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Midterm Review Bio5488 SP2017

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Page 1: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Midterm  ReviewBio5488  SP2017

Page 2: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Question  1  Total  coverage:2x150  bp reads  =  300  bp300  bp x  2e5  reads  =  60e6  bp

Average  coverage:60e6  bp /  12e6  bp =    5x

Poisson  Distribution!

Accurate  Call  %  (at  least  4x)=  1  – {P(0,5)  +  P(1,5)  +  P(2,5)  +P(3,5)}

Page 3: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Question  1  P(l)  =  0.5  

So,  5x  in  a  row  =  0.5  x  0.5  x  0.5  x  0.5  x  0.5  =0.0315

Page 4: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Question  5

ACmGTTCGCTTGAG

5’

3’

CTCAAGCGAACCmGT3’

5’

TGCmCAAGCGAACTC 5’3’

ACmGTTUGUTTGAG UTUAAGUGAAUCmGT

Bisulfite  Treatment

Bisulfite  Treatment

PCR/Sequencing PCR/Sequencing

ACGTTTGTTTGAG TTTAAGTGAATCGT5’ 3’

TGCAAACAAACTC3’ 5’ AAATTCACTTAGCA5’ 3’

3’ 5’

Page 5: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Homology

Page 6: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

How  many  matches?  Mismatches?

How  many  gap  openings?   Extensions?  What  are  the  penalties?

Page 7: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Alanine GCU,  GCA,  GCC,  GCGTryptophan UGG

What  is  the  likelihood   that  W-­‐W  occurs  by  chance  in  either?

What  is  the  percent  identity  of  the  alignments?

Page 8: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Expression

Page 9: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Mixing  up  Type  I/II  error

Page 10: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Power  analysis

• Increasing  sequencing  depth  would  not  increase  the  statistical  power

Page 11: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’
Page 12: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Epigenetics

• Q3• In general: DNAme ~ DNMT3b ChIP.• BUT, for  lowly  expressed  genes,  DNAme would  not  be  that  close  to  zero.  • ALSO, DNAme in  promoter  region  should be  higher comparing  to  highly  expressed  groups

Page 13: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Epigenetics

• Q5:Interaction  between  Dnmt3b / methylated  DNA  and  histone  methyltransferases /  H3K36me3  (recruitment  of  one  by  another); the  associations  are  prior-­‐differentiation-­‐specific;DNA  methylation  in  gene  body  prevents  transcription  from  intragenic  alternative  TSS  (see http://www.nature.com/nature/journal/v543/n7643/full/nature21373.html)

Page 14: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

DNA  binding  specificity

• Strong  binding  to  one  nucleotide?• Frequency:  100%

• For  any  of  the  finger,  background  frequency  is  0.25,  while  real  frequency  is  1.  So:  • Information  content  =  1.0*log2(1.0/0.25)  =  2  bits• so  10  fingers  are  necessary.

• Why  have  specificity  but  degenerate?• Allow  different  level  of  affinity  (diverse  regulatory  activity)• Allow  easy  on/off  

Page 15: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Technologies  used  (and  developed)  to  study  genome  folding

Adapted  from  http://web.uvic.ca/ail/equipment.htmlUnraveling  the  3D  genome:  genomics  tools  for  multiscale  exploration.  Viviana  I.  Risca  and  William  J.  Greenleaf.  Trends  in  Genetics  (2015)

Can  be  divided  into  two  broad  categories:  

1. Imaging1. Bright-­field2. Fluorescence3. EM4. Fluorescence   in-­situhybridization  (FISH),  etc.

2. Genome-­wide1. DamID2. ChIA-­PET3. Chromosome  conformation  capture-­derived,  etc.

Page 16: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

HiC vs.  ChIA-­‐PET

• ChIA-­‐PET:  Chromatin Interaction Analysis by Paired-End Tag Sequencing

Nature Methods 6, 863 (2009)

?

Page 17: Midterm(Review - genetics.wustl.edugenetics.wustl.edu/bio5488/files/2017/03/SP2017_Midterm-Review.pdfQuestion(5 ACmGTTCGCTTGAG 5’ 3’ CTCAAGCGAACCmGT 3’ 5’ TGCmCAAGCGAACTC 5’

Chromatin  interaction

2D  Graph  of   the  same  region