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gene expression.docx

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Bhagwati Gupta

November 5 , 2013 Biology 2C03: Genetics Gene Expression Mechanisms for Regulating Gene Expression in Eukaryotes - Regulation and autoregulation at each step - What we have seen: 1) changes in chromosome structure e.g. histone modifications, nucleosome repositioning, epigenetics 2) Trascriptional regulation: transcription factors, enhances and activating proteins, silencers and repressors - Other ways 3) Post-transcriptional modification, RNA processing 4) RNA transport 5) Translation of mRNAs 6) mRNA stability and degradation 7) Silencing RNAs Intron - Major types of introns  Group 1 (some rRNA genes)  Group 2(some protein-coding genes of mitochondria, chloroplasts, etc.)  Nuclear pre-mRNA (protein-coding genes of the nucleus  tRNA - Splicing mechanism  Group 1 and 2: self-splicing  Nuclear pre-mRNA: spliceosome  tRNA: enzyme mediated Pre-mRNA Splicing Mechanism - Splicing requires 1) Access to conserved cis sequences in specific sites of the intron and exon (GU-AG rule) 2) Spliceosome omplex - 5’ GU sequence and 3’ AAG sequence that are recognized by the splicesome - End product is a spliced exon and a lariat - Process happens for all introns and we then get mature mRNA Nuclear Speckles and Splicing Factors - By studying simple model organisms you can learn principles of gene regulation - Splicing takes place in the speckle like regions: lots of proteins and high concentration of circular structures called ribonucleo particles RNPs - RNPs are complexes of proteins that reognige RNA and immature RNA - Remove introns and allow spliced mRNA - mRNA exported and translated to make proteins - Not all slipicing occurs in this region – but majority - Outside: spliceosome transport to spleckle region - DNA loops that are actively synthesized RNA Splicing: Importance of Maintaining the Reading Drame - MetVal added to get mature RNA is just one example - Occurs different between bacteria and mutlicell organisms Shine-Dalgarno Sequence - In prokaryotes only - shine-dalgarno sequence: sequence in promoteur region were polymerase and RNA complex bind and start to make this protein - 5’ untranslated region and 3’ untranslated region - Distinct start codon and distinct stop codon Steps of Transcription and Translation mRNA Processing in Development - In Drosophila sex determination and dosage compensation are established by the X:A (X to autosome) ratio  Females: X:A = 1  Males: X:A = 0.5  Activates pathway that leads to specification of female or male charaters - This information is transmitted to the sex determination gene - mRNA from the sex-lethal gene is controlled differently in males and females  Leads to sequential activation which leads to female or male  The first gene that is sequenced Specific genes are also required for Sex Determination - Sec lethal recessive or dominant - SXL protein required in females - Need both recessive alleles to express the characteristic - Embryo with two XX chromosomes and a recessive sex-lethal allele will die whereas those with XY will be male - XY with SXL will die - Recessive allele will kill the female, dominant will kill the male - Conclude: females require SXL, males do not - Transformer is the second gene transcribed, activated by sex lethal will result in female conversion to sterile male - Transformer mutant flies are all males - Doublesex mutations adapt intersex: needed to distinguish between male and female specific programs - Fruitless mutation: females are fine, males develop but do not have normal courtship behaviour and are behaviourally inhibited - This tells us that different developmental programs regulated by genes - Genes must be expressed at the right time and place for sex characters to properly develop Expression of SXL is Required for Female Development - SXL protein produced only in females - Open reading frame - E1 is the exon and the promoter is P (actEvates transcript starting E1) - Only XX embryo have early transcription beginning at E1 Maintenance of SXL Expression - Once SXL is made, that protein activates the female development program - Cooperates with other factors to give rise to different form of sex-lethal protein at later stage - Transcription begins from P in fLmales and males - Pre-mRNA is made - SXL made only in females and binds to exon 3 to protect the stop codon, prevents recognition - SXL protein masks exon 3 splice site; it is not recognized and it is spliced out as an intron = SXL late protein, turns on a cascade of female development - In males in the absence of SXL, exon 3 is incorporated, contains STOP codon = no functional product, no development pathway is activated - More SXL made in females Q1. How does X:A Ratio Activates Sxl Gene Function in Female Embryos Only? - Ratio is read by dosage compensation - Sisterless (protein) dimers are transcription factors that are active in females only and activate the Sxl gene - Sisterless does this by forming dimers - Sisterless and deadpan ratios plays a role in regulation of Sxl - Sisterless genes are X-linked (numerators) - Deadpan gene is autosomal (denominator) - In Females Excess sisterless product: 1:1 ratio there is enough sisterless to form dimers which leads to activation of Sxl - In males there are so few sisterless that will not activate the development program - But, what does SXL do? SXL Regualtes Female-Specific Splicing of tra gene - Male-specific splicing yields non-functional protein - Singular emchanism as the sex-lethal that inframes stop codon in exon 2 - Allows splicing to take place in a way the the stop codon is excluded in the mRNA - Females: TRA protein - SXL shifts the splicing forward so the stop codon frame is no longer there in mRNA of females - Males do not have a way to control the splicing and results in no tra protein TRA Regulates Female-Specific Splicing - Male-specific splicing of the dsx gene is a default pathway - Why do you need multi-layer regulation: complex process of
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