Transcript lecture4_456_2015x

Biol 456/656
Molecular Epigenetics
Lecture #4
st
Mon, Aug 31 , 2014
Drosophila Development
https://www.youtube.com/watch?v=DsK9R-yfgF4
https://www.youtube.com/watch?v=ePBghFrPb7Y
Drosophila Embryonic Development
https://www.youtube.com/watch?v=yE0WRBYh_NM
In situ hybridization (ISH)
• Antisense RNA probe or DNA probe
• Probe is labeled for detection (color or
radioactivity)
• Embryo (or any tissue) is prepared (fixed)
• Hybridization (probe binds RNA in situ)
• Image captured with microscope
Figure 3
In situ hybridization: detects RNA in space and time
BDGP In situ database
http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl
http://insitu.fruitfly.org/insitu_image_storage/
img_dir_172/insitu172550.jpe
http://insitu.fruitfly.org/cgibin/ex/report.pl?ftype=1&ftext=CG18408
In situ databases available for different species
Mouse brain:
http://developingmouse.brain-map.org/gene/show/48621
http://www.eurexpress.org/ee/databases/assay.jsp?assayID=euxassay_019787&image=01
http://developingmouse.brainmap.org/gene/show/48621
Eurexpress.com
ISH
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Spatial information of gene expression
Not quantitative
Assayed on gene-by-gene basis
Amenable to high-throughput study (time
consuming)
This is a very small purple slice
(equivalent to 47 genes)
But accounts for half of all
transcript isoforms
# of transcript
isoforms
The pie is equivalent
to all GENES (~15,000)
The pie is equivalent
to all TRANSCRIPT ISOFORMS
TIP: try to “narrate” what the figure is trying to say. For clues, see the “results” text or the
figure legend
“79% of genes in the genome make 5 or less transcript isoforms.”
“0.2% of genes in the genome (47 genes) make > 1000 transcript isoforms”
If you are having trouble understanding a figureBLOW IT UP!
DSCAM
Thousands of predicted spliced isoforms
Try to identify the trends in the data without knowing all the variables and technical
details.
575 AS events
Z scores of psi: measurement of splicing
Cluster analysis
How to read this? Identify the trends.
Seeing the entire genome: what changes with Cd treatment
Reading Papers
• A picture is worth a thousand words…
– only if you can see it (zoom in!)
• Be able to present a paper you have read to
another person in 5-10 minutes, just referring to
figures
• Try different strategies to read a paper
• Know the purpose of your reading
– “big picture/integrating information” reading
– “technical” reading
– “critical” reading