Julius B. Lucks/Meetings and Notes/SMBE2007/introns early introns late

= Scott Roy : Simplification and embellishment of eukaryotic gene structures - creeping intron loss and lineage specific evolution of (alternative) splicing. = Wed Jun 27 08:00:37 EDT 2007

Words to Look Up

 * Fugu

Talk

 * introns-middle
 * spliceosomal introns
 * specific ansecstral (not universal)
 * interrupt coding genes
 * cannot self-splice
 * need spliceosome
 * group II introns
 * bacterial/endosymbiotic genomes
 * interrupt RNA genes ...
 * self-splice
 * Donor(GU)-BranchPoint(A)-Acceptor(AG)
 * BP attacks donor
 * donor attacks the acceptor
 * 1978
 * discov 1977
 * Wally Gilbert - News and Views - Genes and Pieces
 * named introns
 * predicted alternative splicing
 * predicted domain shuffling
 * role in increasing recomb
 * Ford Doolittle (N&V 3 months later)
 * 'like to argue that eukaryotic genome as genes in pieces is primitive form'
 * argued introns early
 * introns-early predictions
 * intron positions correspond to protein structure
 * exons are 3n basepairss
 * if add new exon in middle - causes frameshift
 * introns late prediction
 * spliceosomal system derived from group II introns (transferred from mitochondrion)
 * data
 * protein gene-structure corr p ~ 10^-10
 * p-value exon length ~ 10^-10 (Arlin Stoltzfus group)
 * similarity between spliceosome and type II introns - convinced of introns-late
 * intron loss and gain
 * no clear phylogenetic trend in intron contents
 * could be lots of intron gain, or loss - can't tell direction
 * Coulomb-Huntigton, Majewski, PNAS, 2006
 * 10-15% intron positions shared across fungi, animals and plants

Questions
= Arlin Stoltzfus : The relationship of intron position to protein structural features = Wed Jun 27 08:01:54 EDT 2007
 * UMBI, NIST

Talk

 * functional interpretations
 * 'speed evolution' (Gilbert, 1978)
 * mediate chromatin structure
 * facilitate exon shuffling (Gilbert, 1986)
 * prevent homogenization of orthologs
 * represent a nexus of gene regulation
 * facilitate nonsense-mediated decay (Lynch)
 * Disruptive vs. Formative
 * Disruptive: some point whole protein coding genes
 * some time introns split these
 * Formative
 * assembly of exon coding mini-genes
 * to distinguish, need homology in intron sequences
 * intron seq evolve rapidly
 * exon shuffling creates new chimeric genes
 * generating predictions from the disruptive (insertional) model
 * introns gained non-randomly wrt nucleotide sequence

Conclusions

 * intron positions exhibit substantial corr with structural features
 * sec struct, solvent acc strongest
 * nucleotide model accounts for most of non-randomness
 * sig deviations remained

Questions
= Eugene Koonin : Evolutionary dynamics of introns and their role in eukaryogenesis = Wed Jun 27 08:03:16 EDT 2007

Talk

 * outline
 * evol dynamics of introns - brief summary
 * adaptive intron gain?
 * glimpse of the pre-intron phase of eukaryotic evol
 * role of introns in eukaryogenesis
 * post-mortem on 'introns-early vs introns-late'
 * intron pos highly conserved
 * Carmel, Koonin, Gen. Res, 2007, 'Evolutionary conserved genes preferentially accumulate introns.'
 * chloroplast-derived genes in plants - intronless when entered eukaryotic genome
 * intron density lower than ancestral euk genes, but only by a little bit
 * hypothesis - nucleus evolved as defense device against massive intron invasion
 * why have nucleus - decouples transcription and translation, complicated export, ...
 * prokaryotes have introns too (very few)
 * bacteria - group II introns are retroelements that are deleterious when inserted into important protein-coding genes
 * selfish elements
 * alpha-proteobacterio - rich in group II introns
 * speculation - in wake of mitochon endosymb - symbionts group II introns went on a rampage
 * evol of the nucleus
 * indep compl evidence of mitochond triggering nucleogenesis - unleashed group II introns, but also supplied essential building blocks
 * Mans, Cell Cycle, 2004, 3, 1612 - com genomics, evol and origins of nucl envelope and nucl pore complex
 * Martin, Koonin, Nature, 440, 41, 2006
 * chain of causation for origin of nucleus
 * origin of spliceosome
 * inactivation of RT in invading group II introns - loss of mob - prevention of further damage
 * Koonin, Biol Direct, 2006, 14, 1 - origin of introns and their role in eukaryogenesis: compromise solution ...
 * no introns in protein-coding genes or spliceosome in prokaryotes
 * no support for introns-early from intron phase distribution
 * no support for introns-early from intron-domain correspondence