Dr Paul Bertone
Genomic analysis of pluripotency in embryonic development
Laboratory: Stem Cell Institute, Gleeson Building.
My group is dedicated to understanding stem cell function, the regulation of pluripotency and the properties of corrupted stem cells that give rise to proliferative cancers. In addition to strengthening critical mass in these areas, my background spans both computational and experimental methods, allowing me to develop multidisciplinary approaches to stem cell biology that leverage sophisticated genomic and bioinformatic analyses. I have been an early adopter and inventor of emerging technologies, and play an important role in enhancing the capabilities of the SCI through the application of single-cell profiling, high-throughput sequencing assays, and integrated bioinformatics. I believe that coming from a quantitative mindset brings a valuable perspective to this work, and often inspires experimental protocols designed to produce datasets of unmatched quality and precision. I augment and strengthen the analytical resources of the SCI, and bring novel methods to the Institute of broad utility to multiple labs.
Common marmoset blastocyst immunostained to show pluripotency factor NANOG localised to the inner
cell mass, primitive endoderm specifier GATA6, outer trophectoderm marker CDX2 and nuclei.
We study embryonic and tissue-specific stem cells using a combination of experimental and computational methods, leveraging state-of-the-art genomic technologies to address fundamental aspects of development and disease. We wish to achieve a comprehensive molecular understanding of the naive pluripotent state and to characterise species-specific differences in pluripotent cell specification. We study the emergence of pluripotent cells in rodent, human and non-human primate embryos to define the transcriptional regulatory networks that induce and support naive pluripotency. A second research area entails the analysis of tumour-initiating neural stem cells that drive glioblastoma. We carry out genome-wide analyses to determine chromosomal, mutational and transcriptional aberrations in patient-derived cell lines. These data provide a unified framework for the characterisation and functional analysis of corrupted stem cell populations that support cancer progression.
- Ewan Johnstone
- Giuliano Stirpraro
- Maria Xenophontos
Boroviak T, Loos R, Lombard P, Behr R, Sasaki E, Nichols J, Smith A, Bertone P (2015) Lineage-specific profiling delineates the emergence and progression of naïve pluripotency in mammalian embryogenesis. Dev Cell. 2015 Nov 9;35(3):366-82. PMCID:PMC4643313
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P (2013) Assessment of transcript reconstruction methods for RNA-seq. Nat Methods 10: 1177–84. PMCID:PMC3851240
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P (2013) Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods 10: 1185–91.PMCID:PMC4018468
Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E (2013) Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 494: 77–80. PMCID:PMC3672958
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M (2004) Global identification of human transcribed sequences with genome tiling arrays. Science 306: 2242–6. PMID:15539566