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biol139-lecture34-2011 - BIOL 139 Gene Regulation in...

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Unformatted text preview: BIOL 139 Gene Regulation in Eukaryotes Gene Chapter 18 Text pages 645-653 and 658-661 Text pp 543 - 561 igenetics pp Gene Regulation of Transcription in Eukaryotes: Gene • transcription in eukaryotes is similar to prokaryotes but control is much more complex, usually at initiation (RNAP) • prokaryotes organize genes into operons, eukaryotes generally do not • In eukaryotes 3 RNAPs (I, II and III) in nucleus transcribe different In set of genes All protein-encoding (structural) genes are transcribed by genes RNA polymerase II RNA (all mRNA) How cis-acting and trans-acting factors affect transcription cis-acting trans Enhancers Enhancers Enhancers are: DNA sequences that serve as attachment sites for DNA-binding proteins to regulate initiation of transcription at the promoter region Trans-Acting Factors (Transcription Factors) called transcription factors transcription Encode proteins that interact directly/indirectly with target DNA (cis-element) to activate or repress initiation of transcription (basal) Genes may be located elsewhere in genome located Cis-acting regulatory regions recognized by pol II: no one specific sequence recognized by RNAP II, instead a protein-coding gene may have SEVERAL different cis sequences for recognition and SEVERAL regulation Promoter Core Promoter +1 site Initiation of transcription Core Promoter – always close to the gene’s coding region. Includes an initiation site (+1site) and usually has a “TATA box” initiation “TATA consisting of ≈ 7 nucleotides: TATA(A or T)A(A or T) ∼ -30bp TATA(A TATA Box: - unusual not to have one • required for proper initiation at +1site • if not present get non-specific initiation from ≈ 20 sites Other cis-promoter elements include CAAT box, -75 to -100, GC box -100 or more Cis-acting regulatory regions recognized by pol II: Distal elements upstream (can be 1,000’s of bp away) Distal enhancers, silencers, inhibitors, tissue-specific regulators, activators Enhancer: • most eukaryotic genes regulated by enhancers • regulatory site that can be located far away (>10,000 bp) from the promoter, or can be quite close. • Interact with other transcription factors (TF’s) at core promoter transcription region + RNAP II to stimulate or repress transcription RNAP stimulate or But regulatory elements (cis-elements) need to bind to specific But -elements) proteins (TF’s) to work proteins Here’s where it gets complicated…… 2 categories of Transcription Factors to regulate RNAP II: General (basal) TF and Regulatory TF General Regulatory Basal factors: • required for binding to the promoter region to maintain a promoter basal level of transcription basal • respond to specific cis-elements that are found in nearly all promoters that are recognized by RNAP II (protein-encoding genes) Function is to direct RNAP II to promoter region and help initiate transcription transcription TAFs – TBP-associated factorsTAFs other proteins that bind to TBP TBP – TATA box-binding protein. Essential to the initiation of transcription from all class II genes with a TATA box. TATA Regulatory Transcription Factors: not required for initiation • react to specific sequences in certain genes certain • activators or repressors bind to enhancers activators Regulatory Element Activator TAD TAD DNA-binding domain interacts with cis-element Regulatory Protein (TF) Basal Factor TBP TAD- interacts with other proteins (other TFs, RNAPII etc) Enhancer TATA box Two important structural domains for Two transcription factors (TF) transcription TAD - DNA-binding domain and a DNA-binding transcription-activation domain (TAD) transcription-activation Basal TF’s Transcriptional activators bind to specific enhancers Cis element with basal TF DNA-binding domain -transcription-activation domain (TAD) Protein-protein interaction Transcriptional activators Transcriptional bind to enhancer sequences and can bind enhancer increase transcription 100-fold (or more !) above the basal level above Can increase transcription 100-fold (or more!) above the basal level All transcription factors have two important structural domainsthe DNA-binding domain and the transcription-activation domain (or TAD) Basal factors are required for binding to the promoter to maintain a basal level of transcription TATA box-binding protein. Essential to the initiation of transcription from all class II TATA genes with a TATA box. TATA DNA-binding Proteins: DNA-binding • most eukaryotic activators must form dimers to function dimers Usually a homodimer (2 ID copies of polypeptide) homodimer • 2 subunits • allows recognition to be specific with strong binding specific Homomers – multimeric proteins composed of identical subunits. Two subunits : homodimers subunits. Heteromers – multimeric proteins composed of nonidentical subunits. Two subunits : heterodimers Activator protein dimers Transcriptional repressors diminish transcriptional activity May bind to enhancer element (competitive) to prevent enhancement or may bind to other specific DNA encoded sequences (silencers) to diminish transcription Transcriptional repressors Repressor binds directly to DNA • diminish transcriptional activity diminish Repressor does not directly bind to DNA, but binds to TAD region Repressor Next topic Next Genes and mutation pp 207 - 226, 241-243 pp 377 - 397 igenetics ...
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