Welcome toIntroduction to Bioinformatics

Monday, 15 September

Scenario 2: Regulatory protein / Simulations

SQ 5, 7, 8, 9, 10

Scenario 1: Genomic comparisons

Problem Sets 1M and 1P

Regulatory Protein and their Binding SitesWhat do we talk about?

• Palindromic sequences: relationship to protein binding (SQ7)

• Gene fusions: e.g. ntcA / lacZ (SQ8)

• Simulations?

– Why do them? (SQ10)

– Pitfalls? (SQ9)

• How many promoters? CRP-binding sites? (SQ5)

• How does lac regulation work?

Regulatory Protein and their Binding SitesPalindromic sequences

What is it?

What about with DNA? GCTATCG

Backwards = forwards ROTATOR

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

• DNA is double stranded

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

What is it?

Backwards = forwards

What about with DNA? GCTATCG

ROTATOR

• DNA is double stranded

• DNA is redundant

• DNA has direction (read 5’->3’)

5’- -3’3’- -5’

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

5’- -3’3’- -5’

tRNA

TAT GGCATGCTAGC

TTAAT TCATTAATTA AGTAA

CGTACGATCGG TAT

DNA: cruciform

RNA: stem/loop

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNN

recognizes GTGAGTT

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNN

recognizes GTGAGTT

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNN

Regulatory Protein and their Binding Sites

Palindromic sequencesTTAATGTGAGTTAGCTCACTCATT

AATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNN

Regulatory Protein and their Binding Sites

Palindromic sequences

TTAATGTGAGTTAGCTCACTCATT

AATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNN

NNNNNNNNNNNNN

Regulatory P

rotein and their Binding Sites

Palindromic sequences

TTAATGTGAGTTAGCTCACTCATT

AATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNN

NNNNNNNNNNNNN

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNN

recognizes GTGAGTT

Regulatory Protein and their Binding Sites

Palindromic sequencesTTAA

TGTGAGTT

AGCTCACT

CATT

AATTACAC

TCAATCGA

GTGAGTAA

NNNNNNNN

NNNNNNN

NNNNNNNN

NNNNNNN

NNNNNNNN

NNNNN

NNNNNNNN

NNNNN

Regul

ator

y Pro

tein

and

their

Bin

ding

Site

s

Palin

drom

ic se

quen

ces

TTAATGTGAGTTAGCTCACTCATT

AATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNN

NNNNNNNNNNNNNNN

NNNNNNNNNNNNN

NNNNNNNNNNNNN

Regulatory Protein and their Binding SitesPalindromic sequences

TTAATGTGAGTTAGCTCACTCATTAATTACACTCAATCGAGTGAGTAA

NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

NNNNNNNNNNNNNNNNNNNNNNNNNN

Palindromes: Serve as binding sites for dimeric protein

Regulatory Protein and their Binding SitesSQ7: Is the binding site of NtcA palindromic?

GTA ..(8).. TAC

GTA ..(8).. TAC

5’-GTA ..(8).. TAC-3’3’-CAT ..(8).. ATG -5’

Regulatory Protein and their Binding SitesSQ7: How does NtcA bind to its binding site?

GTA ..(8).. TAC

GTA ..(8).. TAC

5’-GTA ..(8).. TAC-3’3’-CAT ..(8).. ATG -5’

Regulatory Protein and their Binding SitesSQ8: What if NtcA site were attached to lacZ?

GTA ..(8).. TAC

5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

hetQ

NtcA

N RNA Polymerase

Regulatory Protein and their Binding SitesSQ8: What if NtcA site were attached to lacZ?

GTA ..(8).. TAC

5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

hetQ

NtcA

GTA ..(8).. TAC

5’-GTGAGTTAGCTCACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

lacZ

Crp

RNA Polymerase

Operator

N

C

Regulatory Protein and their Binding SitesSQ8: What if NtcA site were attached to lacZ?

GTA ..(8).. TAC

5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

hetQ

NtcAGTA ..(8).. TAC

5’-GTA ..(8).. TACNNNNNNNNNNTANNNTNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CAT ..(8).. ATGNNNNNNNNNNATNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

lacZ

RNA Polymerase

Operator

N

Regulatory Protein and their Binding SitesSQ5: How many genes have promoters? CRP sites?

GTA ..(8).. TAC

5’-GTGAGTTAGCTCACNNTTTACANTANNNNTATGTTNNNNNNNNNNNNNNNNNNNNNNNATGNNNNNNNNNNNNNNNN3’-CACTCAATCGAGTGNNAAATGTANNNNNNATACAANNNNNNNNNNNNNNNNNNNNNNNTACNNNNNNNNNNNNNNNN

lacZ

Crp

RNA Polymerase

Operator

Transcription

How many?

How many?

Regulatory Protein and their Binding SitesSQ10: Issues when modeling genomic DNA?