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<p class=MsoNormal align=center style='margin-bottom:0in;margin-bottom:.0001pt;
text-align:center'><b style='mso-bidi-font-weight:normal'><span
style='font-size:18.0pt;mso-bidi-font-size:14.0pt;line-height:300%'>Quantitative
modeling of a gene's expression from its <span class=SpellE>intergenic</span>
sequence</span></b><b style='mso-bidi-font-weight:normal'><span
style='font-size:16.0pt;mso-bidi-font-size:14.0pt;line-height:300%'><o:p></o:p></span></b></p>
<p class=MsoNormal align=center style='margin-bottom:0in;margin-bottom:.0001pt;
text-align:center'><span style='font-size:12.0pt;mso-bidi-font-size:14.0pt;
line-height:115%'>Md. <span class=SpellE>Abul</span> Hassan Samee</span><sup><span
style='font-size:10.0pt;line-height:115%'>1*</span></sup><span style='font-size:
10.0pt;line-height:115%'> </span><span style='font-size:12.0pt;mso-bidi-font-size:
14.0pt;line-height:115%'>and <span class=SpellE>Saurabh</span> Sinha</span><sup><span
style='font-size:10.0pt;line-height:115%'>1,2</span></sup><span
style='font-size:10.0pt;line-height:115%'><o:p></o:p></span></p>
<p class=MsoNormal align=center style='margin-bottom:0in;margin-bottom:.0001pt;
text-align:center'><sup><span style='font-size:10.0pt;line-height:115%'>1</span></sup><span
style='font-size:12.0pt;mso-bidi-font-size:10.0pt;line-height:115%'>Department
of Computer Science and </span><sup><span style='font-size:10.0pt;line-height:
115%'>2</span></sup><span style='font-size:12.0pt;mso-bidi-font-size:10.0pt;
line-height:115%'>Institute for Genomic Biology, University of Illinois at
Urbana-Champaign, Urbana, Illinois, USA</span><span style='font-size:10.0pt;
line-height:115%'><o:p></o:p></span></p>
<p class=MsoNormal align=center style='margin-bottom:0in;margin-bottom:.0001pt;
text-align:center'><sup><span style='font-size:10.0pt;line-height:115%'>*</span></sup><span
style='font-size:12.0pt;mso-bidi-font-size:10.0pt;line-height:115%'>To whom correspondence
should be addressed, </span><a href="mailto:samee1@illinois.edu"><span
style='font-size:12.0pt;mso-bidi-font-size:14.0pt;line-height:115%'>samee1@illinois.edu</span></a><span
style='font-size:12.0pt;mso-bidi-font-size:14.0pt;line-height:115%'><o:p></o:p></span></p>
<p class=MsoNormal align=center style='text-align:center'><o:p> </o:p></p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><b
style='mso-bidi-font-weight:normal'><span style='font-size:13.0pt;mso-bidi-font-size:
11.0pt;line-height:300%'>Abstract<o:p></o:p></span></b></p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'>Modeling a
gene's expression from its <span class=SpellE>intergenic</span> locus and trans-regulatory
context is a fundamental goal in computational biology. Such models facilitate
our studies of gene regulation at a mechanistic level and can reveal how perturbations
in the regulatory machinery of a gene impact its <span class=SpellE>spatio</span>-temporal
expression. Models of enhancer function, despite their remarkable success in
the past decade, fall short of achieving the broader goal of modeling a gene's
expression from its entire locus. In particular, the distributed nature of <span
class=SpellE><i style='mso-bidi-font-style:normal'>cis</i></span>-regulatory
information and the less understood mechanisms that integrate such information place
gene locus modeling in a different realm than that of modeling an individual
enhancer. Here we report the first quantitative model of a gene's expression
pattern as a function of the sequence of its entire locus. As per this model,
the expression readout of the locus is two-tiered: 1) the combinatorial effect
of transcription factor binding sites within each enhancer is predicted by a
thermodynamics-based model, and 2) independent contributions from multiple
enhancers are linearly combined to produce the gene's expression pattern. The
model does not require any prior knowledge about locations of the enhancers
contributing toward gene expression. We demonstrate that the model captures the
complex multi-domain expression patterns of genes <i style='mso-bidi-font-style:
normal'>even-skipped</i>,<i style='mso-bidi-font-style:normal'> hairy</i>, <i
style='mso-bidi-font-style:normal'>runt</i>, and <i style='mso-bidi-font-style:
normal'>giant</i> along the anterior-posterior axis of the early <i
style='mso-bidi-font-style:normal'>Drosophila</i> embryo. Our findings suggest
the presence of sequence segments in the locus that would contribute ectopic
expression patterns and thus have to be "shut down" by the model. Such segments
were found to be located in inaccessible regions of the locus. We applied our
model to identify the transcription factors responsible for the formation of
stripe boundaries of the studied genes. The resulting network of regulatory
interactions exhibits a high level of agreement with known regulatory
influences on the target genes. Finally, we used the model to analyze interactions
between multiple enhancers in a gene locus. We tested the common assumption of
independent enhancer activities and interrogated how information is integrated
from multiple enhancers to produce a gene expression pattern. We found that
enhancers of the four genes studied in this work act mostly as autonomous entities
to drive expression of their targets.</p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><span
style='font-size:13.0pt;mso-bidi-font-size:11.0pt;line-height:115%'><o:p> </o:p></span></b></p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><b
style='mso-bidi-font-weight:normal'><span style='font-size:13.0pt;mso-bidi-font-size:
11.0pt;line-height:300%'>Data<o:p></o:p></span></b></p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><a
href="http://veda.cs.uiuc.edu/gemstat-gl/data-gl.tar.gz">Data Files</a>. Expression pattern of 23 additional
genes were collected from <a href="http://veda.cs.uiuc.edu/lmcrm/">the companion site for Kazemian et al. (PLoS Biology 2010)</a>.</p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><b
style='mso-bidi-font-weight:normal'><span style='font-size:13.0pt;mso-bidi-font-size:
11.0pt;line-height:300%'>Source<o:p></o:p></span></b></p>
<p class=MsoNormal style='margin-bottom:0in;margin-bottom:.0001pt'><a
href="http://veda.cs.uiuc.edu/gemstat-gl/gemstat_gl.tar.gz">GEMSTAT-GL source code</a>.
See the <a href="http://veda.cs.uiuc.edu/gemstat-gl/readme.txt">ReadMe</a> file and a <a href="http://veda.cs.uiuc.edu/gemstat-gl/run.sh">sample shell script</a> for details of executing the code.
For further help with the code and/or reporting comments/bugs, please e-mail: <a href="mailto:samee1@illinois.edu">Hassan Samee</a>.</p>
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