Fine Structure and Analysis of Eukaryotic Genes.pptVIP

Fine Structure and Analysis of Eukaryotic Genes Split genes Multigene families Functional analysis of eukaryotic genes Split genes and introns The mRNA-coding portion of a gene can be split by DNA sequences that do not encode mature mRNA Exons code for mRNA, introns are segments of genes that do not encode mRNA. Introns are found in most genes in eukaryotes Also found in some bacteriophage genes and in some genes in archae R-loops can reveal introns Examples of R-loops in mammalian hemoglobin genes Comparison of cDNA and genomic clone maps can reveal introns, 1.6.3 Types of exons Finding exons with computers Ab initio computation E.g. Genscan: /GENSCAN.html Uses an explicit, sophisticated model of gene structure, splice site properties, etc to predict exons Compare with genomics and cDNA sequences BLAST2 alignments between cDNA and genomic sequences /blast/ Find exons for HBB Sequence for human beta-globin gene (HBB): Accession number L48217 Thalassemia variant Sequence for HBB mRNA NM_000518 Retrieve those from GenBank at NCBI (or the course website) Get the files in FASTA format Run Genscan and BLAST2 sequences Genscan analysis of HBB gene BLAST2: HBB gene vs. cDNA Introns are removed by splicing RNA precursors Alternative splicing can generate multiple polypeptides from a single gene Alternative splicing can generate multiple polypeptides from a single gene, part 2 Multigene families, e.g. encoding hemoglobin Blot-hybridization analysis showing multiple beta-like globin genes in mammals Maintainingsequence similarity in gene families:Unequal cross-oversand geneconversions Functional analysis of isolated genes Gene Expression: where and how much? A gene is expressed when a functional product is made from it. One wants to know many things about how a gene is expressed, e.g. In which tissues? At what developmental stages? In response to which environmental conditions? At which stages of the cell cycle? How much product is made? RNA blot-hybridizations = No