Seeking computational biologists

Postdoc positions available for computational biologists
In the Bernstein lab we are constantly pushing the limits of transcriptomic and epigenomic technology, including single cell methods. We work together with clinicians, biologists, and chemists across multiple institutions to understand the regulation of the genome, particularly in disease states. We generate terabytes of data from a huge range of tissues and diseases. If you are a talented computational biologist interested in working with us, please email egaskell@broadinstitute.org

Project opportunity in single-molecule imaging methods

Seeking a Postdoc or Graduate Student interested in developing new single-molecule imaging methods for mapping nucleosome modifications

Are you interested in pushing the limits of epigenetic research? Are you excited about the idea of mapping chromatin and transcription factor interactions with single molecule precision? Do you want to answer long standing questions in the field regarding combinatorial histone modifications and chromatin associated proteins? Did you read our Science paper (http://science.sciencemag.org/content/352/6286/717.long) and think wow, that’s amazing, but I could make it better! If this accurately describes you, please email egaskell@broadinstitute.org because we’d like to hire you to work on this project.

Drier et al. describe positive feedback loop generated by enhancer hijacking that drives adenoid cystic carcinoma

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Drier et al. describe how enhancer hijacking rewires the regulation of the oncogenic transcription factor MYB and drives adenoid cystic carcinoma. Translocation of MYB near super-enhancers that are themselves bound by MYB creates a vicious cycle where MYB drives its own transcription. MYB also binds enhancers that drive different regulatory programs in alternate cell lineages in ACC, cooperating with TP63 in myoepithelial cells and a Notch program in luminal epithelial cells. Additional genetic hits to the Notch pathway activate Notch signaling and shift the epigenetic balance between myoepithelial and luminal cells to luminal only high grade ACC. Bromodomain inhibitors that block enhancer function slow tumor growth of low-grade ACC xenografts models in vivo.

Key findings:

  • MYB rearrangements often retain intact MYB transcript, translocating it to the NFIB locus or other loci rich in strong enhancers.
  • The translocated enhancers are driven by MYB binding, yielding oncogenic positive feedback loop driving very high levels of MYB.
  • MYB overexpression support tumorgenicity of both myoepithelial cells and luminal cells in adenoid cystic carcinoma, where MYB cooperates with TP63 in myoepithelial cells and support Notch signaling in luminal cells.
  • Genetic hits to the Notch pathways shift the epigenetic balance toward luminal cells only, yielding high-grade aggressive adenoid cystic carcinoma.
  • The bromodomain inhibitor JQ1, known to block enhancer function and specifically super-enhancer function inhibit growth of lower grade adenoid cystic carcinoma in mice xenografts.

 

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma

Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, Bradner JE, Moskaluk CA, Aster JC, Knoechel B, Bernstein BE. Nature Genetics 2016 Mar;48(3):265-72.

Flavahan, Drier et al., characterize insulator dysfunction in glioma

Will Flavahan, Yotam Drier, et al. demonstrate that hypermethylation-induced loss of genomic insulator function causes the development of oncogenic genome topology configurations in IDH1-mutant glioma. This topological restructuring allows a constitutive housekeeping enhancer to interact with and drive the potent glioma oncogene PDGFRA.

Key Findings:

-The hypermethylator phenotype observed in IDH1-mutant glioma extends to CpGs present in the binding sites of the methylation-sensitive insulator protein, CTCF, leading to loss of key insulators in these cells.
-Loss of an insulator protecting PDGFRA results in oncogene activation and tumor progression.
-Treatment of IDH1 mutant cells with the DNMT inhibitor 5-azacytidine allowed restoration of insulator function and silencing of PDGFRA.
-CRISPR deletion of insulators in IDH1 wild type glioma cells activated PDGFRA expression and increased cellular proliferation in a PDGFRA-dependent manner.

Insulator dysfunction and oncogene activation in IDH mutant gliomas.
Flavahan WA*, Drier Y*, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE. Nature. 2016 Jan 7;529(7584):110-4. doi: 10.1038/nature16490.

Quantitative multiplex ChIP-seq is here

van Galen et al. introduce Mint-ChIP, an approach for multiplexed ChIP-seq on small cell numbers. The approach allows quantitative comparisons of global and locus-specific histone modification levels. The technology is demonstrated by mapping hematopoietic stem cell chromatin landscapes and quantifying changes in leukemia cells treated with epigenetic inhibitors. Detailed protocol now available on the Resources page.

Highlights

– Mint-ChIP enables highly multiplexed ChIP-seq on low-input samples

– Quantitative precision is achieved by normalizing histone modifications to total H3

– Active and repressed regions are mapped in human hematopoietic stem cells

 

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes

van Galen, Peter et al. Molecular Cell.

 

Ryan, Drier et al. link enhancers to oncogene activation in B cell lymphoma

Russell Ryan and Yotam Drier describe PEAR-ChIP, a novel approach for the detection of genomic rearrangements associated with acetylated chromatin. The authors apply this technology to patient samples from several distinct subtypes of B cell lymphoma, revealing therapeutically targetable rearrangements, and uncovering novel mechanisms by which the oncogenes MYC and BCL6 are regulated via native and rearranged enhancers.

Key findings:

  • PEAR-ChIP allows for genome-wide enhancer activity and rearrangement detection in a single protocol
  • PEAR-ChIP analysis of mantle cell lymphoma, diffuse large B cell lymphoma, and chronic lymphocytic leukemia reveals “enhancer hijacking”, enhancer amplification, gene fusion, and inactivating rearrangements affecting numerous cancer genes, including CCND1, BCL2, MYC, BCL6, PDCD1LG2, CIITA, and others.
  • Lymphoma subtype-specific MYC enhancers are active in lymphomas lacking MYC rearrangements, and are associated with SNPs linked to inherited lymphoma risk.
  • Germinal center-specific BCL6 enhancers are activated by the oncogenic transcription factor MEF2B, and can activate MYC via enhancer hijacking in a “pseudo-double-hit” t(3;8)(q27;q24) rearrangement.

 

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma.

Ryan RJ, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE. Cancer Discov. 2015 Jul 30. pii: CD-15-0370.