- Bracht Lab Research Interests: For an organism to survive, the genome, the complete set of DNA in a cell, must be stably maintained and correctly regulated. Given the central importance of the genome, it is surprising that some organisms simply eliminate significant portions of it from some or all cells. Genome changes are also linked to cancer, a fundamentally genomic disease. My lab works on interesting questions surrounding genome dynamics: how does the organism maintain--and sometimes purposefully alter--its genome architecture, and how can it go awry in disease? Genomic methods used in this work include next-generation sequencing of DNA and RNA, cell culture, and computational methods. A particular focus of my laboratory is the role of epigenetics--a genetic code-on-a-code-in controlling genome structure and function.
Paffhausen E*, Alowais Y*, Chao C, Callihan E, Creswell K, Bracht, JR. Discovery of a stem-like multipotent cell fate. American Journal of Stem Cells. In press. (* = co-first authors)
Lindblad KA*, Bracht, JR*, Williams AE, Landweber LF. Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 2017 April 27. (* co-first authors)
Bracht JR*, Wang X*, Shetty K, Chen X, Uttarotai G, Callihan E, McCloud S, Clay D, Wang J, Nowacki M, Landweber LF. Chromosome fusions triggered by noncoding RNA. RNA Biology. 2016 Jun 7:1-12. (* co-first authors)
Chen X*, Bracht JR*, Goldman A, Swart E, Dolzhenko E, Swart E, Clay D, Perlman DH, Doak TG, Stuart A, Amemiya C, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell, Aug. 28, 2014. (*co-first authors)
Bracht JR. Beyond transcriptional silencing: Is cytosine methylation a widely conserved eukaryotic DNA elimination mechanism? BioEssays. April 2014 36(4):346-52.
Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF. Genomes on the Edge: Programmed Genome Instability in Ciliates. Cell. 2013 Jan 31;152(3):406-416.
Swart E, Bracht JR, Magrini V, Minx P,Chen X, Zhou Y, Khurana J, Goldman AD, Nowacki M, Schotanus K, et al. The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with over 16,000 Tiny Chromosomes. PLoS Biology. 2013 Jan 29;11(1).
Fang W, Wang X, Bracht JR, Nowacki M, Landweber LF. Piwi-Interacting RNAs Protect DNA Against Loss During Oxytricha Genome Rearrangement. Cell. 2012 Dec 7;151(6):1243-1255.
Bracht JR*, Perlman DH, Landweber LF*. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biology. 2012 Oct 17;13(10):R99. *corresponding.
The Bracht lab investigates the process of genome rearrangement in the ciliate Oxytricha trifallax: Genomic methods used in this work include next-generation sequencing of DNA and RNA, cell culture, and computational methods.
Honors, Awards, and Fellowships
NSF I-Corps Teams. Using genomics to detect pathogens. National Science Foundation. (2016-2017)
K22 Transition Career Development Award (National Institutes of Health, National Cancer Institute): Model systems for the investigation of DNA methylation and drug repurposing (2014-2017)
F32 NRSA Postoctoral Fellowship: Epigenetic regulation of programmed genome instability in O. trifallax (2012-2014)
Area of Expertise
cell biology, genomics, computational genomics
As an assistant professor in AU's Dept. of Biology, Bracht researches how genome architecture is established and maintained in healthy cells and how it goes awry in disease. He uses a unicellular eukaryote, the ciliate Oxytricha trifallax, as a model system for the role of epigenetics — information on the DNA molecule but outside the DNA sequence — in controlling genome architecture.