The Johnson Laboratory

Dr. Steven Johnson and studentSix feet of DNA is contained in almost every cell of your body. In order to fit into a nucleus with a diameter of 1/300,000th its length, the DNA is highly compacted with proteins to form chromatin. This extreme compaction must be highly ordered to allow DNA to function in its roles in transcription and replication. The first order of this compaction is the nucleosome composed of 147 base pairs of DNA wrapping around a core of eight histone proteins. The position and density of nucleosomes on the genome play a major role in regulating genic expression. Densely packed, tightly bound nucleosomes form heterochromatin (which is transcriptionally inactive) and less dense, loosely packed nucleosomes form euchromatin in which the genes can be turned on and off as appropriate. Many decades of research in several labs has demonstrated that the underlying DNA sequence itself can influence where nucleosomes form in the genome.

In my lab we study chromatin architecture (specifically by looking at nucleosome positioning and its relation to the underlying DNA sequence in the genome) with the goal of learning how to modulate chromatin architecture by subtly manipulating the underlying DNA sequence so as to regulate gene expression. We are using both in vivo and in vitro approaches in our studies coupled with ultra-high-throughput DNA sequencing technologies. We have comprehensive nucleosome position maps for human tissues as well as for the nematode worm C. elegans (a common model organism for human genetics and disease), and are continuing studies to look at nucleosome positioning in specific cell types at different developmental stages. We are also using in vitro nucleosome reconstitution assays to define and test putative nucleosome attractive or repulsive sequences. These sequences can then be tested in vivo in the worm for their potential to regulate genic expression both temporally and spatially in C. elegans. Because of the highly conserved nature of histone proteins within the domain Eukaryotae and the absolute conservation of the chemical structure of DNA between all forms of life, what we learn from these basic studies in the worm may enable us to subtly manipulate gene expression in human cells and tissues with the potential to overcome the universal problem of gene silencing which occurs with DNA-based disease treatments such as those seen in current applications of gene-therapy.

Stained Glass C. elegans made by Steve Johnson.  Owned by Andrew Fire, Stanford University