Matthew Blow’s research involves applying high throughput experimental and computational approaches to understand genome function. Current work is in three ongoing projects.
In the Functional Encyclopedia of Bacteria and Archea (FEBA) project, we are collaborating with the Deutschbauer group at LBNL to apply transposon mutagenesis, high throughput growth assays and novel DNA sequencing approaches to annotate gene function across dozens of diverse bacteria. This project addresses a major outstanding challenge in genome biology and aims to assign gene function information to thousands of genes of previously unknown function.
In a second project, we plan to expand on these approaches for discovery and transfer of novel pathways for phosphate solubilization. We will first use transposon mutagenesis to discover bacterial genes involved in phosphate solubilization. We will then use DNA synthesis and genome engineering to introduce these capabilities to plant root-associated bacteria. The long-term goal of this project is to engineer bacterial strains that increase the bio-availability of phosphorus from natural sources, and reduce dependency on added fertilizers.
Finally, we are using novel capabilities on the pacific biosciences sequencing platform to directly sequence DNA modifications bacteria, and explore the epigenomic landscape of bacteria. Sequencing from hundreds of diverse bacteria has revealed patterns of DNA modification that extend beyond known roles in DNA restriction systems, and hint at a widespread and hitherto underappreciated role of methylation in bacterial genome regulation.
|Matt Blow, PI||Christine Shulse,
|Christine is engineering plant-associated bacteria to release phosphate from soils, in order to improve plant growth.|
- Attanasio C, (2 authors), Blow MJ, (14 authors), Pennacchio LA. 2014. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research 24(6):920-9.
- Nord AS, Blow MJ, (11 authors), Visel A. 2013. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell 155(7):1521-31.
- Attanasio C, Nord AS, Zhu Y, Blow MJ, (15 authors), Visel A. 2013. Fine tuning of craniofacial morphology by distant-acting enhancers. Science 342(6157):440
- Visel A, (8 authors), Blow MJ, (14 authors), Rubenstein JL. 2013. A high-resolution enhancer atlas of the developing telencephalon. Cell 152(4): 895-908.
- May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA, Visel A. 2012. Large-scale discovery of enhancers from human heart tissue. Nature genetics 44(1): 89-93.
- Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio LA. 2010. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 464(7287): 409-412.
- Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel A, Pennacchio LA. 2010. ChIP-Seq identification of weakly conserved heart enhancers. Nature genetics 42(9): 806-810.
- Visel A*, Blow MJ*, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. 2009. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457(7231): 854-858.
- Blow MJ, Zhang T, Woyke T, Speller CF, Krivoshapkin A, Yang DY, Derevianko A, Rubin EM. 2008. Identification of ancient remains through genomic sequencing. Genome research 18(8): 1347-1353.
- Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. 2006. RNA editing of human microRNAs. Genome biology 7(4): R27.
- Stephens P, (10 authors), Blow M, (45 authors), Futreal PA, Wooster R, Stratton MR. 2004. Lung cancer: intragenic ERBB2 kinase mutations in tumours. Nature 431(7008): 525-526.
- Blow M, Futreal PA, Wooster R, Stratton MR. 2004. A survey of RNA editing in human brain. Genome research 14(12): 2379-2387.