Ch 6t - Chapter 6: Understanding Function within a Genome...

Info iconThis preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
Chapter 6: Understanding Function within a Genome Molecular Genetics Lecture Outlines Studying transcriptome changes: Fig. 6.1: SAGE (serial analysis of gene expression). You could just clone all the cDNAs from a transcriptome and then sequence them to detemine which genes were turned on, but this would take a long time. Instead, clone little tiny 12-bp pieces of each cDNA into a “concatomer” (all the pieces stuck together in a row as a long chain of DNA). You know the ID of each tiny piece, so by sequencing the concatomer, you know all the cDNAs that are turned on. How to generate the concatomer? Start by binding the mRNAs with oligo dT bound to cellulose beads, then make the cDNAs right on column. Get rid of the bulk of each cDNA by digestion with a 4-base target restriction endonuclease (like Alu I), leaving you with a 256-base (average size) cDNA piece stuck on the column – the other pieces are washed off. Then, ligate a Bsm FI site onto the end of each cDNA piece. Bsm FI is unusual in that it cuts 10-14 bases away from the target. Thus, when you cut with this enzyme, you’ll release cDNA pieces about 12 bp long – just the size you needed! Ligate them all together as a concatomer and sequence the concatomer. Fig. 6.2 & 6.3 & 6.6: Analysis with chips and arrays. Chips contain random oligomers; arrays contain actual cloned cDNA sequences. Arrays contain sequences of actual mRNAs (cDNA) that are spotted onto the silicon wafer. With both analyses, add labeled cDNA to the chip or array and see which spots of the chip or array bind the cDNA. Look for changes in patterns between transcriptomes – transcriptomes from different tissues or from the same tissue in different pathological states. With the chip, you figure out what mRNA each oligo represents; with the array, you already know. Fig. 6.7: With chips & arrays, you can track the abundance of particular mRNAs under particular conditions and over time. Then you can express the relatedness of mRNAs by a dendrogram (tree-graph) and this relatedness is not by sequence but by function. Fig. 6.8:
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.

This note was uploaded on 04/15/2008 for the course BIO 4306 taught by Professor Kearney during the Spring '08 term at Baylor.

Page1 / 3

Ch 6t - Chapter 6: Understanding Function within a Genome...

This preview shows document pages 1 - 2. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online