BIOL 311 Human Genetics Fall 2006 Lecture Regulation of Gene Expression Reading Chap 10 Lecture outline 1 Levels of control 2 Histone modification 3 RNA polymerase II transcription 4 Transcription factors 5 Steroid receptors 6 Alternate promoters and alternate splicing 7 Epigenetic mechanisms Lecture 1 Levels of control of gene expression transcriptional control control determines whether or not transcription is initiated requires promoter of gene transcription factors bind to promoter and recruit RNA polymerase to initiate transcription post transcriptional regulation of gene expression control after pre mRNA synthesis can involve control of RNA processing mRNA transport translation mRNA stability protein processing protein targeting protein stability epigenetic mechanisms changes that are heritable but not due to changes in the order of bases on DNA main mechanism is DNA methylation Methylation represses gene expression and determines which allele of a gene is expressed for certain genes immunoglobulin genes genes on X chromosome etc 2 Histone modification histones are basic proteins that help compact DNA act as generalized repressors of transcription dense packed chromatin transcriptionally inactive to open up the chromatin structure chemical groups are added to histones to make conditions more favorable for transcription Histone acetylation 1 Add acetyl group to epsilon NH2 group of lysines on histone H3 and H4 Acetylation reduces the positive charge of histone side chains HATs Histone acetylated histone HDACs histone deacetylases Many other types of modifications of histones occur methylation phosphorylation ubiquitination ADP ribosylation Fig 10 1 Some histone modifications shown histone code 3 RNA polymerase II transcription Eukaryotes have different RNA polymerases to transcribe different categories of gene rRNA genes RNA polymerase I transcribes 18S 5 8S 28S rRNA genes tRNAs 5S rRNA some snRNAs transcribed by RNA polymerase III protein coding genes and some snRNAs transcribed by RNA polymerase II RNA polymerase II 12 subunits catalyzes RNA synthesis associates with about 40 other subunits that are transcription factors TFIID TATA binding protein Also TFIIB A F E H 4 Transcription factors basal transcription factors proteins that assist transcription in many tissues tissue specific transcription factors proteins only present in certain tissues that enhance or repress transcription bind DNA may activate transcription directly or bind to other proteins coactivators that activate transcription transcription factors often have conserved domains that mediate protein interactions DNA binding domains Zinc fingers Fig 10 6 cys2his2 type and cys4 type Homeodomain helix turn helix Fig 10 8 Helix loop helix Fig 10 8 Protein interaction domain Leucine zipper 2 Activation domains more difficult to define Glutamine rich Proline rich 5 Steroid receptors Respond to small molecules ligands in environment Fig 10 10 Ligand Glucocorticoids Estrogen Thyroid hormone Vitamin D Retinoic acid Receptor GR ER TR VDR RAR Have similar DNA binding domains cys4 zinc fingers Ligand binding activates receptor Recognition sites on DNA are similar Receptor ligand interactions mostly occur in the cytoplasm Other transcription factors mediate environmental responses Chemical signal cAMP Serum growth factor Phorbol esters Transcription factor CREB ATF SRF serum response factor AP 1 dimer of fos jun Transcription factors often carry out the final stage of activation triggered by an environmental signal Signal receptor cell signaling i e kinase cascade activate transcription factor moves to nucleus to activate gene expression 6 Alternate promoters and alternate splicing human genome project 35 000 human genes initial predictions were for 80 000 100 000 why the discrepancy Single gene can have multiple transcription start sites some genes alternate splicing many genes when different selections of exons are used in making different mRNAs from the same gene Example of multiple promoters Dystrophin gene 79 exons 2 4 Mb Xp21 location Altered in two forms of muscular dystrophy 3 Duchenne s MD severe form usually due to large deletions in gene Becker s MD milder form usually due to small mutations in gene At least 7 distinct promoters for dystrophin gene Active in different tissues First three promoters when used produce large transcript encoding 427 kDa protein Alternate splicing and alternate poly A addition sites produce many different premRNAs encoding different proteins Various alternate splicing scenarios Fig 10 15 Alternate splicing of Wilms tumor protein Wilms tumor kidney tumor WT1 gene altered in some inherited kidney cancers Single gene encodes 24 isoforms o Three possible start codons o RNA editing in exon 6 some RNA bases altered in pre mRNA o Alternative splicing Produces isoforms with different functions DsCam Drosophila gene with 38 000 possible isoforms 7 Epigenetic mechanisms Heritable states which do not depend on DNA sequences Examples DNA methylation Chromatin remodeling Histone modification Fig 10 18 Mechanism of DNA methylation CpG target sequence Keep the same pattern of methylation as DNA is replicated and passed on Why is DNA methylated Protect from transposons NO Regulate gene expression Generally silences gene expression Recruits HDAC leads to deactylation of histone helping to shut off gene expression 4