Lecture_3_motifs

Promoter sequence regulates the expression of the

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Unformatted text preview: binding to a specific loca,on in the respec,ve gene’s regulatory region Gene Regula,on Promoter Gene encoding protein Gene Regula,on Promoter transcription Messenger RNA Gene encoding protein transcription Messenger RNA Protein Promoter sequence: regulates the expression of the gene. Promoter sequence: regulates the expression of the gene. 2 9/2/13 Transcrip,on Factor Binding Sites •  Transcrip,on factor binding sites can be located anywhere within the regulatory region •  Transcrip,on factor binding sites may vary slightly across different regulatory regions since non- essen,al bases could mutate Mo,fs and Transcrip,onal Start Sites ATCCCG! gene TTCCGG! gene ATCCCG! gene ATGCCG! gene ATGCCC! gene Mo,f Illustra,ons: Mo,f Logos •  Mo,fs can mutate on non important bases •  The five mo,fs in five different genes have muta,ons in posi,on 3 and 5 •  Representa,ons called mo#f logos illustrate the conserved and variable regions of a mo,f Mo,f Logos: An Example TGGGGGA! TGAGAGA! TGGGGGA! TGAGAGA! TGAGGGA! (http://www-lmmb.ncifcrf.gov/~toms/sequencelogo.html) Iden,fying Mo,fs Iden,fying Mo,fs: Complica,ons •  Genes are turned on or off by regulatory proteins •  We do not know the mo,f sequence •  These proteins bind to upstream regulatory regions of genes to either a]ract or block an RNA polymerase •  Regulatory protein (TF) binds to a short DNA sequence called a mo,f (TFBS) •  We do not know where it is located rela,ve to the genes start •  So finding the same mo,f in mul,ple genes’ regulatory regions suggests a regulatory rela,onship amongst those genes •  Mo,fs can differ slightly from one gene to the next •  How to discern it from “random” mo,fs? 3 9/2/13 A Mo,f Finding Analogy The Gold Bug Problem •  Given a secret message: 53++!305))6*;4826)4+.)4+);806*;48!8`60))85;]8*:+*8! 83(88)5*!; 46(;88*96*?;8)*+(;485);5*!2:*+(;4956*2(5*-4)8`8*; 4069285);)6 !8)4++;1(+9;48081;8:8+1;48!85;4)485!528806*81(+9;48; (88;4(+?3 4;48)4+;161;:18...
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