PROJECT SUMMARY
The human body comprises of trillion of cells, which are the building blocks of life. Each cell is highly organized,
with various constituents within localizing to specific regions. Location within a cell is a cardinal organizing
principle of gene control and function, especially for RNAs that code for proteins or serve regulatory roles as
non-coding RNAs. Each cell type has its distinct RNA-species profile, and where these RNAs are located within
the cell can dictate their folding, editing, splicing, translation, degradation, binding partners, catalytic activity, and
even the fate of the proteins that they encode. Unsurprisingly, perturbations in RNA localization result in disease
conditions including cancers and neuropathologies. In spite of the vital importance of subcellular RNA localization
in gene expression, investigating such phenomena simultaneously for many RNA species has been challenging.
To address these long-standing issues, Dr. Furqan Fazal and others have recently developed a technique called
APEX-seq that can track the location of thousands of RNAs in living human cells with high-temporal and
nanometer-spatial resolution. APEX-seq has the transformative potential to provide high-resolution snapshots of
tens of thousands of endogenous cellular RNA species, free from artifacts of overexpression, cell fixation or
recombinant tagging. This proposal outlines a five-year career program for Dr. Fazal as he investigates principles
of RNA subcellular localization, and reaches milestone goals that will transition him into an independent
investigator. By improving the APEX-seq technique and amalgamating it with a number of cutting-edge tools
including massively-parallel reporter assays and deep-learning-based approaches, Dr. Fazal will dissect how
sequences within RNAs direct them to different locations, and how cells actively control RNA subcellular
localization to regulate gene function. This work will be carried out at Stanford University, where Dr. Fazal will
be mentored by Dr. Howard Chang, a pioneer in developing new genomics tools, and Dr. Joanna Wysocka, a
leading authority in vertebrate development and non-coding genomic regulatory elements. Both mentors have
highly-successful track records of placing postdoctoral fellows into independent academic positions at leading
institutions around the nation and world. Additional support will be available through collaboration with Drs. Shen,
Boettiger and Kundaje who will provide training and expertise in genetics, imaging, statistics and computation.
An advisory committee comprising of world-leading investigators Drs. Ting, Kool, Li, Bryant and Bassik will also
monitor progress and provide expertise. Further acquisition of scientific and professional skills will be achieved
by utilizing the educational resources available through the Stanford University School of Medicine and Office of
Postdoctoral Affairs. Stanford provides an outstanding intellectually-stimulating environment with all facilities and
resources necessary for success, and all proposed training will complement Dr. Fazal’s previous knowledge in
genomics and biophysics and facilitate his transition into a multidisciplinary RNA biologist in the field of spatial
transcriptomics.