Editing BioMicroCenter:Research (section)

=== Elucidating Brn targeting of Sox2 in embryonic stem cells - [http://web.mit.edu/biology/www/facultyareas/facresearch/jaenisch.html JAENISCH LAB] - [http://web.mit.edu/biology Biology] and [http://web.mit.edu/ki KI]===
In mammals, a few thousand transcription factors regulate the differential expression of greater than 20,000 genes to specify ~200 cell types during development.  How this is accomplished has been a major focus of biology for many years.  Transcription factors bind sequence-specific regulatory elements, including proximal promoters and distal enhancers, to control gene expression.  Emerging evidence indicates that transcription factor binding at distal enhancers plays important roles in the establishment of tissue-specific gene expression programs during development.  Combinatorial binding among groups of transcription factors can further increase the diversity and specificity of regulatory modules governed by a particular factor.   The identification of regulatory modules comprised of groups of transcription factors which occupy important regulatory regions of genes which govern cell fate determination would shed light on how developmental decisions are made.<BR><BR>
Work from the Jaenisch and Young labs elucidated the role of  a group of three transcription factors, Oct4, Sox2, and Nanog, in regulating cell identity in embryonic stem cells (ESCs) using ChIP-on-Chip technology in 2005.  Recently, Michael Lodato from the Jaenisch lab, in collaboration with the Boyer lab, has studied the genome-wide role of Sox2 in neural progenitor cells (NPCs).   Their work showed that Sox2 occupied a distinct set of targets in NPCs relative to it targets in ESCs, and further that Sox2 switched partner factors during this transition: form Oct4 and Nanog in ESCs to Brn2, and Oct4 family member, in NPCs. <BR><BR>  
Taking advantage of the expertise in the BioMicro Center, they were able to examine the effect of the NPC-specific Sox2 partner factor, Brn2, on Sox2 binding in ESCs, where Sox2 normally partners with Oct4.  The BioMicro Center Staff utilized the IP-Star Automated ChIP System to facilitate the automation of a large number of ChIP-Seq experiments, successfully querying the genome-wide occupancy of Sox2, Brn2, Histone H3 Lysine 4 monomethylation, Histone H3 Lysine 27 acetylation, total Histone H3, and p300 in both control and Brn2-induced ESCs in a rapid and controlled manner.  Thus, not only could the binding of Sox2 and Brn2 be investigated, but due to the availability of the IP-STAR automated ChIP system the Jaenisch Lab could investigate changes to the epigenome as well.  The BioMicro Center then prepared Illumina libraries from these samples ran them in a single lane of an Illumina flow cell, saving time and immensely reducing the cost to the Jaenisch Lab.  Finally, the BioMicro Center implanted quality control metrics on both the samples before loading on the sequencer and on the quality of the data generated during the run. <BR><BR>
Using this data, the Jaenisch Lab was able to define a set of regions where ectopic Brn2 could recruit endogenous Sox2 (Figure x), and they are currently investigating the effects of this binding on the chromatin status of these regions.   The technical expertise of the staff of the BioMicro Center contributed significantly to the successful completion of this project during both the planning and execution of these experiments.  <BR><BR>