BSCI222 Exam IIILectures 17-22Lecture 17 & 18: Gene Expression in Eukaryotes Chapter 17(2-7,1,17,18);14(16-18);16(8,9); 18(1-4,7,8,11,1,16-8,20,22,26,29)o Differences from prokaryote regulationoo Nucleuso Large amounts of non-coding DNAo Intronso Coupled (prokaryote) vs. uncoupled transcription/translationo Polycistronic (prokaryote) vs. monocystronico Lots of RNA modificationo Multicellularityo Chromatin Modification of chromatin structure occurs in eukaryoteso DNase I Hypersensitivityo Several changes in chromatin are observed when genes become transcriptionally activeo When they become transcriptionally active, regions around the gene become highly sensitive to the action of DNase Io DNase I hypersensitive sites frequently develop about 1000 nucleotides upstream of the start site of transcriptiono Relaxation of chromatin allows regulatory proteins access to binding sites on the DNAo Histone modificationo Two domains:  A globular domain that associates with other histones and the DNA A positively charged tail domain that probably interacts with the negatively charges phosphate groups on the backbone of the DNAo Tails are modified by the addition or removal of phosphate groups, methyl groups, or acetyl groupso Histone code because they encode information that affects howgenes are expressedo Methylation of Histoneso Addition of methyl groups to the tails of the histoneso Addition can bring about the activation or repression of transcriptiono Addition of three methyl groups to lysine 4 in the tail of the H3 histone protein  most commono Acetylation of Histoneso Addition of acetyl groups usually stimulates transcriptiono Acetylation of histones controls flowering in ArabidopisFLC gene suppresses flowering until after an extended period of coldnessFLD stimulates flowering by repressing the action of FLC FLD encodes a deacetylase enzyme which removes acetyl groups from histone proteins in the chromatin surrounding FLCThe removal of acetyl groups from histones alters chromatin structure and inhibits transcriptiono Chromatin Remodelingo Chromatin-remodeling complexesSome transcription factors and other regulatory proteins alter chromatin structure without altering the chemical structure of histones directlySWI-SNF found in yeasto Major modes of Regulation o Transcriptional control o Post-transcriptional control o Translational control o Transcriptional controlo InitiationAccess to promoters—controlling chromatin (chromatin modification ^^^^)Rate of assembly of initiation-RNA Pol II-Pre-initiation complex=gun-Rate of assembly can vary-Activator proteins—Transcription factorso Stimulate and stabilize the basal transcriptionapparatus at the core promotero Mediator- transcriptional activator proteins make contact with the mediator and affect the rate at which transcription is initiatedo Two functions: 1) capable of binding DNA at a specific base sequence (usually a consensus sequence in a regulatory promoter or enhancer) and 2) able to interact with other components of the transcriptional apparatus and influence the rate of transcriptiono Bind sequences in promoters, distal enhancerso Recruit components to promoterRate of transition to elongation-Activators interact with mediator-Mediator interacts with Pol II-Mediator is like a switchboard-A mediator is a multi-protein complex-Integrates signals that affect Pol IICarboxy terminal domain of Pol II is phosphorylated—does this trigger the switch to elongation?-Consists of tandem repeats of YSPTSPSHow to prevent ‘shorts’ – activators interacting with the wrong intitiation complex?-INSULATORS! -Most enhancers are capable of stimulating any promoter in their vicinities. Their effects are limited, however, by insulators which are DNA sequences that block or insulate the effect of enhancers in a position-dependent manner-Genetic insulators prevent activators from interactingwith the wrong o Post Transcriptional regulation alternative splicingT-antigen geneSF2 enhances the production of mRNA encoding the small tantigen SF2 has two binding domains: one domain is an RNA-binding region and the other has alternating serine and arginine amino acidsSplicing can be regulated by splicing activators and repressors-Example from slideshow: exon 4 has weak 3’ splice site – too weak and splicing doesn’t occur-In females the Tra protein is expressed and acts as a splicing activator-3 + 5 and 3 + 4 + 5o Translational control—global Phosphorylating elF2 inactivates it all –translation stopsMechanisms of gene regulation by RNA interference-Small interfering RNAs and microRNAs regulate gene expression through at least 4 distinct mechanisms 1)cleavage of mRNA 2) inhibition of translation 3) transcriptional silencing 4) degradation of mRNA-RNA cleavageo RISCs that contain an siRNA pair with mRNA molecules and cleave the mRNA near the middle of the bound siRNA o Cleavage is sometimes referred to as ‘slicer activity’o After cleavage, the mRNA is further degraded-Inhibition of translationo Some miRNAs regulate genes by inhibiting the translation of their complementary mRNAso The exact mechanism by which mrRNAs repress translation is not known-Transcriptional silencingo Other siRNAs silence transcription by altering chromatin structureo siRNAs combine with proteins to form a complex called RITs which is analogous to RISCo The siRNA component of RITS then binds to its complementary sequence in DNA or an RNA molecule in the process of being transcribed and represses transcription by attracting enzymes that methylate the tails of histone proteins -Slicer-independent degradation of mRNAo A final mechanism by which miRNAs regulate gene expression is by triggering the decay of mRNA in a process that does not require slicer activitySome genes are regulated by processes that affect translation or by modifications of proteinsEpigenetics-Imprinting—same genotype & different phenotype-Heritable changes in gene expression not associated with changes in the DNA code-Human exampleo If deletion is inherited from father: prader-willi syndrome, mother: angelman syndromeSame genotypes, different phenotypes-Mechanisms:o DNA methylationUsually occurs at CpGs, methyltransferaseBecause it occurs at CpGs, patterns can be copied following replicationSo methylation patterns can be inheritedMethylated DNA is transcriptionally inactiveo Chromatin modification-Many diseases