Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression;...

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Today • Building a genome – Nucleotides, GC content and isochores – Gene structure and expression; introns – Evolution of noncoding RNAs • Evolution of transcription – Transcription & Translation – Recoding and RNA editing – Evolution of the genetic code

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Transcript of Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression;...

Page 1: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Today• Building a genome

– Nucleotides, GC content and isochores– Gene structure and expression; introns– Evolution of noncoding RNAs

• Evolution of transcription– Transcription & Translation– Recoding and RNA editing– Evolution of the genetic code

Page 2: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

The four nucleotides of DNA

Page 3: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Watson & Crick actually got it wrong …

Page 4: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

GC content versus optimal growth temperature

Genome-wide

Ribosomal RNAs

Page 5: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Environmental signature on GC content

Page 6: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Structure of human isochores

Page 7: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Lack of isochores in lizards

Page 8: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

GC-content correlates with recombination rate

Page 9: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

A

B

C{ AAAAAA {

Influences gene from afar….

D

EF G

GH

{

A._______________B. _______________C. _______________D. _______________E. _______________F. _______________G. _______________H. _______________I. _______________

I I

Anatomy of a eukaryotic gene

Page 10: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Introns cleaved out by the spliceosome

Page 11: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Phylogenetic distribution of introns implies recent origin

Page 12: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Intron phase and size

Page 13: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Rotem Sorek et al. Genome Res. 2003; 13: 1631-1637

Figure 3 Human-mouse alignment of the KCND3 gene, corresponding to RefSeq NM_004980 (from VISTA browser, http://pipeline.lbl.gov/vistabrowser/)

Intronic regions adjacent to exons are often conserved

Page 14: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

2005: Widespread transcription in the human genome

revealed by microarray analysis

Page 15: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Fast forward 2010: Expression tracks known genes closely

Page 16: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Number of regulatory genes (R) vs. total number of genes (G)

Circles - Bacteria; triangles - Archaea R = 0.00002G2

Mycoplasmagenitalium

Bradyrhizobiumjaponicum

Page 17: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Does ‘noncoding DNA’ increase genomic complexity?

Page 18: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Was eukaryotic complexity released by noncoding RNAs?

Page 19: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

MicroRNAs - a new class of small RNAs with big roles in development

and evolution

Page 20: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Translational repression by microRNAs

Page 21: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

microRNAs as cladistic characters

Page 22: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Explosive diversity of cichlid fish

Page 23: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Rapid evolution of microRNA targets – a link with speciation?

Page 24: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

The ‘universal’ genetic code

Page 25: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.
Page 26: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Translation

Page 27: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Phe 12s rRNAVal

16s rRNA

LeuIle

Gln

Met

Trp

Ala

Asn

Cys

Tyr

COI

SerAspCOII

LysATP8

ATP6COIII

GlyNADH3

Arg

NADH4L

NADH4

His

Ser

Leu

NADH5

Cyt b

Thr

Control Region

Pro

NADH6

Glu

noncoding

Structure of vertebrate mitochondrial DNA (~17,000 bp)

rRNA genes

tRNA genes

ATP synthase genes

Cytochrome bc1 complex

Cytochrome Oxidase

NADH:Ubiquinone Oxidoreductase

NADH1

NADH2

Page 28: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Four ways to change the coding of amino acids from RNA

Page 29: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

Wobble rules in various organisms

base modifications in tRNAs can increase decoding breadth

Page 30: Today Building a genome –Nucleotides, GC content and isochores –Gene structure and expression; introns –Evolution of noncoding RNAs Evolution of transcription.

A code that minimizes polarity changes better than the universal code


Group II Introns: Mobile Ribozymes that Invade DNAcshperspectives.cshlp.org/content/3/8/a003616.full.pdf · Finally, trans-splicing group II introns are variants caused by genomic

Group II Introns: Mobile Ribozymes that Invade DNAcshperspectives.cshlp.org/content/3/8/a003616.full.pdf · Finally, trans-splicing group II introns are variants caused by genomic

A unique group of self-splicing introns in bacteriophage T4nopr.niscair.res.in/bitstream/123456789/15315/1/IJBB 38(5) 289-293… · A unique group of self-splicing introns in bacteriophage

A unique group of self-splicing introns in bacteriophage T4nopr.niscair.res.in/bitstream/123456789/15315/1/IJBB 38(5) 289-293… · A unique group of self-splicing introns in bacteriophage

Long-term evolution of the S788 fungal nuclear small ...dblab.rutgers.edu/home/downloads/Files/Haugen et al RNA 2004.pdfRNA secondary structures of these introns revealed a very similar

Long-term evolution of the S788 fungal nuclear small ...dblab.rutgers.edu/home/downloads/Files/Haugen et al RNA 2004.pdfRNA secondary structures of these introns revealed a very similar

Splicing RNA: Mechanisms. Splicing of Group I and II introns Introns in fungal mitochondria, plastids, Tetrahymena pre-rRNA Group I –Self-splicing –Initiate.

Splicing RNA: Mechanisms. Splicing of Group I and II introns Introns in fungal mitochondria, plastids, Tetrahymena pre-rRNA Group I –Self-splicing –Initiate.

REVIEW Open Access Bacterial group I introns: mobile RNA ... · 2/15/2018 · REVIEW Open Access Bacterial group I introns: mobile RNA catalysts Georg Hausner1, Mohamed Hafez2,3 and

REVIEW Open Access Bacterial group I introns: mobile RNA ... · 2/15/2018 · REVIEW Open Access Bacterial group I introns: mobile RNA catalysts Georg Hausner1, Mohamed Hafez2,3 and

Origin and Evolution of Group I Introns in Cyanobacterial ... · the trees were built by a neighbor-joining algorithm (33). The robustness of the tree topologies was tested by bootstrap

Origin and Evolution of Group I Introns in Cyanobacterial ... · the trees were built by a neighbor-joining algorithm (33). The robustness of the tree topologies was tested by bootstrap

National Center for Biotechnology Information Evolution of eukaryotic genomes: remarkable conservation and massive loss of genes and introns Eugene V.

National Center for Biotechnology Information Evolution of eukaryotic genomes: remarkable conservation and massive loss of genes and introns Eugene V.

NATURAL SELECTION AT MAJOR HISTOCOMPATIBILITY …webpages.icav.up.pt/ptdc/BIA-BEC/104981/2008/25.pdf · e-mail: austin@hugaus3.bio.psu.edu KEY WORDS: adaptive evolution, introns,

NATURAL SELECTION AT MAJOR HISTOCOMPATIBILITY …webpages.icav.up.pt/ptdc/BIA-BEC/104981/2008/25.pdf · e-mail: [email protected] KEY WORDS: adaptive evolution, introns,

Introns and Exons DNA is interrupted by short sequences that are not in the final mRNA – Called introns – Exons = RNA kept in the final sequence.

Introns and Exons DNA is interrupted by short sequences that are not in the final mRNA – Called introns – Exons = RNA kept in the final sequence.

An evaluation of the evolution of the gene structure of ... · The gene structure of three exons and two introns is remarkably conserved. However, additional lineage-specific introns

An evaluation of the evolution of the gene structure of ... · The gene structure of three exons and two introns is remarkably conserved. However, additional lineage-specific introns

Organellar Introns Organellar genomes contain 3 types of introns: 1. Group I 2. Group II (evolutionary precursors to nuclear mRNA/spliceosomal introns)

Organellar Introns Organellar genomes contain 3 types of introns: 1. Group I 2. Group II (evolutionary precursors to nuclear mRNA/spliceosomal introns)

DNA Replication--- transcription--- translation · When the RNA molecules are formed, both the introns and exons are copied from the DNA. However, introns are cut out of RNA molecules

DNA Replication--- transcription--- translation · When the RNA molecules are formed, both the introns and exons are copied from the DNA. However, introns are cut out of RNA molecules

Introns increase gene expression in cultured maize cellsgenesdev.cshlp.org/content/1/10/1183.full.pdf · Introns increase gene expression in cultured maize cells Judy Callis, ~ Michael

Introns increase gene expression in cultured maize cellsgenesdev.cshlp.org/content/1/10/1183.full.pdf · Introns increase gene expression in cultured maize cells Judy Callis, ~ Michael

Introns: structure and functions

Introns: structure and functions

Plant intron sequences: evidence for distinct groups of introns

Plant intron sequences: evidence for distinct groups of introns

The Vertebrate Genome: Isochores and Evolution ' - Molecular

The Vertebrate Genome: Isochores and Evolution ' - Molecular

Evolution of the U2 Spliceosome for Processing …...the non-canonical (and canonical) introns of F. borealis are spliceosomal. Figure 3. Splicing Inhibitor Assay (A) RT-PCR was used

Evolution of the U2 Spliceosome for Processing …...the non-canonical (and canonical) introns of F. borealis are spliceosomal. Figure 3. Splicing Inhibitor Assay (A) RT-PCR was used

Addition of Multiple Introns to a Cas9 Gene Results …...2020/04/03  · Addition of Multiple Introns to a Cas9 Gene Results in Dramatic Improvement in Efficiency for Generation of

Addition of Multiple Introns to a Cas9 Gene Results …...2020/04/03  · Addition of Multiple Introns to a Cas9 Gene Results in Dramatic Improvement in Efficiency for Generation of

Group I introns

Group I introns

Excision of Intron Sequences. Splicing Removal of introns must be very precise. Conserved sequences for removal of the introns of nuclear mRNA genes.

Excision of Intron Sequences. Splicing Removal of introns must be very precise. Conserved sequences for removal of the introns of nuclear mRNA genes.