Our laboratory is built upon a team of scientists with diverse backgrounds, expertise and interests. We train to seamlessly bridge the experimental, computational and statistical sciences towards decoding the human genome. Our logo and scientific approach is inspired by (yet far less important than) the Delta Force teams trained across air, land and sea to safely accomplish goals as a team. Similarly, we are a small team of scientists using diverse approaches to accurately extract information from the dark regions of the human genome. This requires extensive intra- and inter-laboratory collaborations to support these research operations -- thus, our long standing motto: Innovation through Integration. Our environment is welcoming and encouraging of people from all backgrounds, training and research interests. Diversity is the engine of evolution and of our science!
For more than a decade, we have had a hobby of "gene-hunting" for new genes in the human and mouse genomes (genomic cartography). Specifically, we aim to identify members of a new(er) class of genes termed long noncoding RNA (lncRNA).
We are less interested in the number of lncRNA genes in the genome and more focused on using all the information we can to identify the ones most likely to function in human health and disease. These efforts require creative computational and experimental solutions that we pursue in parallel.
RNA, CHROMTAIN and NUCLEAR ORGANIZATION
Remarkably, 2m of linear DNA must be packaged into to the small confines of the nucleus. To ensure proper cell state, each cell must organize its DNA, RNA, and proteins within the nucleus in ways that differ in each cell type. More than 25 years ago, it had been suspected that RNA itself might be a key organizing factor that shapes this dynamic nuclear floor plan. Indeed, many lncRNAs (e.g. XIST, FIRRE, NEAT1) play important roles in maintaining and establishing nuclear domains.
We are applying single molecule RNA FISH, live cell imaging CLING-FISH, CRISPR-Display, HiC, rChIP and fRIP technology to understand how lncRNAs facilitate intra- and inter-chromosomal interactions in space and time.
GENETIC MODELS OF LNCRNA
"The laws of genetics have never depended upon knowing what the genes are chemically and would hold true even if they were made of green cheese" - Ed Lewis
The ultimate demonstration of the functional contribution of a lncRNA is through genetic testing. If DNA containing a lncRNA is removed and the organism is affected, then it must be important, no matter its molecular mode of action. We further use "genetic rescue" models to identify those lncRNAs that have RNA based physiological functions. To date our laboratory has examined over 40 unique genetic modifications of lncRNAs -- however we are now out of this business -- for now.
THE MOLECULAR GRAMMAR OF LNCRNAs
For protein-coding genes we know the letters (amino acids), words (domains) and sentences (structures). Thus, to near fluency, we can read a sequence and make some inference of function for a given protein.
In contrast, we have almost no vernacular for lncRNAs owing to the different "syntax" compared to proteins. By way of analogy, proteins transmit information through a lexicon and RNA through a symbolic language like hieroglyphics.
Towards this goal we have developed a Massively Parallel RNA Assay (MPRNA) strategy that test hundreds of thousands of individual RNA sequences and structures for function. Thus we can rapidly identify RNA "hieroglyphs" and look for commonalities and meanings -- as we can for proteins today.
Our research has a long-standing history of developing or refining new computational and or experimental solutions to identify new functionalities in the human genome. Computationally, we have developed solutions for RNA-sequencing in bulk and single cell populations, fRIP-sequencing and one of the first machine learning approaches to identify functional polymorphisms in the human population. We have refined numerous computational approaches to develop lncRNA catalogs, characterization of global lncRNA properties and live cell image tracking of chromosomal movements.
Experimentally we have developed several new approaches to gain unique insights into the human genome. This includes PIP-seq, fRIP-seq, and MPRNA towards our ultimate goal of understanding the molecular syntax of lncRNA biology. We have also developed two distinct applications of CRISPR-CAS9 systems. Specifically, CRISPR-Display that serves as a drone to carry RNA cargo to specified regions of the genome. As well as live cell imaging approaches such as CLING-FISH and SNP-CLING (Crispr Live Cell Imaging) to monitor how chromosomes fold and interact in living cells.