415 Clinical Research Building
415 Curie Boulevard
Philadelphia, PA 19104-6145
Office: 215-898-1958
arjunrajlab@gmail.com
Our lab aims to develop a quantitative understanding of the molecular biology of the cell. Interests include chromosome structure and gene expression, non-coding RNA, and global regulation of gene expression. Applications include genetics, cancer and stem cells.
We have contributed to the understanding of mechanisms that create and control cell-to-cell variability in gene expression. In particular, our work was amongst the first to use quantitative single molecule RNA detection techniques to describe the phenomenon of transcriptional bursts, in which we found that transcription is a pulsatile process consisting of pulses of activity interspersed with periods when the gene is completely inactive (Raj et al. PLOS Bio 2006, Leveque and Raj Nat Meth 2013a). We also contributed to the mathematical modeling of this field (Raj et al. PLOS Bio 2006). We have now shown how these pulses relate to homeostatic mechanisms that maintain transcript concentration despite changes in cell volume and DNA content (Padovan-Merhar et al. Mol Cell 2015). We have also shown that variability can be used as a tool for dissecting mechanisms of transcriptional control of molecules such as long non-coding RNA (Maamar et al. Genes and Dev. 2013).
We have contributed to the understanding of how cell-to-cell variability can lead to phenotypic consequences. Specifically, we showed that variability in transcription can lead to random cell fate decisions in bacteria (Maamar and Raj et al. Science 2008), and that variability in gene expression can lead to phenotypic variability in metazoan development (Raj and Rifkin et al. Nature 2010). More recently, we have linked gene expression variability to single cell non-genetic resistance mechanisms in melanoma (Shaffer et al. Nature, in press).
We have contributed to methodological approaches to measuring expression and transcription in single cells via RNA fluorescence in situ hybridization (RNA FISH). First, we developed a method that greatly simplifies the detection of individual RNA molecules by RNA FISH (Raj et al. Nat Meth 2008). We have since pushed the method to high multiplexing in the detection of chromosome structure and gene expression simultaneously (Levesque and Raj, Nat Meth 2013a). We also have enabled the detection of single nucleotide variants on individual RNA molecules (Levesque et al. Nat Meth 2013b), which allows for mutation detection and measurements of allele-specific expression. Further, we have developed an ultra-fast variant of RNA FISH that enables use in diagnostic and point of care settings (Shaffer et al. PLOS ONE 2013).
FIRST NAME: | LAST NAME: | TITLE: | EMAIL: |
---|---|---|---|
Arjun | Raj | PI | arjunraj@seas.upenn.edu |
Naveen | Jain | grad student | naveen.Jain@uphs.upenn.edu |
Karun | Kiani | grad student | karun.kiani@pennmedicine.upenn.edu |
Lauren | Becj | grad student | laurenbeck13@gmail.com |
Allison | Cote | 2019 PhD | allcote@mail.med.upenn.edu |
Margaret | Dunagin | lab manager | dunagin@seas.upenn.edu |
Ben | Emert | grad student | Benjamin.Emert@uphs.upenn.edu |
Amanpreet | Kaur | postdoc | amankaur@upenn.edu |
Ian | Mellis | 2019 PhD | iamellis@mail.med.upenn.edu |
Eric | Sanford | grad student | eric.sanford@pennmedicine.upenn.edu |
Connie | Jiang | grad student | connie.jiang@pennmedicine.upenn.edu |
Eduardo | Torre | 2019 PhD | edatorre@gmail.com |
Yogesh | Goyal | postdoc | yogesh.goyal0308@gmail.com |
Ian | Dardani | grad student | idardani@seas.upenn.edu |
Jess | Li | grad student | jessi.li.ljx@gmail.com |
Amy | Azaria | undergrad | amazaria@seas.upenn.edu |
Phil | Burnham | postdoc | phil.burnham.50@gmail.com |
Chris | Cote | tech | chrisjamescote@gmail.com |
Sam | Reffsin | grad student | reffsin@seas.upenn.edu |
Lee | Richman | grad student | leepr@upenn.edu |
Max | Betjes | visiting graduate student | maxbetjes@gmail.com |
Ryan | Boe | grad student | ryanboelab@gmail.com |