Steven M. Johnson
The following two specific Aims are from my 2011 MEG. We made great progress and completed Aim 1 and modified our Aim 2. Below I will give a status report for each Aim.
Aim 1: Perform in vitro nucleosome (invitrosome) reconstitution on naked C. elegans genomic DNA using unmodified recombinant histone octamer to produce a modification-‐free genome-‐wide baseline map of nucleosome position preferences.
We completed this Aim and have published the results with analysis by collaborators at Rutgers and Princeton this year.
Locke, G., Haberman D., Johnson, S.M., and Morozov, A.V. (2013) Global remodeling of nucleosome positions in C. elegans. BMC Genomics, 14:284. BYU authors in bold
Aim 2: Reconstitute invitrosomes on enzymatically methylated C. elegans genomic DNA to analyze effects of DNA methylation on nucleosome formation.
Two undergraduate students, Scott Wilkes and Kade McQuivey were the initial students working on this project. They accomplished the methylation of the C. elegans genome and validation of the methylation by bisulfite sequencing. They both graduated and a new master’s student Ashley Wright took up the project in 2012 and was commencing the work when a paper came out in Nucleic Acids Research (January 2013) publishing experiments almost identical to our proposed experiments (using invitrosomes to answer the major questions). After careful evaluation of the newly published paper we concluded that they had adequately answered the questions we sought to address and Ashley shifted to related research on how end-‐bias of in vitro reconstituted nucleosome can be overcome. We have completed the wet-‐lab and informatics analysis of this project and are currently writing the manuscript for submission at the beginning of 2014. The funds for this original aim have been used to support Ashley and for materials and reagents for this modified aim.
Wright, AN., Kempton, CE., Bodily, P. and Johnson, SM. Efficient recovery of lost invitrosomes through comparative defined-end analysis. In prepairation BYU authors in bold
Overall, great progress was made in these in vivo studies in the lab. Additionally, all the students mentioned above submitted abstracts for and attended UCUR conferences (Wilkes and McQuivey) or the International C. elegans Meeting (Wright). This was a tremendous opportunity for them to talk about their research with people outside of the lab and in other fields of research and expand their scientific and future employment horizons. We greatly appreciate the MEG funding that made these projects and experiences possible.