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A critical directive of the BioMicro Center is to provide a cutting-edge research core for members of the MIT community. Creating and maintaining the BioMicro Center at the forefront of technology improves our ability to support MIT faculty in grant applications, manuscript publishing and in the recruitment of new faculty members. In part, this goal is achieved through ongoing collaborations with many labs at MIT. A selection of these collaborations taken from the annual reports of the BioMicro Center is presented below.


Large-scale discovery and functional analysis of distal enhancer elements - BOYER LAB - [Biology and [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.

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.

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.

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.

Chris Burge (Biology) We study mechanisms of posttranscriptional gene regulation using a combination of computational and experimental methods. A long-term goal is to understand the RNA splicing code: how the precise locations of exons and splice sites are identified in primary transcripts, and how this code is altered in cell- and condition-specific alternative splicing. Current efforts are focused on identifying splicing cis-regulatory elements and associated splicing factors, and understanding the context-dependent activities and functional interactions between these elements. We also study the roles that microRNAs (miRNAs) play in gene regulation, with an emphasis on determining the rules for miRNA-directed targeting of mRNAs. We are beginning to study the relationship between alternative cleavage and polyadenylation, which is commonly used to generate alternative mRNA isoforms differing in their 3' UTRs, and miRNA regulation. (expanded research description)

Sally Chisholm (Biology) The general goal of the research in my lab is to advance our understanding of microbial ecology and evolution in the oceans. In recent years we have focused our attention on a single group, the cyanobacterium Prochlorococcus, which is the smallest and most abundant microbe in ocean ecosystems — sometimes accounting for half of the total chlorophyll. This “minimal phototroph” can convert CO2, sunlight, and inorganic nutrients into a living cell with as few as 1700 genes. We have been developing Prochlorococcus, and the phage that infect them, as a model system for understanding life processes across all scales of spatial and temporal organization, from the genome to the biosphere, and from daily to evolutionary time scales. In so doing, we hope to develop a unified understanding of this one small representative of the diversity of life. (expanded research description)

Peter Dedon (expanded research description)