The laboratory of Job Dekker PhD (HHMI, UMass Med School) is seeking outstanding candidates to join a multidisciplinary team of molecular biologists, statisticians and bioinformaticians.  Email to Job Dekker: job.dekker@umassmed.edu

 

We are a highly interdisciplinary lab, combining experimental and computational efforts to study how genomes function.  We are funded by the Howard Hughes Medical Institute and NIH. Recently we established the Center for 3D Structure and Physics of the Genome, as part of the NIH 4D Nucleome Consortium, to study the spatial organization of the human genome.



The Dekker Lab is one of the leading labs in the world that studies how the genome is organized in three dimensions in the cell nucleus.  To explore and study genome folding we first developed several genomics technologies such as 3C, 5C and Hi-C (Dekker, Science 2002, Dostie Genome Res. 2006, Lieberman Aiden, van Berkum, Science 2009).  These technologies employ deep sequencing to produce massive genome-wide chromatin interaction maps that we then analyze using a whole suite of computational and bioinformatic methods that we developed ourselves, and in collaboration with our close collaborators in the laboratory of Leonid Mirny (MIT).  (See Lajoie, Nature Methods 2009, Imakaev, Nature Methods 2012).



Our research has revealed new insights into the mechanisms of long-range gene regulation by distal enhancers (Sanyal, Nature 2012), the compartmentalization of chromatin in distinct functional domains (Nora, Nature 2012), the internal organization of the chromatin fiber (Dekker, JBC 2008), the structure of mitotic chromosomes (Naumova, Science 2013), and the overall organization of entire genomes inside the nucleus (Gibcus, Mol. Cell 2013).



Recently NIH started the 4D Nucleome initiative (https://commonfund.nih.gov/4dnucleome/index).  Our lab heads one of the largest centers in this network.  In our center we employ state-of-the-art genomics, imaging, genome engineering, computational modeling and bioinformatic approaches to study the structure and biophysics of the human genome.  We are looking for enthusiastic bioinformaticians and computational biologists to participate in and lead the analysis component of our Center.  In these positions, you would be playing a key role in the Center, as well as in the international 4D Nucleome Consortium to explore this exciting new area of genome sciences.

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Academic Background

Job Dekker received his B.S. (1993) and his Ph.D. (1997) from the University of Utrecht, The Netherlands. From 1998 to 2003, he was a post-doctoral fellow at Harvard University during which time he was awarded an NWO-TALENT stipendium, an EMBO long-term fellowship and a fellowship from The Medical Foundation / Charles A. King Trust. Dr. Dekker joined the University of Massachusetts Medical School as an Assistant Professor in the Program of Gene Function and Expression in the spring of 2003. In 2008 he was promoted to Associate Professor, and in 2011 to Professor. He is a recipient of a 2007 W. M. Keck Foundation Distinguished Young Scholar in Medical Research Award, and the 2011 ASBMB Young Investigator Award. In 2011 he became co-director (with Dr. Marian Walhout) of the newly established Program in Systems Biology.  Job Dekker was appointed Investigator of the Howard Hughes Medical Institute in 2015.

For more information about the Dekker lab, to access tools and view and download published datasets please visit our website: http://jobdekkerlab.umassmed.edu

Job Dekker is a member of the Center for Cancer Systems Biology (CCSB) at the Dana-Farber Cancer Institute. For more information about CCSB see: http://ccsb.dfci.harvard.edu.

Spatial Organization of Genomes

We study how a genome is organized in three dimensions inside the nucleus.  The spatial organization of a genome plays important roles in regulation of genes and maintenance of genome stability.  Many diseases, including cancer, are characterized by alterations in the spatial organization of the genome.  How genomes are organized in three dimensions, and how this affects gene expression is poorly understood.  To address this issue we study the genomes of human and yeast, using a set of powerful molecular and genomic tools that we developed.

From linear sequence to three-dimensional organization

Although the DNA of chromosomes is a linear sequence, the living genome does not function in a linear fashion.  This is most clearly illustrated by the fact that genes are often regulated by elements that can be located far away along the genome sequence. Recent evidence shows that regulatory elements can act over large genomic distances by engaging in direct physical interactions with target genes, resulting in the formation of chromatin loops.  Based on these observations we have proposed that the spatial organization of the genome resembles a three-dimensional network that is driven by physical associations between genes and regulatory elements, both in cis (along the same chromosome) and in trans (between different chromosomes) (Dekker (2006), Nature Methods, 3(1): 17-21).

How does the spatial organization of a genome relate to its regulation and function?

In each cell type a distinct set of genes is expressed and therefore the spatial organization of the genome will likely be cell-type specific.  Insights into the mechanisms that modulate the spatial organization of the genome will greatly contribute to a better understanding of tissue-specific gene regulation and may reveal causes of human diseases that are due to defects in these processes.

In order to understand the spatial organization of a genome we try to answer the following questions.  Which regulatory elements interact with each of the genes in the human genome?  What drives the specificity of these interactions?  Can we identify proteins that mediate these interactions?  How do interactions between regulatory elements and genes result in activation and repression of genes?  How do defects in these interactions result in human disease?  Can we use information about chromatin interactions to generate three-dimensional models of chromosomes?

Tools we developed for mapping the spatial organization of genomes: 3C, 5C and Hi-C

We developed Chromosome Conformation Capture (3C), which is used to detect physical interactions between genomic elements (Dekker et al. Science, 2002).  Using 3C we, and others, discovered that gene regulation is mediated by the three-dimensional organization of chromosomes that brings genes and their regulatory elements in close spatial proximity.  3C is now widely used and already has had a major impact on studies of genome regulation.

Large-scale detection of long-range chromatin interactions will be instrumental in mapping genome-wide networks of communication between genomic elements and the determination of the three-dimensional folding of the genome.  My group was the first to combine 3C with ultra-high-throughput DNA sequencing, thereby dramatically increasing the scale at which interactions between genomic loci can be studied.  Specifically, we have developed 5C, a high-throughput version of 3C for large-scale mapping of chromatin interaction networks (Dostie et al. Genome Res. 2006).  To enable the community to adopt 5C and related technologies we have developed "my5C", a publicly available set of computational tools for design of 5C studies and for visualization and analysis of any large chromatin interaction data sets (my5C.umassmed.edu; Lajoie et al. Nature Methods 2009).

Ultimately we aim to obtain detailed insights into the three-dimensional arrangements of complete genomes at Kb resolution.  To this end we developed the Hi-C technology: a genome-wide and unbiased method that combines 3C with deep sequencing (Lieberman-Aiden, van Berkum et al. Science 2009).  We have applied Hi-C to generate the first comprehensive and unbiased long-range interaction maps of the human genome.  Hi-C data reveal both known hallmarks of nuclear organization (e.g. formation of chromosome territories, and preferred co-location of particular pairs of chromosomes) as well as novel folding principles of chromosomes.  First, we found that the human genome is divided over two types of spatial compartments, one containing active chromatin, and one containing all inactive segments of the genome.  Second, we discovered a novel higher order chromatin folding motif: at the megabase scale, our data are consistent with a model in which chromatin is described by a polymer state known as the fractal globule: a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.   This conformation is an extremely efficient solution for packing long chromosomes inside the nucleus.  Hi-C data for GM06990 lymphoblastoid cells and for K562 erythroleukemia cells is available in a user friendly format at our website: http://hic.umassmed.edu.

Topologically Associating Domains

Using 5C technology, and in collaboration with the laboratory of Dr. Edith Heard, we discovered that mammalian chromosomes are composed of Topologically Associating Domains (TADS; Nora et al. Nature 2012). TADs are hundreds of Kb in size and are characterized by frequent interactions between loci located within the same TAD, but much lower interaction frequencies between loci located in different TADs. We found that TADs are determined by cis-acting boundary regions and spatially separate adjacent TADS. Furthermore, TADs represent functional units as genes located within TADs show related gene expression patterns. We propose that TADs are fundamental structural and functional building blocks of chromosomes.

Gene regulation by long-range looping interactions

The most direct way in which chromosome folding affects gene regulation is through the formation of long-range looping interactions between gene promoters and distal gene regulatory elements such as enhancers. As part of the ENCODE project, we recently completed a comprehensive analysis of looping interactions between genes and distal elements throughout 1% of the human genome (Sanyal, Lajoie et al. Nature 2012). We discovered >1,000 long-range interactions between promoters and distal sites that include elements resembling enhancers, promoters and CTCF-bound sites. We observed significant correlations between gene expression, promoter-enhancer interactions and the presence of enhancer RNAs. Long-range interactions display striking asymmetry with a bias for interactions with elements located ~120 Kb upstream of the TSS. Long-range interactions are often not blocked by sites bound by CTCF and cohesin implying that many of these sites do not demarcate physically insulated gene domains. Further, only ~7% of looping interactions are with the nearest gene, suggesting that genomic proximity is not a simple predictor for long-range interactions. Finally, promoters and distal elements are engaged in multiple long-range interactions to form complex networks. Our results start to place genes and regulatory elements in three-dimensional context, revealing their functional relationships.

Building three-dimensional models of chromosomes

As a first step towards studying the spatial organization of entire chromosomes we have used 3C to determine the three-dimensional structure of yeast chromosome III (Dekker et al. (2002), Science, 295: 1306-1311).  We generated a matrix of interaction frequencies and developed mathematical tools to determine a population-average three-dimensional model of this ~320 kb chromosome based on the pattern of chromatin interactions (Figure 3).  Chromosome III emerged as a contorted ring, due to prominent interactions between the sub-telomeric regions. 

More recently, we worked with the laboratory of Dr. Marc A. Marti-Renom to use chromatin interaction data to build spatial models of chromosomal domains and even complete genomes. For instance, using 5C data for the human alpha-globin domain, we discovered that chromatin folds in globular domains of several hundreds of Kb (Baù, Sanyal, A. et al. Nat. Struct. Mol. Biol.) 2011 . These are probably equivalent to TADs (see above). In collaboration with Mark Umbarger and George Church we were able to generate a three-dimensional model of the complete genome of the bacterium Caulobacter crescentus, which led to the identification of cis-elements that determine the folding of the entire genome (Umbarger, Toro et al. Mol. Cell 2011.

For more information on the work in my laboratory, please see our lab website at http://my5c.umassmed.edu/welcome/welcome.php

Figures

Figure 1.   (a) Genes (blue rectangles) and regulatory elements (red circles) are linearly organized along chromosomes (top), but as a result of specific interactions between elements (indicated by arrows, both in cis and in trans) a complex three-dimensional network is formed inside the cell (bottom).  (b) Schematic representation of the 3C assay.  Chromatin is cross-linked, digested with a restriction enzyme and then ligated.  Specific ligation products can be detected by PCR.  [Figure from Dekker (2006), Nature Methods, 3(1): 17-21].

Figure 2.   Schematic representation of the human beta-globin locus.  Activation of the g-globin genes in K562 cells involves interactions between the LCR and the activated genes resulting in a large (~40 kb) chromatin loop.  The LCR also interacts with an element located downstream of the locus (3’HS1).

Figure 3. Spatial organization of yeast chromosome III (~ 320 kb) as determined by Chromosome Conformation Capture (3C). 3C was applied to determine the frequency with which several loci along the chromosome interact.  Interaction frequencies were then used to model the average spatial organization of the chromosome.  Interactions between the telomeres result in the formation of a ring-like structure with a diameter of around 300 nm.

Laboratory Personnel

Karrie Brown, Executive Secretary to the chair

Houda Belaghzal, Graduate Student

Johan Gibcus, Instructor

Noam Kaplan, Postdoctoral Fellow

Bryan Lajoie, Bioinformatician Level III

Yu (Sunny) Liu, Postdoctoral Fellow

Marlies Oomen, Graduate Student

Allana Schooley, Postdoctoral Fellow

Anne-Laure Valton, Postdoctoral Fellow

Liyan Yang, Research Associate Level II

Ye Zhan, Research Associate Level II

 

Rotation Projects

Multiple rotation projects are available in several areas related to long-range gene regulation and higher order chromosome organization.  Projects include thorough analyses of the biochemical mechanisms of long-range gene regulation of specific disease-related genes, as well as large-scale analyses of chromosome organization using high-throughput genomics technologies (5C and Hi-C).  The lab employs a wide range of experimental approaches, including cell culture, protein biochemistry, microscopy, genomics as well computational approaches such as bioinformatics and modeling.  Specific rotation projects are determined dependent on the interest of the student.