R. Nicholas Laribee
264 Cancer Research Building
- Ph.D., Indiana University School of Medicine, Bloomington, IN, Microbiology and Immunology
- B.S., Indiana University-Bloomington, Bloomington, IN, Biology
Epigenetics, gene regulation and signal transduction
Epigenetics; Chromatin; Gene transcription; nutrient signaling; mTORC1
While DNA is the purveyor of genetic information, the human genome is not composed solely of DNA. Instead, it is packaged with histone proteins to form individual nucleosomes which is the basic unit of chromatin found in all eukaryotic cells. Individual nucleosome particles, and their internucleosomal interactions, form compacted three-dimensional structures that allow genomes to be packaged into nuclei. This genomic compaction into chromatin is essential for compressing and storing the genetic material in nuclei; however, the physical state of chromatin is resistant to biochemical reactions requiring access to the underlying DNA template. Therefore, eukaryotic cells ranging from yeast to man have evolved highly conserved biochemical mechanisms that control chromatin structure and function to regulate these DNA-templated processes. These mechanisms include histone post-translational modifications, DNA methylation, ATP-dependent chromatin remodeling, histone chaperone-dependent nucleosome regulation and the incorporation of histone variants.
The modulation of chromatin structure is typically regarded as “epigenetic” regulation due to the potential for these altered chromatin states to be propagated through multiple cell divisions and, in some cases, through multiple organismal generations. Epigenetic regulation can be significantly influenced by environmental factors, including such things as diet and stress. Similarly, changes in cellular metabolism also contribute to the regulation of chromatin as many of the cofactors needed in enzymatic reactions necessary for DNA and histone modifications are generated as a consequence of cellular metabolism. As such, the dysregulation of epigenetic processes through many different mechanisms can either contribute to, or cause, a number of human diseases including cancer, cardiovascular disease, and many neurodevelopmental disorders. Furthermore, the process of aging alters epigenetic pathways that impair the maintenance of the chromatin fiber. Aging-dependent chromatin alterations ultimately lead to the physical degradation of chromatin and can be a contributing factor in the enhanced susceptibility to diseases such as cancer that occurs in older individuals. Therefore, determining how epigenetic processes function is essential for understanding how the environment affects human health and disease. Our laboratory uses budding yeast as a genetic and biochemical model to understand the molecular mechanisms by which the environment affects chromatin regulation. Yeast provide unparalleled genetic and biochemical approaches for teasing apart the complex nature of these processes yet the information gained from these studies is highly applicable to the corresponding pathways in human cells as these processes are highly conserved. For example, human replication-independent histone H3, one of the core histone proteins contained in the nucleosome, differs from yeast histone H3 by only three amino acids! Our laboratory has several on-going projects to dissect these mechanisms which are outlined briefly below.
The Ccr4-Not complex is a nine subunit protein complex conserved from yeast to man. This complex functions in every step of the gene expression process, including the regulation of chromatin structure, to control cell growth, proliferation and development. In mammals, this complex is required for the maintenance of embryonic stem cells and is essential for embryogenesis. Our laboratory is currently defining how nutrient signaling through the mechanistic target of rapamycin complex 1 (mTORC1) pathway utilizes this multiprotein complex to regulate gene transcription necessary for cell growth and proliferation. We have several ongoing projects related to the function of this complex in eukaryotic cells as described below.
1. Role of mTORC1-regulated histone post-translational modifications in gene transcription. Our laboratory recently published a genetic screen of a library of histone H3 and histone H4 mutants to identify those individual histone residues exhibiting genetic interactions with the mTORC1 signaling pathway (Chen et al, Epigenetics & Chromatin, 2013). We identified several sites on both histone H3 and H4 that are functionally linked to mTORC1, including the identification of an absolutely essential and novel role for histone H3 lysine 37 (H3K37) in mTORC1-dependent cell growth control. Mutation of H3K37 to alanine (H3K37A) causes cell death by necrosis when mTORC1 signaling is decreased which is a surprising result since pharmacological mTORC1 inhibition typically results in cytostatic, but not cytoxic, effects. We have determined that one role for H3K37 in the mTORC1 signaling pathway may be to anchor high mobility group (HMG) proteins to chromatin and that specific disruption of HMG chromatin binding induces cell death. Our laboratory is exploring the concept that mTORC1 signaling actively regulates multiple histone post-translational modifications that promote HMG chromatin binding and suppression of necrosis as well as those modifications that function in mTORC1-dependent transcriptional regulation. Our long term goals with this project are to both understand how mTORC1 regulates histone modifications to affect chromatin structure as well as identify chromatin pathways to target pharmacologically to enhance the anti-cancer activities of mTORC1 inhibitors.
- Fasken, MB, Laribee, RN, Corbett, AH. Nab3 facilitates the function of the TRAMP complex in RNA processing via recruitment of Rrp6 independent of Nrd1. PLoS Genet, 11 (3), e1005044, 2015.
- Laribee, RN, Hosni-Ahmed, A, Workman, JJ, Chen, H. Ccr4-not regulates RNA polymerase I transcription and couples nutrient signaling to the control of ribosomal RNA biogenesis. PLoS Genet, 11 (3), e1005113, 2015.
- Workman, JJ, Chen, H, Laribee, RN. Environmental signaling through the mechanistic target of rapamycin complex 1: mTORC1 goes nuclear. Cell Cycle, 13 (5), 714-25, 2014.
- Chen, H, Workman, JJ, Tenga, A, Laribee, RN. Target of rapamycin signaling regulates high mobility group protein association to chromatin, which functions to suppress necrotic cell death. Epigenetics Chromatin, 6 (1), 29, 2013.
- Chen, H, Fan, M, Pfeffer, LM, Laribee, RN. The histone H3 lysine 56 acetylation pathway is regulated by target of rapamycin (TOR) signaling and functions directly in ribosomal RNA biogenesis. Nucleic Acids Res, 40 (14), 6534-46, 2012.
- Kerr, SC, Azzouz, N, Fuchs, SM, Collart, MA, Strahl, BD, Corbett, AH, Laribee, RN. The Ccr4-Not complex interacts with the mRNA export machinery. PLoS One, 6 (3), e18302, 2010.
- Fuchs, SM, Laribee, RN, Strahl, BD. Protein modifications in transcription elongation. Biochim Biophys Acta, 1789 (1), 26-36, 2009.
- Laribee, RN, Shibata, Y, Mersman, DP, Collins, SR, Kemmeren, P, Roguev, A, Weissman, JS, Briggs, SD, Krogan, NJ, Strahl, BD. CCR4/NOT complex associates with the proteasome and regulates histone methylation. Proc Natl Acad Sci U S A, 104 (14), 5836-41, 2007.
- Laribee, RN, Fuchs, SM, Strahl, BD. H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev, 21 (7), 737-43, 2007.
- Xiao, T, Shibata, Y, Rao, B, Laribee, RN, O'Rourke, R, Buck, MJ, Greenblatt, JF, Krogan, NJ, Lieb, JD, Strahl, BD. The RNA polymerase II kinase Ctk1 regulates positioning of a 5' histone methylation boundary along genes. Mol Cell Biol, 27 (2), 721-31, 2007.
- Laribee, RN, Klemsz, MJ. Histone H4 HDAC activity is necessary for expression of the PU.1 gene. Biochim Biophys Acta, 1730 (3), 226-34, 2005.
- Laribee, RN, Krogan, NJ, Xiao, T, Shibata, Y, Hughes, TR, Greenblatt, JF, Strahl, BD. BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex. Curr Biol, 15 (16), 1487-93, 2005.
- Chang, HC, Zhang, S, Thieu, VT, Slee, RB, Bruns, HA, Laribee, RN, Klemsz, MJ, Kaplan, MH. PU.1 expression delineates heterogeneity in primary Th2 cells. Immunity, 22 (6), 693-703, 2005.
- Zhang, B, Laribee, RN, Klemsz, MJ, Roman, A. Human papillomavirus type 16 E7 protein increases acetylation of histone H3 in human foreskin keratinocytes. Virology, 329 (1), 189-98, 2004.
- Laribee, RN, Klemsz, MJ. Loss of PU.1 expression following inhibition of histone deacetylases. J Immunol, 167 (9), 5160-6, 2001.
- Liu, Y, Jones, M, Hingtgen, CM, Bu, G, Laribee, N, Tanzi, RE, Moir, RD, Nath, A, He, JJ. Uptake of HIV-1 tat protein mediated by low-density lipoprotein receptor-related protein disrupts the neuronal metabolic balance of the receptor ligands. Nat Med, 6 (12), 1380-7, 2000.