Jacob Jaffe is the assistant director of the Proteomics Platform at the Broad Institute. Proteomics is the study of the full complement of proteins encoded in the human genome along with changes made to the proteins after they are created, known as post-translational modifications.
In the cell’s nucleus, DNA wraps around chromatin proteins called histones, which can carry a variety of post-translational modifications, often thought of as chromatin “marks.” Jaffe’s primary research interest is the biochemistry of these histone marks, which are part of the cell’s “epigenome” – inherited genetic elements other than DNA. It has recently been shown that certain combinations of chromatin marks greatly influence the activity of DNA with which they are associated. Through techniques developed in the Proteomics Platform, Jaffe has been able to characterize a full complement of these marks. He aims to understand how chromatin marks change in models of cellular differentiation and disease, and explore the idea of epigenetic signatures that can differentiate among cancers.
As assistant director of the platform, Jaffe also directs research aimed at elucidating protein-protein, protein-DNA, and protein-small-molecule interactions. The core enabling technology of Jaffe’s work is mass spectrometry, which allows precise identification and quantification of thousands of proteins in an unbiased manner. Jaffe is an expert in the quantitative analysis of the proteome using stable-isotope labeling techniques (such as SILAC or iTRAQ), as well as algorithmic development for statistical modeling of proteomics data.
Jaffe joined the Broad in 2004 after earning a Ph.D. in biology/biochemistry from Harvard University in the laboratories of Broad Senior Associate Member George Church and Howard Berg.Select Publications
Riddle NC, et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb;21(2):147-63.
Markljung E, et al. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol 2009 Dec;7(12):e1000256.
Rudomin EL, Carr SA, Jaffe JD. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). J Proteome Res. 2009 Jun;8(6):3154-60.
Jaffe JD, et al. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol Cell Proteomics. 2008 Oct;7(10):1952-62.