Exploring the gene expression regulation by single molecule RNA imaging

The RNA molecules are the central players for gene regulation. For the coding region of our genome, RNA serves as intermediate messenger molecular in form of mRNA. The expression and localization of mRNA in the cell determine the temporal and spatial regulation of protein expression. It has become apparent from genome wide sequencing analyses that a vast majority of human genome (about 98%) does not code for proteins, nevertheless, about 80% of non coding genome is functional and is transcribed into RNA. These non-coding RNAs (ncRNAs) comprise of ribosomal RNAs, Short non-coding RNAs, (also known as microRNAs) and long non-coding RNAs (lncRNAs). These ncRNAs also play a central role by regulating gene expression at the level of transcription as well as translation.

Our lab's overall theme is to image mRNAs and lncRNAs using single molecule in situ Hybridization (smFISH) technique to visualize their intracellular distribution in the cells. This technique employs a set of small oligonucleotide probes which tile along the length of RNA molecule and each probe has same fluorophore at its terminal end. These probes when bind specifically to target RNAs, enables each mRNA molecule to be seen as a bright, diffraction-limited spot in a fluorescence microscope. Different mRNA species can be distinguished from each other, using sets of probes labeled with differently colored fluorophores. The images thus obtained are processed using custom written algorithms to address questions about where, how much and with whom, the RNA of interest is located.

We used this technique in past to understand mRNA transport in neurons, splicing and most recently we established a method called "Fusion FISH" for imaging the fusion mRNAs that are formed as products of chromosomal translocations. By coupling this single-molecule imaging technique with automated image-analysis computer programs, the location of affected cells among the normal cells in a tissue sample can be readily determined, and the number of gene fusion transcripts in each individual affected cell can be counted.

Selected Publications

Awards and Honors

• Recipient of NIH Director’s Early Independence Award 2012
• Stanley S. Bergen, Jr., M.D. Medal of Excellence for academic excellence and leadership in the Graduate School of Biomedical Sciences, UMDNJ, 2012.
• NJMS Faculty Organization Outstanding Graduate Student Award for outstanding performance, academic excellence, research accomplishments and service in the graduate program, 2012.
• First Prize for Best Poster, 3rd Annual Postdoctoral Appreciation Week Symposium Robert Wood Johnson Medical School, Piscataway, New Jersey, 2011
• Executive Women of New Jersey Graduate Merit Award for Outstanding Candidate Pursuing an Advanced Degree in Science, Technology, Engineering, Math or Environmental Science, 2011
• First Prize for Best Poster Presentation, UMDNJ Inter-School Technology Symposium Robert Wood Johnson Medical School, 2011
• Best Poster Prize, 24th Annual International RNA Symposium, Hunter College, City University of New York, 2011
• Best Oral Presentation Prize, 17th Annual Graduate Student Research Symposium UMDNJ, Newark, New Jersey, 2010
• Mentor Appreciation Award, Bergen Academy High School, 2008
• National Scholarship Award for Postgraduate Students, Ministry of Human Resource Development of India, 2003 - 2004

Education

2011 Ph.D. in Cell Biology and Neurobiology, University of Medicine and Dentistry of New Jersey, New Jersey

2005 M.S. with honors in Molecular Biology, Panjab University, India

2003 B.S. with honors in Microbiology, Panjab University, India

Positions

2013-Present. Assistant Professor, Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School

2012-2013. Assistant Professor, Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey.