Scientific Papers

For more papers, visit a faculty member's page from the listing on Whitehead Faculty and access the PubMed link.

The history of the Y chromosome in man.

Nat Genet. 2016 May 27;48(6):588-9.

Hughes, J.F.*, and Page, D.C.*

Studies of the Y chromosome over the past few decades have opened a window into the history of our species, through the reconstruction and exploitation of a patrilineal (Y-genealogical) tree based on several hundred single-nucleotide variants (SNVs). A new study validates, refines and extends this tree by incorporating >65,000 Y-linked variants identified in 1,244 men representing worldwide diversity.


Mule regulates the intestinal stem cell niche via the Wnt pathway and targets EphB3 for proteasomal and lysosomal degradation.

Cell Stem Cell. 2016 May 11.

Dominguez-Brauer, C., Hao, Z., Elia, A.J., Fortin, J.M., Nechanitzky, R., Brauer, P.M., Sheng, Y., Mana, M.D., Chio, II, Haight, J., Pollett, A., Cairns, R., Tworzyanski, L., Inoue, S., Reardon, C., Marques, A., Silvester, J., Cox, M.A., Wakeham, A., Yilmaz, O.H., Sabatini, D.M.*, van Es, J.H., Clevers, H., Sato, T., and Mak, T.W.

The E3 ubiquitin ligase Mule is often overexpressed in human colorectal cancers, but its role in gut tumorigenesis is unknown. Here, we show in vivo that Mule controls murine intestinal stem and progenitor cell proliferation by modulating Wnt signaling via c-Myc. Mule also regulates protein levels of the receptor tyrosine kinase EphB3 by targeting it for proteasomal and lysosomal degradation. In the intestine, EphB/ephrinB interactions position cells along the crypt-villus axis and compartmentalize incipient colorectal tumors. Our study thus unveils an important new avenue by which Mule acts as an intestinal tumor suppressor by regulation of the intestinal stem cell niche.


Comparative transcriptomics across the prokaryotic tree of life.

Nucleic Acids Res. 2016 May 6.

Cohen, O., Doron, S., Wurtzel, O.*, Dar, D., Edelheit, S., Karunker, I., Mick, E., and Sorek, R.

Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to 'transcriptional noise'. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5'UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at, setting a framework for comparative studies of the microbial non-coding genome.


Induced pluripotent stem cells meet genome editing.

Cell Stem Cell. 2016 May 5;18(5):573-86.

Hockemeyer, D., and Jaenisch, R.*

It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments-the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology-have fundamentally reshaped our approach to biomedical research, stem cell biology, and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided and set the stage for their success.


Epigenetics: Cell-type methylomes in the root.

Nat Plants. 2016 May 4;2(5):16061.

Gehring, M.*

A new study combines cell sorting with DNA methylation and RNA profiling to identify novel epigenomic features in plant roots.


The shrinking mitochondrion.

Scientist. 2016 May 1; 30: 22-23.

Johnston, I., and Williams, B.*

Scanning the mitochondrial genomes of thousands of species is beginning to shed light on why some genes were lost while others were retained.


Polyspermic fertilization resulting in multipolarity in a sea star zygote.

Mol Reprod Dev. 2016 May;83(5):375.

Swartz, S.Z.*


A specialized flavone biosynthetic pathway has evolved in the medicinal plant, Scutellaria baicalensis.

Sci Adv. 2016 Apr; 2(4): e1501780.

Zhao, Q., Zhang, Y., Wang, G., Hill, L., Weng, J.K.*, Chen, X.Y., Xue, H., and Martin, C.

Wogonin and baicalein are bioactive flavones in the popular Chinese herbal remedy Huang-Qin (Scutellaria baicalensis Georgi). These specialized flavones lack a 4'-hydroxyl group on the B ring (4'-deoxyflavones) and induce apoptosis in a wide spectrum of human tumor cells in vitro and inhibit tumor growth in vivo in different mouse tumor models. Root-specific flavones (RSFs) from Scutellaria have a variety of reported additional beneficial effects including antioxidant and antiviral properties. We describe the characterization of a new pathway for the synthesis of these compounds, in which pinocembrin (a 4'-deoxyflavanone) serves as a key intermediate. Although two genes encoding flavone synthase II (FNSII) are expressed in the roots of S. baicalensis, FNSII-1 has broad specificity for flavanones as substrates, whereas FNSII-2 is specific for pinocembrin. FNSII-2 is responsible for the synthesis of 4'-deoxyRSFs, such as chrysin and wogonin, wogonoside, baicalein, and baicalin, which are synthesized from chrysin. A gene encoding a cinnamic acid-specific coenzyme A ligase (SbCLL-7), which is highly expressed in roots, is required for the synthesis of RSFs by FNSII-2, as demonstrated by gene silencing. A specific isoform of chalcone synthase (SbCHS-2) that is highly expressed in roots producing RSFs is also required for the synthesis of chrysin. Our studies reveal a recently evolved pathway for biosynthesis of specific, bioactive 4'-deoxyflavones in the roots of S. baicalensis.


Generation of fluorogen-activating designed ankyrin repeat proteins (FADAs) as versatile sensor tools.

J Mol Biol. 2016 Mar 27;428(6):1272-89.

Schutz, M., Batyuk, A., Klenk, C., Kummer, L., de Picciotto, S., Gulbakan, B., Wu, Y.F., Newby, G.A.*, Zosel, F., Schoppel, J., Sedlák, E., Mittl, P.R., Zenobi, R., Wittrup, K.D., and Plückthun, A.

Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biological molecules of interest. Recently, a novel class of fluorescence based probes, fluorogen-activating proteins (FAPs), has been reported. These binding proteins are based on antibody single-chain variable fragments and activate fluorogenic dyes, which only become fluorescent upon activation and do not fluoresce when free in solution. Here we present a novel class of fluorogen activators, termed FADAs, based on the very robust designed ankyrin repeat protein scaffold, which also readily folds in the reducing environment of the cytoplasm. The FADA generated in this study was obtained by combined selections with ribosome display and yeast surface display. It enhances the fluorescence of malachite green (MG) dyes by a factor of more than 11,000 and thus activates MG to a similar extent as FAPs based on single-chain variable fragments. As shown by structure determination and in vitro measurements, this FADA was evolved to form a homodimer for the activation of MG dyes. Exploiting the favorable properties of the designed ankyrin repeat protein scaffold, we created a FADA biosensor suitable for imaging of proteins on the cell surface, as well as in the cytosol. Moreover, based on the requirement of dimerization for strong fluorogen activation, a prototype FADA biosensor for in situ detection of a target protein and protein protein interactions was developed. Therefore, FADAs are versatile fluorescent probes that are easily produced and suitable for diverse applications and thus extend the FAP technology.


*Author affiliated with Whitehead Institute for Biomedical Research

© Whitehead Institute for Biomedical Research         Nine Cambridge Center    Cambridge, MA 02142