PLANT GENETICS and MOLECULAR BIOLOGY
Department of Cell Biology & Molecular Genetics
Types of genes: ribosomal RNA (rRNA) 18S-5.8S-28S cluster, 5S tRNA mRNA Types of RNA polymerase Pol I (18S-5.8S-28S rRNA cluster) Pol II (mRNA) Pol III (tRNA and 5S rRNA) Functional elements in a gene (mRNA) -coding region codes for protein -5’ untranscribed region Promoter- initiates transcription TATA box: (TATAA) Initiator or inr element: (PyPyCAPyPyPyPy) -5’ untranslated region 5’ cap: 7’ methylated guanosine on end of mRNA- no DNA sequence element needed translation start site: optimal GTCGACCATGGTC -3’ untranslated region polyadenylation site: site where mRNA is cleaved and polyA tail is added sequence in some mammalian genes: AAUAA-N10-35¯ -Internal to coding region introns- DNA sequence that does not code for amino acids because it is removed from mRNA by splicing -plant consensus: 5’ splice site:GíGUAAGUAU Branch point: YNRAY 3’ splice site: U/A G/A UAGýGU underlined are invariant í is 5’ exon-intron boundary ý is 3’ intron-exon boundary Protein splicing- another twist on splicing. Intein is internal portion of a protein which can catalyze its removal from the protein. Gene Expression- how to modulate expression for each gene Transcription -elements that modulate transcription are usually upstream in the 5’ untranscribed region -enhancer elements produce overall higher transcription -signal-specific activators-induce transcription to specific stimuli -Higher order regulation -chromatin structure- organized around nucleosomes -DNA- 2nm -Histones 2a,2b, 3, 4 wrap 146 bp 10nm -histone H1- 6 nucleosomes per turn 30 nm -loops attach to scaffold every 30,000-90,000 bp , 700 nm scaffold- two proteins, one is topoisomerase -packaging- important for expression euchromatin-active heterochromatin-inactive -controlled by cytosine methylation (CpG)- associated with inactivated genes histone acetylation (activates)/deacetylation (inactivates) mRNA stability -determines half-life of mRNA -mechanisms: a) polyA shortening- determined by sequence in 3’UTR eg. UUAUUUA U/A U/A shortens half-life b) nonsense codon shortens halflife eg. DSR cryptic element (TGYYGATGYYYY in yeast) in coding region c) endonuclease site in 3’UTR or coding region eg. iron response cleavage at GAACAAG -a and b result in decapping and degradation by 5’-3’ exonuclease Alternate intron-exon splicing produces different products from one gene -e.g. Drosophila sex determination -protein can mask or enhance use at specific splice sites Links: Transcription topics - PLSC731 NDSU PLACE database- cis-acting elements in vascular plants
List of Gene finding programs-predict transcriptional start sites, intron/exon boundaries
Last revised: March 6, 2000- Straney