Transcriptional Control of
Neural Diversity
Jane E. Johnson, PhD
UT Southwestern Medical Center
Department of Neuroscience
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Nervous System •  Brain •  Spinal cord •  Sensory systems •  Neurons •  Oligodendrocytes •  Astrocytes Tuj1!
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B. Signaling factors pattern the neural tube
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C. Transcription factor expression is patterned
by signaling factors (particularly homeodomain
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Overview of the generation of different
neural cell types during development
Progenitor
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Neural stem
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Ascl1
Neuron
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Oligodendrocyte
Ascl1 is expressed in and required for subsets of
neuronal and oligodendrocyte progenitors
Transcription Factor Machinery and
Epigenetics
In biology, and specifically genetics, epigenetics is the study of inherited changes in
phenotype (appearance) or gene expression caused by mechanisms other than changes in
the underlying DNA sequence, hence the name epi- (Greek: ! - over, above) -genetics.
These changes may remain through cell divisions for the remainder of the cell's life and
may also last for multiple generations. However, there is no change in the underlying
DNA sequence of the organism;[1] instead, non-genetic factors cause the organism's
genes to behave (or "express themselves") differently. (Wikipedia: epigenetics)
Transcription factor
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Back to the biological question of
transcription control of neural development
Progenitor
cell
Neural stem
cell
Ascl1
Neuron
$me Ascl1
Oligodendrocyte
Ascl1 is expressed in and required for subsets of
neuronal and oligodendrocyte progenitors
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Ascl1 Regulates the Expression of Notch Ligand Delta-­‐
like 3 (Dll3) through a proximal promoter Henke et al., 2009 Chromatin Immunoprecipitation (ChIP)
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How to get a genomewide
understanding of Ascl1 targets?
Chromatin Immunoprecipitation (ChIP)
followed by sequencing (ChIP-seq)
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Ascl1 ChIP-Seq: Dll3
Window from UCSC Genome Browser with millions of 36 bp sequence
reads from the ChIP-seq data mapped to the mouse genome. Ascl1 bound
region is boxed and shows its location in the proximal promoter of Dll3.
Ascl1 ChIP-Seq: Dll3
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Using the USCS Genome Browser you can zoom in to see the sequence
under the peak that has highly conserved Ascl1 binding sites.
Ascl1 ChIP-Seq: Dll1
ChIP-seq data reveals a previously characterized Ascl1 binding site in
the Dll1 promoter (black box) as well as an novel site within an intron of
Dll1 (red box).
De Novo Motif Analysis
~2,000 high confidence binding sites called so many novel
targets of Ascl1 identified that can be studied for their
function in neural development.
This motif matrix appeared in every peak and defines a
more restricted recognition sequence for Ascl1.
Normal regulators of development show up in cancer cells
Ascl1 in glioblastoma and multiple neuroendocrine tumors
Tumor forming cells 


Ascl1 is highly expressed neuroendocrine cancers (Small cell
lung cancer, medullary thyroid carcinoma, pheochromocytoma)
Ascl1 likely contributes to the progressive development and
behavior of the tumor cells but not the initial event.
Knocking down levels of Ascl1 in tumor cell lines results in cell
death and inhibition of growth.
What are the transcriptional targets of Ascl1 that explain
the biological behavior and may be novel therapeutic targets?
ChIP-seq with Ascl1 in the Small Cell Lung Carcinoma cell
lines reveals Ascl1 bound to some similar regions as has been
identified in the developing neural tube ie Dll1 and Dll3.
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SCLC versus embryonic neural tube
Ascl1 Binding Sites
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200 binding regions shared
Why such a difference in number and location?
Suspect epigenetic differences as major player.
Transcription factor
accessibility
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Compare Ascl1 binding sites in the different tissues
with respect to the epigenetic marks
Hawkins 2010 Future
Coupling higher order chroma$n changes with $ssue specific factors to gain mechanis$c insights into the transcrip$onal control of developmental processes. Determine how these interac$ons change when things go awry in the cell as in cancer-­‐-­‐-­‐leading to new therapeu$c targets for treatment. Strategies to harness the biological ac$vi$es of transcrip$on factors to direct differen$a$on of stem cells or reprogram cells to specific lineages. i.e. recently shown that fibroblasts can be reprogrammed directly to neurons with Ascl1 being a cri$cal component of the cocktail.