The ability of the retinoblastoma protein (pRB) to restrict the cell cycle is well known. Since KDM5A/RBP2/JARID1A is associated with pRB/E2F, one may wonder about its recruitment and its role in the cell cycle. In our study we determined how KDM5A uses its demethylating capability on cell cycle genes during differentiation. We also wanted to know if the demethylation function of KDM5A is non-redundant. It was previously shown that KDM5A and E2F colocalize. We aimed to know at what point of the cell cycle KDM5A is recruited, and whether E2F plays a role in KDM5A recruitment or vice-versa. We focused on the genomic localization of KDM5A in mouse ES cells and human U937 cells at different stages of development.
In this study I analyzed KDM5A ChIP-seq data in mouse embryonic stem (ES) cells to determine the location and distribution of these targets in various genomic features. I classified KDM5A locations based on distances and analyzed microarray expression data to test correlations in binding and expression, and to identify KDM5A targets that are activated upon cellular differentiation in absence of KDM5A. Also, I analyzed public ChIPseq and ChIP-on-chip data to determine genome-wide overlap and the specific locations of KDM5A and E2F. This overlap of targets and the functional clustering approaches pointed to KDM5A recruitment to E2F-dependent mitotic genes and functions of common interest. When I coupled these ﬁndings to gene expression data, I observed that these genes are repressed, indicating a contribution of KDM5A to cell cycle regulation. However, I have also identified E2F independent recruitment of KDM5A and those interesting targets functions.
This study was conducted in international collaboration between a wet lab and a bioinformatics lab in the USA and Spain, respectively. The experimental part of this study was done mainly by Michael Beshiri & Katherine B. Holmes under supervision of Dr. Elizabeta Benevolenskaya, at the Department of Biochemistry and Molecular Genetic, University of Illinois at Chicago, USA and William G. Kaelin Jr., at Dana–Farber Cancer Institute in Boston. The bioinformatics part was supervised by Dr. Nuria Lopez Bigas, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, Spain.
Overall we found that KDM5A is co-recruited with components of the DREAM complex at E2F targets. However, KDM5A and E2F4 independently contribute to repression of cell cycle genes during differentiation, but they act co-operatively to repress cell-cycle genes. KDM5A recruitment to the E2F-dependent cell cycle genes occur at the later stage (96h) of differentiation. This function of gene repression by KDM5A is a methylation-dependent function. This function of KDM5A is non-redundant and cannot be compensated by KDM5A homolog KDM5B.
This work just has been published in PNAS:
Michael L. Beshiri, Katherine B. Holmes, William F. Richter, Samuel Hess, Abul B. M. M. K. Islam, Qin Yan, Lydia Plante, Larisa Litovchick, Nicolas Gévry, Nuria Lopez-Bigas, William G. Kaelin, Jr. and Elizaveta V. Benevolenskaya Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation. PNAS 2012.