Editing BioMicroCenter:Research (section)

=== Large-scale discovery and functional analysis of distal enhancer elements - [http://web.mit.edu/biology/www/facultyareas/facresearch/boyer.html BOYER LAB] - [http://web.mit.edu/biology Biology] and [http://web.mit.edu/ki KI]===
The overall goal of the Boyer lab is to understand how a single cell can ultimately specify the diversity of cell types during mammalian development. An exciting and emerging area of biology in the post-genomics era has been the genome-wide identification of non-coding regulatory elements in what was once known as “junk DNA”. Enhancers are key cis-regulatory elements that can affect gene transcription independent of their orientation or distance that are required for tissue specific patterning of gene expression during development, though only few examples had been known. Global identification of these regions as well as their contribution to target gene expression has been challenging because enhancers can often reside thousands of base pairs away from their target of regulation.<BR><BR>
The Boyer lab has recently discovered that specific histone modification patterns could identify enhancers by genome-wide ChIP-Seq in embryonic stem cells (ESCs) as well as in a range of differentiated cell types and moreover, that these patterns distinguish enhancers as either active or poised (or inactive). Remarkably, genes connected to active enhancers code for genes with cell type specific functions and more importantly, poised enhancers could predict future developmental potential of that cell by marking genes that have the potential to become activated. However, it had been unclear how enhancer states were correlated during lineage commitment. Using cutting edge high-throughput sequencing methods, the Boyer lab has now defined a large set (~80,000) of both poised and active enhancers throughout the genome based on chromatin modification patterns derived from four key time points  during cardiomyocyte differentiation. The differentiation system provides a unique opportunity to study enhancer state transitions during embryonic patterning of cardiomyocytes, which ultimately comprise the majority of the cell types in the developing heart. <BR><BR>
The BioMicro Center was instrumental in providing the technical expertise necessary for the generation of the large number of high quality sequencing libraries from chromatin immunoprecipitated material. The BioMicro Center adapted the use of the IP-Star automated ChIP system (currently under evaluation) to facilitate automation of ChIP followed by library generation on the SPRI-TE. Additionally, the Boyer lab was able to barcode each experimental sample so that multiple sequencing libraries could be run in a single lane of an Illumina flow cell. Barcoded libraries were then analyzed by a number of quality control measures developed by the BioMicro Center to ensure the highest quality of sequence. These steps represented substantial improvements over previous protocols and allowed us to perform many experiments in a cost and time-efficient manner.<BR><BR>
Together with the BioMicro Center, the Boyer lab analyzed the substantial amount of sequencing data and developed new algorithms to identify and to functionally dissect the role of distal enhancer elements in regulating gene expression patterns during lineage commitment.  As a result of this study, they found that enhancer utilization is highly cell type specific and that enhancer state transitions are dynamic and non-random and likely occur during short windows of developmental time. These exciting findings have provided new details about how tissue specific expression patterns are established early in development and how mutations in these elements may contribute to cardiac diseases.