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MGY299Y1 Lecture Notes - Dna-Binding Domain, Heat Map, Chromatin

Molecular Genetics and Microbiology
Course Code
Timothy Hughes

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Generic models or regulation of transcription
- Models come from bacteria
- For yeasts, the regulatory elements cant be moved too far away or it wont work
Models of action
- Enhancer: acts at a distance, piece of DNA that when put into report construct, can put in any orientation
anywhere relative to the transcription start site and it will turn on transcription
o Sequence of DNA that have many TF binding sites
- Silencer: similar to enhancer except its the negative regulator. Locally recruit repressive elements. Can spread,
but not many of these silencers present
- Insulator: blocks activity as go down the chromosome. The enhancer cannot get to promoter beucz theres
insulator in btw. Usually influence the DNA its on, so there may be a linear DNA scanning by them.
- Locus control region: not very common to have this arrangement in the genome
- Question skipped =D
Major areas of research
- Cataloging is done by diff methods
- Big area of research
- Many different proteins working together
Gene co-expression reflects gene function in mouse
- 2D Clustering diagram, aka heat map
- Genes that are needed in specific places are expressed there
- Most of the conserved/functional regions in the genome are the regulatory elements
81 DNA-binding domains in representative sequenced eukaryotes
- Putative TF: contains a domain that among characterized proteins is a TF
- Genes/binding sites are multiplied--> duplication
How do we determine sequence specificity of a DNA-binding protein?
- Could look in vivo or in vitro (pools of DNA or microarray)
- All bind to DNA sequences just the affinity is different
- Fav sequence: GGAATTTCC
- TF have to work together because the middle of the fav sequence is more flexible, so different proteins are able
to bind no specificity if only one protein, so need them to work together
Most mammalian TFs without known sequence specificity are C2H2 ZFs
- Direct:
- Sequence identity and motif: when proteins have more than 2/3 identical, generally they will have
indistinguishable biochemical identities (a rule of thumb)
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