Lecture, chapter 12 - RNA processing

Today we finished chapter 12, on RNA processing.

We discussed the process of intron splicing, in which snRNPs ("snurps") play an important role, the different mechanisms of alternative splicing (promoter selection, tail site selection, exon cassette selection, trans-splicing), base modification (methylation and pseudo-urydilation), RNA editing, export of RNA to the cytoplasm, and mRNA degradation (in prokaryotes and eukaryotes).

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Lab 14a - Bionformatics

Screenshot of a typical BLAST output
(click on pic for a full size image)
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Today we had an extremely shallow introduction to the universe of bioinformatics. We had an overview of the main genetic information repositories in the U.S., Europe, and Japan (see previous post), with emphasis on the NCBI website, specially on its main database, GenBank, and one of its main tools, BLAST.

The goal for this lab is for students to get acquainted with BLAST, by "blasting" nucleic acid and protein sequences (the verb 'to blast' makes reference to using the BLAST feature in the NCBI website).

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Bioinformatics links for lab 14

The following links will provide fast access to the web pages you need to do your bionformatic exercises:

• National Center for Biotechnology Information (NCBI)
• DNA Data Bank of Japan (DDBJ)
• European Bioinformatics Institute (EBI)

• GenBank statistics
• Clustal W
• Phylogeny software

• NCBI's Coffee Break

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Lecture, chapter 12 - RNA processing

Today we started covering chapter 12, on RNA processing.

We discussed the kinds of processing that different RNA molecules undergo, in both eukaryotes and prokaryotes. We compared the kinds of RNA found in bacteria (regulatory RNA and tmRNA) with those find in eukaryotes (snRNA, snoRNA, scRNA, miRNA, siRNA...), of course, besides the "classics": tRNA, rRNA and mRNA, present in all cells.

We discussed mRNA processing more in depth than in previous chapters, and we introduced the basics of rRNA and tRNA post-transcriptional processing. When focused on mRNA we talked about 5'-capping and polyadenylation ("tailing"). On Friday, we'll talk about intron splicing.

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