Nova regulates brainspecific splicing to shape the synapse

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Nova regulates brain-specific splicing to
shapethe synapse

• VOLUME 37 NUMBER 8 AUGUST 2005 NATURE
  GENETICS
• ???
• 2006.10

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introduce

• cis elements (sequences)
• 5 Splice Site and 3 Splice Site
• ESE (Exonic Splicing Enhancer) and ESS (Exonic
  Splicing Silencer)
• ISE (Intronic Splicing Enhancer) and ISS
  (Intronic Splicing Silencer).
• Many sequences function is distinct in different
  gene and different position.

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introduce

• trans elements
• U1,U2
• Other splicing regulate elements (proteins even
  RNA). SR proteins, hnRNPA1, fox1 nova, etc.

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summary

• they carried out genome-wide quantitative
  analysis of alternative splicing using a custom
  Affymetrix microarray to assess the role of the
  neuronal splicing factor Nova in the brain.

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summary

• they used a stringent algorithm to identify 591
  exons that were differentially spliced in the
  brain relative to immune tissues, and 6.6 of
  these showed major splicing defects in the
  neocortex of Nova2-/- mice. they tested 49 exons
  with the largest predicted Nova-dependent
  splicing changes and validated all 49 by RT-PCR.

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summary

• They analyzed the encoded proteins and found that
  all those with defined brain functions acted in
  the synapse (34 of 40, including neurotransmitter
  receptors, cation channels, adhesion and scaffold
  proteins) or in axon guidance (8 of 40).
  Moreover, of the 35 proteins with known
  interaction partners, 74 (26) interact with each
  other. Validating a large set of Nova RNA targets
  has led us to identify a multi-tiered network in
  which Nova regulates the exon content of RNAs
  encoding proteins that interact in the synapse.

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significance

• No study has undertaken a genome-wide analysis to
  address statistically the functional coherence of
  genes coregulated at the level of alternative
  splicing.

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Nova1 and nova2

• neuron-specific KH-type RNA binding proteins.
• Nova-RNA structural studies Nova knockout mice,
  RNA cross-linking and immunoprecipitation (CLIP)
  and biochemical analysis suggested that Nova
  might preferentially target RNAs encoding
  proteins with roles in neuronal inhibition.

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Back ground

• To address this hypothesis systematically, they
  undertook a genome-wide screen to identify and
  validate Nova-dependent alternatively spliced
  transcripts in brain.

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analyse array data
The algorithm to calculate the change in fraction
of exon inclusion (?I) is based on the decrease
in probe set 12-12a and increase in probe set
12-13 normalized signals between the two
compared samples
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Array analysis

• Data were quantified as the change in the
  fraction of exon inclusion (?I), where a ?I value
  of 0.5 indicates a 50 increase and a ?I value of
  0.5 indicates a 50 decrease in exon inclusion in
  the first of the two compared samples.
• They identified 4,776 different spliced exons
  from 3,008 genes.

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Nova2 is not expressed in thymus(??), and nova1
is not expressed in neocortex(???) . Therefore,
the ?I wont be too large.
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Comparison of spinal cord(??) VS thymus (??) and
cmparison of midbrain(??) VS thymus. They have
identified 1,239 changes with ?Igt0.2 that were
common to both spinal cordthymus and
midbrain-thymus comparisons. When they expanded
this analysis to compare splicing in all brain
regions with splicing in either thymus or
spleen, we found that 12 (591 of 4,776) of
exons showed the same differential splicing
pattern in all comparisons (?Igt 0.2.
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They found 53 exons with ?I gt0.20 in both
samples (Fig. 2c). Moreover, all 41 exons with?I
gt0.24 in one triplicate correlated (R2 0.94)
with predicted changes in the second triplicate.
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These splicing changes did not follow a normal
distribution but affected a specific subset of
alternative exons(blue line). kgt3 represents a
distribution with significant outliers.
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RT-PCR validate
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RT-PCR results for 49 exons confirmed the
direction and magnitude of splicing change
predicted by the microarray, In conclusion, all
the exons with large predicted change (?I gt0.2)
and 95 of the exons with no predicted change
(?Ilt0.1) could be validated by RT-PCR.
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A table of all the 49 exons
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RT-PCR validate

• Of the 49 Nova2-regulated transcripts validated
  in this study, 31 are expressed both in brain and
  in immune tissues.
• 97 (30/31) have the same splicing pattern in
  Nova2-/- neocortex as in immune tissues,
  suggesting that Nova2 promotes brain-specific
  splicing.

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analysis

• Of the 49 exons validated splicing changed, 33
  also had predicted splicing changes in all other
  Nova2-/- brain regions, 7 also had predicted
  splicing change in wild-type versus Nova1
  knockout brain tissue, 5 transcripts identified
  with Nova-dependent differential splicing in the
  cortex and spinal cord.

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Nova regulates splicing of RNAs encoding synaptic
functions

• program GoMiner were used to analyse the function
  of Nova-regulated transcripts.
• gene functions associated with Nova-regulated
  (n48) exons were compared with the complete set
  of microarray alternative exons from genes
  expressed in brain (n2710).

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• Functions with the most significant enrichment
  among Nova-regulated transcripts were proteins
  act at the cell membrane, most often at the
  cell-cell junctions, suggesting they may all act
  in the synapse(??).

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The genes with potential synaptic functions
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The synaptic module of 41 proteins encoded by
validated Novaregulated RNAs. The proteins
encoded by validated RNAs identified by the
microarray are shown in orange, and those
validated in previous studies8,9 are shown in
yellow. Proteins encoded by RNAs identified by
multiple Nova CLIP tags9 are shown in blue, and
other proteins in the same networks that are not
known to be regulated by Nova are shown in
white. Red arrows denote positive regulatory
interactions, and blue bars denote negative
regulatory interactions. All proteins shown are
not necessarily present in a single synapse
(symbolized by interruptions in the membranes).
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finally

• they identified a new gene regulatory module
  consisting of transcripts coregulated at the
  level of alternative splicing. Nova-regulated
  transcripts encode proteins that form an
  interaction module in the synapse.

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My feeling

• The array is just a beginning, much more
  bioinformatics and other works have to do to
  validate and analysis the array data.

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Thank you!!!

• ???
• 2006.10