Genomes and chromosomes in flux

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Genome organization

• 11-27-2006

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Outline

• Genomic features
• Reference genome
• Comparing genomes
• The epigenome

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Describing a reference genome

• Genomic features to be identified
• Genes, exons, introns, UTRs, promoters,
  enhancers, insulators, non-coding RNAs (siRNA,
  miRNA), telomeres, SSRs, centromeres, transposons
  (MITEs, DNA elements, retroelements, helitrons)
• Meta-analysis
• Colinearity, duplication rates,
  expansion/contraction of gene families, gene
  number

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Comparing genomes within a species

• List of terms used to compare genomes within a
  species
  
• SNP, IDP, CNV (NIPS)
• How do these apply to marker types such as RFLP,
  CAPS etc
  

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Composition of plant genomes
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Meyers et al., 2001 Genome Res.
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Fine scale genome organization in maize
View 1 Widely separated genes with many
retrotransposons between genes
SanMiguel et al., 1998
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Transposons

• DNA elements
• Retrotransposons
• MITEs
• Helitrons - contains 5' TC and 3' CTRR termini as
  well as two short palindromic sequences near the
  3' terminus that potentially can form a 20-bp
  hairpin

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Transposable elements

• Transposable elements are mobile pieces of DNA
• Generally divided into two classes based on
  mechanism of transposition
  
• DNA transposons
• (Mu, Ac, En/Spm in maize)
• Compromise 2 of the maize genome
• move via a DNA intermediate (cut-and-paste)
• TIRs (Terminal inverted repeats)
• Retrotransposons
• Compromise 60 of the maize genome
• move via a RNA intermediate (copy-and-paste)
• LTRs (Long terminal repeats)

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Retrotransposon features
Gypsy-like retroelements
gag
protease
rt
endo
LTR
LTR
Copia-like retroelements
gag
protease
rt
endo
LTR
LTR

• Retrotransposons must be expressed in order to
  transpose
  
• The LTR sequences of retrotransposons act as
  promoters
  
• Each retrotransposon contains two promoters

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Helitrons

• Recently discovered as a new class of repetitive
  elements in Arabidopsis and C. elegans genome
  sequence
  
• Very hard to find bioinformatically
• Defined by 5 CT, 3 CTTR and secondary structure
  near 3 end
  
• Move via rolling circle replication
  (copy-and-paste with DNA intermediate)

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Defining the epigenome

• Epigenome any information encoded within the
  genome that is not based on sequence
  
• Defining epigenome likely includes DNA
  methylation, histone modifications, associated
  RNA, nucleasome arrangement and tertiary
  structure of DNA

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Hon RNA PolIV PcG
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Figure 5 Somatic instability of the peloric
phenotype correlates with demethylation of Lcyc.
a, Flowers from a peloric plant showing somatic
instability. Arrows point to extra spurs on the
lateral petals of the semipeloric flowers. The
almost wild-type flower on the left has an extra
dorsal stamen within the flower. b, DNA from
young leaves of wild-type () and peloric (P)
individuals digested and blotted as for Fig. 4b.
The first two lanes corresponds to DNA from
parental individuals lane 3, DNA from an F2
unstable mutant (U) lanes 46, DNA from cuttings
from the unstable plant with peloric (P),
semipeloric (SP) and near wild-type ()
phenotypes. Of the cuttings, only those with near
wild-type phenotype show extensive demethylation
of Lcyc. Based on the relative intensity of the
2.2-kb and 2.4-kb bands, semipelorics appeared to
less heavily methylated than pelorics, consistent
with their less extreme phenotype.
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