1. Molecular Epigenetics
Biol 456/656
Molecular Epigenetics
Lecture #4
Mon, Aug 31st, 2014

2. Drosophila Development

3. Drosophila Embryonic Development

4. 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

5. Figure 3
In situ hybridization: detects RNA in space and time

6. http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl BDGP In situ database

7. http://insitu. fruitfly. org/cgi-bin/ex/report. pl

8. In situ databases available for different species
Mouse brain:

10. Eurexpress.com

11. ISH Spatial information of gene expression Not quantitative
Assayed on gene-by-gene basis
Amenable to high-throughput study (time consuming)

13. to all TRANSCRIPT ISOFORMS
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”

14. If you are having trouble understanding a figure-
BLOW IT UP!

15. DSCAM
Thousands of predicted spliced isoforms

16. Try to identify the trends in the data without knowing all the variables and technical
details.

17. 575 AS events
Z scores of psi: measurement of splicing
Cluster analysis
How to read this? Identify the trends.

18. Seeing the entire genome: what changes with Cd treatment

19. 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