Hoorcollege 7
-> each protein domain recognizes a relatively short sequence, but duplication or tandem
multimerization results in longer sequence targets
helix-turn-helix proteins -> eiwit komt ertussen in de grote groeve van het DNA
- proteins can “read” DNA sequence via interaction in major groove
- helix-turn-helix protein
- homeodomain protein
- leucine zipper protein
- helix-loop-helix protein
- b sheet DNA recognition proteins
- zinc finger proteins
transcription factors can bind to DNA cooperatively
- when they bind together to the DNA, the affinity is higher
- when they bind separately to the DNA, the affinity is lower
nucleosomes can promote cooperative binding of transcription factors to DNA
conclusions:
- eukaryotic gene transcription is regulated on a per gene basis
- transcription factors recognize specific sequences and act cooperatively to regulate
transcription
~5-10% of all genes code for transcriptional regulators
RNA seq -> identify exons and illustrate differential gene expression in different cell types
regulatory DNA defines gene expression patterns during development and cell differentiation
- the genome is the same in all cell types, but different genes are active in different
tissues because different transcription factors bind to them
, ChIP assay: chromatin immunoprecipitation
- to which sequence within the genome does a TF bind?
- which TF binds to a given regulatory element?
finding regulatory sequences -> use of reporter genes
- stuk DNA pakken uit genoom en plakken achter een gen dat makkelijk zichtbaar is
- zodra deze wordt afgeschreven en zichtbaar is in de cel kun je ook direct zien wat
dat stuk DNA doet (like LacZ or GFP)
discovering gene expression patterns ->use of RNA in situ hybridization
- look at expression of mRNA in certain tissues
-> regulatory elements controlling the expression of TF and developmental regulators
diverged in early vertebrate evolution
-> cis-regulatory elements of an eukaryotic genen can be spread over long distances and
come together through DNA looping
the large size of gene control regions complicates molecular definition of a ”gene”
most eukaryotic genes are controlled independently of each other
-> eukaryotic transcription regulators bind weakly to each other and assemble into
complexes on the DNA
heel veel regulatoren kunnen als enhancers én als repressors dienen
-> transcription activators alter chromatin structure before DNA transcription/replication
histone acetyltransferase histone kinase and chromatin remodeling complex are
transcription co-activators
-> each protein domain recognizes a relatively short sequence, but duplication or tandem
multimerization results in longer sequence targets
helix-turn-helix proteins -> eiwit komt ertussen in de grote groeve van het DNA
- proteins can “read” DNA sequence via interaction in major groove
- helix-turn-helix protein
- homeodomain protein
- leucine zipper protein
- helix-loop-helix protein
- b sheet DNA recognition proteins
- zinc finger proteins
transcription factors can bind to DNA cooperatively
- when they bind together to the DNA, the affinity is higher
- when they bind separately to the DNA, the affinity is lower
nucleosomes can promote cooperative binding of transcription factors to DNA
conclusions:
- eukaryotic gene transcription is regulated on a per gene basis
- transcription factors recognize specific sequences and act cooperatively to regulate
transcription
~5-10% of all genes code for transcriptional regulators
RNA seq -> identify exons and illustrate differential gene expression in different cell types
regulatory DNA defines gene expression patterns during development and cell differentiation
- the genome is the same in all cell types, but different genes are active in different
tissues because different transcription factors bind to them
, ChIP assay: chromatin immunoprecipitation
- to which sequence within the genome does a TF bind?
- which TF binds to a given regulatory element?
finding regulatory sequences -> use of reporter genes
- stuk DNA pakken uit genoom en plakken achter een gen dat makkelijk zichtbaar is
- zodra deze wordt afgeschreven en zichtbaar is in de cel kun je ook direct zien wat
dat stuk DNA doet (like LacZ or GFP)
discovering gene expression patterns ->use of RNA in situ hybridization
- look at expression of mRNA in certain tissues
-> regulatory elements controlling the expression of TF and developmental regulators
diverged in early vertebrate evolution
-> cis-regulatory elements of an eukaryotic genen can be spread over long distances and
come together through DNA looping
the large size of gene control regions complicates molecular definition of a ”gene”
most eukaryotic genes are controlled independently of each other
-> eukaryotic transcription regulators bind weakly to each other and assemble into
complexes on the DNA
heel veel regulatoren kunnen als enhancers én als repressors dienen
-> transcription activators alter chromatin structure before DNA transcription/replication
histone acetyltransferase histone kinase and chromatin remodeling complex are
transcription co-activators
