture 1 November 2012
Yitzhak (Tzachi) Pilpel1
![Page 2: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/2.jpg)
Course requirements
• Attendance and participation
• Five reading assignments
• A final take home papers reading-based exam
• website
In total 13 or 14 meetings (not 17…)No meeting on Nov 15th
2
![Page 3: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/3.jpg)
Genomics marked the beginning of a new age in
biology and medicine
1900
1953
1977
1980
1983
1990
1994-98
1998
2000
2005
Watson and Crick identify DNA(the double helix) as the Chemical basis of heredity
DNA markers used to map human disease genes to chromosomal regions
Human Genome Projects (HPG) begins-an international effort to map and sequence all the genes in the human genome
DNA markers used to map human disease genes to chromosomal regions
Release of Human Genome Project
Sanger and Gilbert derive methods of sequencing DNA
Huntington disease gene mapped to chromosome 4
Genetic and physical mapping
Working Draft of the human genome sequencing complete
Rediscovery of Mendel's laws helps establish the science of genetics
Source: Health Policy Research Bulletin, volume 1 issue2, September 2001
3
![Page 4: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/4.jpg)
The genome browser
Link4
![Page 5: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/5.jpg)
Number of protein coding genes20,210
19,735
13,601
5,616
20,568
482Mycoplasma genitalium
Mouse Fruit fly Mustered(Arabidopsis)
Worm (C elegans)
Yeast(S Cerevisiae)
5
![Page 6: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/6.jpg)
How comes we have so few genes give that we are so complex???
19,735
21,710•We have many non-protein coding genes
•Our genes are longer and more complex
•Regulation of human genes activity is more complex
•Repeats (formerly known as “junk DNA” (yet not garbage) contribute to complexity
•Combinatorial interactions among genes and products
6
![Page 7: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/7.jpg)
The hierarchical structure of the genome
Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.
7
![Page 8: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/8.jpg)
Expressing the genome
8
![Page 9: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/9.jpg)
The Central Dogma: a cellular context
915
![Page 10: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/10.jpg)
DNA mRNA Protein
Inactive DNA
The Central Dogma of Molecular BiologyExpressing the genome
RNA
10
![Page 11: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/11.jpg)
Evolution
11
![Page 12: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/12.jpg)
Corrected view of evolution
12
![Page 13: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/13.jpg)
The tree of life
13
![Page 14: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/14.jpg)
How genomes evolve?
Consider two distinct possibilities:
•Genomes evolve by lots of de-novo “inventions”
•Genomes evolve predominantly by mixing and matching existings
parts 14
![Page 15: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/15.jpg)
Classification of protein structures
15
![Page 16: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/16.jpg)
Very slow growth in number of protein folds
Very few structural “inventions”
16
![Page 17: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/17.jpg)
Comparing a certain family (e.g. kinases) in different species reveals few
“inventions”
17
![Page 18: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/18.jpg)
Analogy:
•Technology
•Language
18
![Page 19: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/19.jpg)
Some basic evolutionary operations
• Mutating existing DNA
• Change gene expression profiles
• Duplications of existing material (genes, chromosomes, genomes)
• Transfer of genes from one organism to another
• Functionalization of “junk DNA”
• Reverse transcription??19
![Page 20: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/20.jpg)
Stress condition induce high DNA replication error rate
Because most newly arising mutations are neutral or deleterious, it has been argued that the mutation rate has evolved to be as low as possible, limited only by the cost of error-avoidance and error-correction mechanisms. But up to one per cent of natural bacterial isolates are 'mutator' clones that have high mutation rates. We consider here whether high mutation rates might play an important role in adaptive evolution. Models of large, asexual, clonal populations adapting to a new environment show that strong mutator genes (such as those that increase mutation rates by 1,000-fold) can accelerate adaptation, even if the mutator gene remains at a very low frequency (for example, 10[-5]). …
20
![Page 21: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/21.jpg)
Some basic evolutionary operations
• Mutating existing DNA
• Change gene expression profiles
• Duplications of existing material (genes, chromosomes, genomes)
• Transfer of genes from one organism to another
• Functionalization of “junk DNA”
• Reverse transcription??21
![Page 22: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/22.jpg)
A slight change in expression program can make a big change: olfactory receptor can “smell the egg”
22
![Page 23: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/23.jpg)
Science. 2003 Mar 28;299(5615):2054-8.Identification of a testicular odorant receptor mediating human sperm chemotaxis.Spehr M, Gisselmann G, Poplawski A, Riffell JA, Wetzel CH, Zimmer RK, Hatt H.SourceDepartment of Cell Physiology, Ruhr University Bochum, 150 University Street, D-44780 Bochum, Germany.AbstractAlthough it has been known for some time that olfactory receptors (ORs) reside in spermatozoa, the function of these ORs is unknown. Here, we identified, cloned, and functionally expressed a previously undescribed human testicular OR, hOR17-4. With the use of ratiofluorometric imaging, Ca2+ signals were induced by a small subset of applied chemical stimuli, establishing the molecular receptive fields for the recombinantly expressed receptor in human embryonic kidney (HEK) 293 cells and the native receptor in human spermatozoa. Bourgeonal was a powerful agonist for both recombinant and native receptor types, as well as a strong chemoattractant in subsequent behavioral bioassays. In contrast, undecanal was a potent OR antagonist to bourgeonal and related compounds. Taken together, these results indicate that hOR17-4 functions in human sperm chemotaxis and may be a critical component of the fertilization process.
23
![Page 24: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/24.jpg)
Some basic evolutionary operations
• Mutating existing DNA
• Change gene expression profiles
• Duplications of existing material (genes, chromosomes, genomes)
• Transfer of genes from one organism to another
• Functionalization of “junk DNA”
• Reverse transcription??24
![Page 25: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/25.jpg)
nonfunctionalization
neofunctionalization subfunctionalization
duplication
Gene duplication might provide redundancy
25
![Page 26: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/26.jpg)
500 1000 1500 2000 2500 3000 3500 4000 4500 5000 5500-2
-1.5
-1
-0.5
0
0.5
1
1.5
2
chromosome III duplicates in heat
Gene Index
log 2(e
xpre
ssio
n ev
o39
/ evo
30)
all genes
chromosome III genes
P value < 10e-100
26
![Page 27: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/27.jpg)
Heat shock tolerance correlates with chromosome III copy number
0
0.5
1
1.5
2
2.5
3
3.5
Rela
tive
Surv
ival
WT Two copies
Evolved 3 copies
WT One copyWT, 3 copies27
![Page 28: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/28.jpg)
• Chromosomes are easily gained and lost in yeast evolution
• A more fine-tuned solution may follow chromosome duplication
• A sticking similarity between repetitive experiments
• A chromosome-condition specificity?
Conclusions from the experiment
28
![Page 29: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/29.jpg)
29
![Page 30: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/30.jpg)
Many gene duplicate distances Correspond to 60-70 mya!!
Sequences similarity between gene pairs
30
![Page 31: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/31.jpg)
Some basic evolutionary operations
• Mutating existing DNA
• Change gene expression profiles
• Duplications of existing material (genes, chromosomes, genomes)
• Transfer of genes from one organism to another
• Functionalization of “junk DNA”
• Reverse transcription??31
![Page 32: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/32.jpg)
Horizontal (“lateral”) gene transfer: transfer genes between organisms –
mostly in stress
32
![Page 33: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/33.jpg)
Some basic evolutionary operations
• Mutating existing DNA
• Change gene expression profiles
• Duplications of existing material (genes, chromosomes, genomes)
• Transfer of genes from one organism to another
• Functionalization of “junk DNA”
• Reverse transcription??33
![Page 34: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/34.jpg)
Evolution of transcriptional switches
Similar function
Neutral selection
Disrupted function
Low ratepurifying selection
TF1
TF2
Altered function
Low ratepurifying selection
TF1
Gained function
TF1
CACGCGTACACGCGTT
TF1
CACGAGTTCACGCGTT
CACACGTTCACGCGTTCACACGTTCACGCGTT
Low ratepurifying selection
34
![Page 35: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/35.jpg)
Evolution of transcription networks
35
![Page 37: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/37.jpg)
Repetitive elements in the human genome
•Alu are repetitive retrotransposons elements in the Human genome. •Alu elements are about 300 base pairs long and are therefore classified as short interspersed elements (SINEs) •There are over one million Alu elements interspersed throughout the human genome•About 10% of the human genome consists of Alu sequences. 37
![Page 38: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/38.jpg)
Retro-transposition
38
![Page 39: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/39.jpg)
Alus may contain binding sites for TFs, microRNAs…
Alus
Alus 39
![Page 40: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/40.jpg)
Can the phenotype shape the genotype?
Classical Darwinian theory
Lamarckian Theory
Genotype Phenotype
Genotype Phenotype
40
![Page 41: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/41.jpg)
The Central Dogma: a cellular context
4115
![Page 42: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/42.jpg)
42
![Page 43: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/43.jpg)
cell division
celldeath
Attack a virus differentiate
proteinsynthesis
* * *
Cell membrane
Nucleus
43
![Page 44: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/44.jpg)
* * *From parts to networks…
44
![Page 45: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/45.jpg)
Reporter gene reveal spatio-temporal expression programs
45
![Page 46: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/46.jpg)
In uni-cellulars response to environmental signals affect gene expression dramatically
Genes
Gasch et al Mol Biol Cell. 2000 Dec;11(12):4241-57.46
![Page 47: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/47.jpg)
The transcriptome during the cell cycle
Spellman et al Mol Biol Cell. 1998 Dec;9(12):3273-9747
![Page 48: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/48.jpg)
Coding DNA strandNon-coding strandRNA
48
![Page 49: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/49.jpg)
Transcription regulation
• The hardware
• The software
• The input
• The output
49
![Page 50: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/50.jpg)
The initiation machinery complex
50
![Page 51: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/51.jpg)
Transcription factors bind the DNA
51
![Page 52: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/52.jpg)
ATACGAT
Keys (regulators) can scan the genomes in search for their locks (recognition sites)
52
![Page 53: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/53.jpg)
Transcription regulation
• The hardware
• The software
• The input
• The output
53
![Page 54: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/54.jpg)
http://esg-www.mit.edu:8001/esgbio/pge/lac.html
In the absence of Lactose
54
![Page 55: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/55.jpg)
http://esg-www.mit.edu:8001/esgbio/pge/lac.html
In the presence of Lactose
The Lac Operon (Jacob and Monod)
55
![Page 56: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/56.jpg)
http://esg-www.mit.edu:8001/esgbio/pge/lac.html
In the absence of Glucose
56
![Page 57: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/57.jpg)
The logic of the Lac operon regulation
CAPsite
Operator
Glu
cose
Lac
tose
+ -
- +
- -
+ +
Activity
OFF
ON
OFF
OFF
Lactose
n y
OFF
n y
OFF ON
Glucose
57
![Page 58: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/58.jpg)
Genomic Regulatory Logic
58
![Page 59: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/59.jpg)
DNA binding proteins for unique pathways
59
![Page 60: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/60.jpg)
A global map of combinatorial expression control
mRPE72
SWI5
SFF '
MCM1
SFFMCM1'
ECB SCB
MCB
PAC
mRRPE
mRRSE3
GCN4
BAS1
LYS14
RAP1
mRPE34
mRPE57
mRPE6mRPE58
STRE
RPN4 ABF1
PDR
CCA
PHO4
AFT1
STE12
MIG1
CSRE
HAP234
ALPHA1'
ALPHA1
ALPHA2
mRPE8
mRPE69
Heat-shockCell cycleSporulationDiauxic shiftMAPK signalingDNA damage
*High connectivity
*Hubs*Alternative partners in various conditions
60
![Page 61: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/61.jpg)
Transcription regulation
• The hardware
• The software
• The input
• The output
61
![Page 62: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/62.jpg)
5’- TCTCTCTCCACGGCTAATTAGGTGATCATGAAAAAATGAAAAATTCATGAGAAAAGAGTCAGACATCGAAACATACAT
5’- ATGGCAGAATCACTTTAAAACGTGGCCCCACCCGCTGCACCCTGTGCATTTTGTACGTTACTGCGAAATGACTCAACG
5’- CACATCCAACGAATCACCTCACCGTTATCGTGACTCACTTTCTTTCGCATCGCCGAAGTGCCATAAAAAATATTTTTT
5’- TGCGAACAAAAGAGTCATTACAACGAGGAAATAGAAGAAAATGAAAAATTTTCGACAAAATGTATAGTCATTTCTATC
5’- ACAAAGGTACCTTCCTGGCCAATCTCACAGATTTAATATAGTAAATTGTCATGCATATGACTCATCCCGAACATGAAA
5’- ATTGATTGACTCATTTTCCTCTGACTACTACCAGTTCAAAATGTTAGAGAAAAATAGAAAAGCAGAAAAAATAAATAA
5’- GGCGCCACAGTCCGCGTTTGGTTATCCGGCTGACTCATTCTGACTCTTTTTTGGAAAGTGTGGCATGTGCTTCACACA
AlignACE ExampleAlignACE Example
…HIS7 …ARO4…ILV6…THR4…ARO1…HOM2…PRO3
300-600 bp of upstream sequence per gene are searched in
Saccharomyces cerevisiae.
62
![Page 63: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/63.jpg)
5’- TCTCTCTCCACGGCTAATTAGGTGATCATGAAAAAATGAAAAATTCATGAGAAAAGAGTCAGACATCGAAACATACAT
5’- ATGGCAGAATCACTTTAAAACGTGGCCCCACCCGCTGCACCCTGTGCATTTTGTACGTTACTGCGAAATGACTCAACG
5’- CACATCCAACGAATCACCTCACCGTTATCGTGACTCACTTTCTTTCGCATCGCCGAAGTGCCATAAAAAATATTTTTT
5’- TGCGAACAAAAGAGTCATTACAACGAGGAAATAGAAGAAAATGAAAAATTTTCGACAAAATGTATAGTCATTTCTATC
5’- ACAAAGGTACCTTCCTGGCCAATCTCACAGATTTAATATAGTAAATTGTCATGCATATGACTCATCCCGAACATGAAA
5’- ATTGATTGACTCATTTTCCTCTGACTACTACCAGTTCAAAATGTTAGAGAAAAATAGAAAAGCAGAAAAAATAAATAA
5’- GGCGCCACAGTCCGCGTTTGGTTATCCGGCTGACTCATTCTGACTCTTTTTTGGAAAGTGTGGCATGTGCTTCACACA
AAAAGAGTCA
AAATGACTCA
AAGTGAGTCA
AAAAGAGTCA
GGATGAGTCA
AAATGAGTCA
GAATGAGTCA
AAAAGAGTCA
**********
AlignACE ExampleAlignACE Example
MAP score = 20.37
…HIS7
…ARO4
…ILV6
…THR4
…ARO1
…HOM2
…PRO3
The Best MotifThe Best Motif
63
![Page 64: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/64.jpg)
Transcription regulation
• The hardware
• The software
• The input
• The output
64
![Page 65: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/65.jpg)
Expression regulation of genes determines complex spatio-temporal patterns
65
![Page 66: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/66.jpg)
Monitor expression during
cell cycle
0 5 10 15-2
-1
0
1
2
3
4
Time
mR
NA
exp
ress
ion
leve
l
G1 S G2 M G1 S G2 M 66
![Page 67: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/67.jpg)
Time-point 1
Tim
e-po
int 3
Tim
e-po
int 2
-1.8
-1.3
-0.8
-0.3
0.2
0.7
1.2
1 2 3
-2
-1.5
-1
-0.5
0
0.5
1
1.5
1 2 3
-1.5
-1
-0.5
0
0.5
1
1.5
1 2 3
Time -pointTime -point
Time -point
Nor
mal
ized
Exp
ress
ion
Nor
mal
ized
Exp
ress
ion
Nor
mal
ized
Exp
ress
ion
Genes can be clustered based on time-dependent expression profilesGenes can be clustered based on time-dependent expression profiles
67
![Page 68: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/68.jpg)
The K-means algorithm
• Start with random positions of centroids.
Iteration = 0
68
![Page 69: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/69.jpg)
K-means
• Start with random positions of centroids.
• Assign data points to centroids
Iteration = 1
69
![Page 70: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/70.jpg)
K-means
• Start with random positions of centroids.
• Assign data points to centroids.
• Move centroids to center of assigned points.
Iteration = 1
70
![Page 71: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/71.jpg)
K-means
• Start with random positions of centroids.
• Assign data points to centroids.
• Move centroids to center of assigned points.
• Iterate till minimal cost. Iteration = 3
71
![Page 72: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/72.jpg)
The diauxic shift
Time 72
![Page 73: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/73.jpg)
Genetic reprogramming of the yeast metabolism upon glucose deletion
73
![Page 74: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/74.jpg)
Glucose
Pyruvate
2 ADP+Pi
2 ATP
NAD+
NADH
EthanolLactateFermentFerment
AcetylCoA
TCA
NAD+NADHRespirate
At the beginning – whenglucose is abundant
74
![Page 75: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/75.jpg)
Glucose
Pyruvate
2 ADP+Pi
2 ATP
NAD+
NADH
EthanolLactateFermentFerment
O2O2
AcetylCoA
TCA
NAD+NADHRespirate
~20 hours laterwhen glucose is depleted
75
![Page 76: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/76.jpg)
The promoter sequences of co-expressed genes
5’- TCTCTCTCCACGGCTAATTAGGTGATCATGAAAAAATGAAAAATTCATGAGAAAAGAGTCAGACATCGAAACATACAT
5’- ATGGCAGAATCACTTTAAAACGTGGCCCCACCCGCTGCACCCTGTGCATTTTGTACGTTACTGCGAAATGACTCAACG
5’- CACATCCAACGAATCACCTCACCGTTATCGTGACTCACTTTCTTTCGCATCGCCGAAGTGCCATAAAAAATATTTTTT
5’- TGCGAACAAAAGAGTCATTACAACGAGGAAATAGAAGAAAATGAAAAATTTTCGACAAAATGTATAGTCATTTCTATC
5’- ACAAAGGTACCTTCCTGGCCAATCTCACAGATTTAATATAGTAAATTGTCATGCATATGACTCATCCCGAACATGAAA
5’- ATTGATTGACTCATTTTCCTCTGACTACTACCAGTTCAAAATGTTAGAGAAAAATAGAAAAGCAGAAAAAATAAATAA
5’- GGCGCCACAGTCCGCGTTTGGTTATCCGGCTGACTCATTCTGACTCTTTTTTGGAAAGTGTGGCATGTGCTTCACACA
…HIS7 …ARO4…ILV6…THR4…ARO1…HOM2…PRO3
76
![Page 77: Regulatory Genomics Lecture 1 November 2012 Yitzhak (Tzachi) Pilpel 1](https://reader035.vdocument.in/reader035/viewer/2022062519/56649e395503460f94b2ae74/html5/thumbnails/77.jpg)
Promoter Motifs and expression
profilesCGGCCCCGCGGA
CTCCTCCCCCCCTTC TGGCCAATCA
ATGTACGGGTG
77