Section: Research

Postdoctoral Position Available

Job Dekker, Ph.D.

Academic Role: Assistant Professor

Faculty Appointment(s) In:
   Biochemistry and Molecular Pharmacology
   Program in Gene Function and Expression

Other Affiliation(s):
   Interdisciplinary Graduate Program

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 to explore the spatial organization of genomes

In order to determine the spatial organization of chromosomes at high resolution we have developed the Chromosome Conformation Capture technology, commonly referred to as 3C (Dekker et al. (2002), Science, 295: 1306-1311).  3C is used to detect physical interactions between pairs of genomic loci.  3C is now widely used and has proven to be a very powerful tool to detect cis- and trans-interactions between genes and regulatory elements.  

In order to dramatically increase the throughput of the analysis of chromatin interactions we have developed the 3C-Carbon Copy (5C) technology that can be used to analyze millions of chromatin interactions in parallel (Dostie et al. (2006), Genome Research, 16(10): 1299-1309).  5C was the first method that combines 3C with microarray detection.  5C is highly versatile and can also be used in conjunction with ultra-high-throughput single molecule DNA sequencing. 

We are currently using 3C and 5C to map and study the networks of chromatin interactions that underlie long-range gene regulation in the human genome.

Chromatin looping in the human beta-globin locus

The human beta-globin locus consists of five beta-globin-like genes (e, Ag, Gg, d and b) and one beta-globin pseudogene (y).  These genes are developmentally regulated by a single element, the Locus Control Region (LCR) located upstream of the gene cluster.  This locus has served as a powerful model system to study long-range gene regulation.  The LCR was found to directly interact with the expressed beta-globin-like genes resulting in the formation of large chromatin loops.  For instance in K562 cells, that express high levels of g-globin, we found that the LCR strongly interacts with the g-globin genes but not with the other beta-globin-like genes (Dostie et al. (2006), Genome Research, 16(10): 1299-1309).  Interestingly, the LCR also interacts with a genomic element located downstream of the globin genes, although the role of this interaction is currently unclear.  A schematic representation of these looping interactions is presented in Figure 2. 

We continue to study the human beta-globin locus to understand the molecular and biochemical mechanisms that drive developmental dynamics of long-range gene regulation.

Three-dimensional organization of chromosomes and chromatin domains

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. 

We have also analyzed the effect of gene activation on the general organization of a 150 kb chromatin domain around the FMR1 gene on the human X-chromosome.  We found that gene activation results in chromatin decondensation throughout a surprisingly large 50 kb region surrounding the active promoter (Gheldof et al. (2006), PNAS 103(33): 12463-12468). The molecular mechanisms that drive these large-scale conformational changes are currently being studied.

We continue to employ 3C and 5C to study the overall spatial organization of chromosomes and chromosome domains in yeast and human cells.

Office: LRB 519
Phone: 508-856-4371
E-mail: Job.Dekker@umassmed.edu
Keywords: Cell Biology, DNA Replication, Gene Expression

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Postdoctoral Position Available A postdoctoral position is available to study in this laboratory. Contact Dr. Dekker for additional details