About

Lab Focus 

Our lab studies a newly identified mRNA species; isolated 3'UTR sequences expressed in the absence of their cognate coding regions.  

Previously, our laboratory focused on the the study of dopaminergic neuron (DA neuron) development, the key neurons that die in Parkinson’s disease. While using transcriptome analysis to identify molecular differences between subtypes of dopamine neurons using we made the surprising discovery of the widespread expression of isolated 3’ UTR sequences (i3'UTRs) in the absence of  their cognate coding sequences (CDS) (Neuron 2015).  Although these findings contradict traditional dogma which dictates that CDS and cognate UTR sequences are connected from the time of RNA maturation to degradation, similar results showing discordant expression of 3'UTRs and CDS sequences were reported first in 2011, and verified again recently in late in 2017.  Our studies showed that the often dramatic differential  3'UTR/CDS ratio is not particular to development or to neurons but appears to occur in all tissues, all ages and for all genes examined. Using two-color in situ hybridization with a red probe to the 3'UTR and green probe to the cognate CDS we find that some cells show very high 3'UTR/CDS expression, but in others very high CDS/3'UTR. This differential 3’UTR/CDS expression patterns shows purposeful (not random) expression in that it is consistent in particular cells, is spatially patterned, and changes with developmental or biological state. We also find that when cognate  3’UTR and CDS sequences are co-expressed, they may be localized to different subcellular compartments within a particular cell. 

These findings raised a number of questions. In our lab we have chosen to focus on the biological role of isolated 3'UTRs (i3'UTRs). As i3'UTRs are >200bp and do not code for protein, they are essentially a new species of long non-coding RNAs (lncRNAs), and numerous studies show that lncRNAs can affect the precise spatial and temporal regulation of gene expression and other cellular, developmental, and disease-related events.

We hypothesize that i3'UTRS play important roles in developmental events and we are testing this hypothesis in neural stem cells (NSCs), in hair and skin stem cells (HF-SCs) and during neural differentiation. Each of these projects utilizes similar techniques to manipulate and study i3'UTRS. We expect that their misimpression with have discrete and important biological effects on various developmental programs. 

For both the NSC and HF-SC projects we have a particular focus on the stem cell regulator and marker genes Oct4, Sox2, Klf4, Myc and nanog, collectively known as OSKM+ as well as important players or control genes in either neural or hair development. For neural diffnertiaton we focus on both central neurons such as cortical and dopaminergic as well as on the peripheral sensory neurons, DRGs. 

s. three of which are the focus of her laboratory:  (i) how dynamic or stable is the 3’ UTR/CDS ratio in cells in vitro and in vivo, under different biological conditions; (ii) what is the role of the dramatic increase in 3’ UTR/CDS in some of the key DA neuron determinant genes during development; and (iii) does two-color in situ hybridization help illuminate the roles of Sox C proteins (Sox4, 11, and 12) in neuronal development. Sox C genes are important developmental regulatory genes.  Previous in situ hybridization using probes to random regions in these genes show widespread, almost ubiquitous expression in the developing brain (bottom right). Two color in situ hybridization to the CDS and cognate 3’UTR of Sox genes has instead revealed exquisite patterns, gradients and cell type specific expression of each of these genes (see below) suggestive of important functions for particular developing neurons. Viral overexpression of UTR sequences and examination of Sox C knockout mice will allow testing of these predictions

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