R. Nicholas Laribee

Assistant Professor

Office: 264 CANCER RESEARCH BUILDING
19 SOUTH MANASSAS
MEMPHIS TN 381033403
Tel: (901) 448-2609
rlaribee@uthsc.edu

Education

  • Ph.D., Indiana University School of Medicine, Bloomington, IN, Microbiology and Immunology
  • B.S., Indiana University-Bloomington, Bloomington, IN, Biology

Research Interest/Specialty

 Epigenetics, gene regulation and signal transduction

Research Keywords

 Epigenetics; Chromatin; Gene transcription; nutrient signaling; TORC1; sirtuins; Ccr4-Not

Research Description

Although DNA encodes an organism’s genetic information, the genome is not composed solely of DNA.  Instead, it is packaged with histone proteins to form individual nucleosomes.  The nucleosome is the basic unit of chromatin found in all eukaryotic cells.  Individual nucleosomes, and their inter-nucleosomal interactions, create compacted, three-dimensional architectures that package the genome into the nucleus.  While this compaction is essential for storing the genetic material, the physical state of chromatin is resistant to biochemical reactions requiring access to DNA, including the gene expression machinery.  Therefore, eukaryotic cells ranging from yeast to man have evolved highly conserved biochemical mechanisms that control chromatin structure and function to permit regulated gene transcription, DNA replication, and DNA repair.  These mechanisms include histone post-translational modifications, DNA methylation, ATP-dependent chromatin remodeling, histone chaperones, and the incorporation of histone variants.

Chromatin modifications are typically regarded as “epigenetic” due to the potential for altered chromatin states to be propagated through multiple cell divisions and, in some cases, through multiple organismal generations.  Epigenetic regulation is significantly influenced by environmental factors, including such things as diet and various stressors.  Indeed, altered epigenetic regulation is one of the main mechanisms by which the environment influences phenotype.  Similarly, changes in cellular metabolism also contribute to epigenetic regulation as many of the cofactors needed in enzymatic reactions necessary for DNA and histone modifications are generated through cellular metabolism.   The dysregulation of epigenetic processes contributes to a number of diseases including cancer, cardiovascular disease, and many neurodevelopmental disorders.  Furthermore, degradation of chromatin structure directly contributes to the aging process and enhances the susceptibility for age-associated diseases such as cancer. Therefore, determining how the environment controls epigenetic processes, and how they function in gene expression, is essential for understanding how the environment impacts human health.  Our laboratory uses budding yeast as a genetic and biochemical model to understand these mechanisms.  Yeast provide unparalleled genetic and biochemical approaches for teasing apart the complex nature of these processes, yet the information gained from these studies is directly applicable to the corresponding pathways in human cells.  Our laboratory has several on-going projects to dissect these mechanisms which are outlined briefly below.

Role of the Ccr4-Not complex in cell growth and proliferation.  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 epigenetic regulation, 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.  Dysregulation of human Ccr4-Not is linked to multiple cancers, as well as to autism spectrum disorders, and cardiovascular disease.  Our laboratory is currently defining how nutrient signaling through the target of rapamycin complex 1 (TORC1) pathway utilizes Ccr4-Not to regulate gene transcription.  We have several ongoing projects related to the function of this complex that are described below.

1.  Ccr4-Not is a novel transcriptional co-regulatory for RNA polymerase I (Pol I).  Ccr4-Not is a known RNA polymerase II (Pol II) transcriptional co-regulator that can both positively and negatively regulate Pol II transcription in poorly understood ways.  Our laboratory recently identified a novel role for Ccr4-Not as a Pol I transcriptional co-regulator.  Specifically, we found that loss of the Ccr4-Not specific mRNA deadenylase subunit Ccr4, or the ubiquitin ligase Not4 subunit, increases Pol I transcription and ribosomal RNA (rRNA) biogenesis only under nutrient rich conditions. It does so in part by increasing Pol I interactions with the essential transcription factor, Rrn3, to form the transcription initiation competent form of the Pol I holoenzyme.  Surprisingly, in Ccr4-Not mutants, the  Rrn3-Pol I complex is resistant to disruption by decreased TORC1 signaling, thus implicating Ccr4-Not as essential for bridging TORC1 signaling to Pol I transcriptional regulation.  Ccr4-Not additionally functions to promote Pol I transcription elongation through complex genetic and functional interactions with non-essential Pol I elongation subunits.  We continue to delineate how Ccr4-Not to control cell growth and proliferation by regulating Pol I transcription.  Our ultimate goal is to expand these studies into human cell line models to determine how Ccr4-Not disruption dysregulates Pol I activity to contribute to cancer. 

 2.  The biological functions of the Not4 ubiquitin ligase.  Ccr4-Not contains the evolutionarily conserved Not4 ubiquitin ligase which is unique within the eukaryotic proteome as it is the only RING domain containing ubiquitin ligase that also has a putative RNA recognition motif (RRM) domain.  Whether this RRM domain binds RNA and, how RNA binding might modulate the ubiquitin ligase function of this protein, remains unknown.  Furthermore, this ubiquitin ligase only has a few identified substrates and none of these substrates can individually explain the severe phenotypes that occur upon loss of Not4.  Our laboratory is currently exploring both the role of this domain in Not4 function, as well as attempting to identify novel substrates for this ligase in order to understand its critical role in cell growth and proliferation.

 3.  Role of Ccr4-Not in control of chromatin structure.  Ccr4-Not interacts with multiple chromatin regulators yet how these interactions affect chromatin structure and function to control gene expression are unknown.  We are exploring the role of Ccr4-Not in these aspects of chromatin regulation and how they contribute to gene transcription mediated by both RNA Pol I and Pol II complexes.

Mechanisms of environmentally-induced epigenetic regulation.  The environment has a profound effect on human development and disease.  While environmentally-induced genome alterations due to DNA mutation are well-defined mechanisms by which the environment affects health, a number of complex diseases cannot be explained solely through this simple mechanism.  Many diseases, including most cancers, cardiovascular disease and neurodevelopmental disorders are thought to be caused by both genetic (ie. DNA mutation) and epigenetic dysfunction.  Because epigenetic dysregulation affects organismal phenotype without altering DNA sequence, these processes are potentially reversible which makes them ideal targets for drug development.  We utilize the TORC1 pathway, which is regulated by environmental nutrients and stress, as a model for elucidating mechanisms by which environmental information is transmitted to chromatin for controlling cell growth, proliferation and survival.  Dysregulated TORC1 signaling contributes to virtually all cancers, as well as other diseases such as neurodevelopmental disorders, cardiovascular disease, and metabolic syndrome. Therefore, defining how TORC1 regulates epigenetic processes will both illuminate how the environment affects phenotype and will identify novel areas for pharmacological intervention in disease therapy.

1.    Role of TORC1-regulated chromatin states in maintaining cell viability.  Our laboratory recently performed a chemical genomic screen of a library of histone H3 and histone H4 mutants to identify those epigenetic pathways exhibiting genetic interactions with TORC1.  We identified several sites on both histone H3 and H4 that are functionally linked to TORC1, including the identification of an absolutely essential and novel role for histone H3 lysine 37 (H3K37) in TORC1-dependent cell viability. We have determined that one role for H3K37 in the TORC1 signaling pathway is to anchor high mobility group box (HMGB) proteins to chromatin and that specific disruption of HMG chromatin binding induces cell death when TORC1 is inhibited.  Our laboratory is exploring the novel concept that TORC1 signaling actively regulates specific chromatin states that promote HMGB binding to actively prevent cell death. Our long term goals with this project are to define these TORC1-regulated chromatin states, understand how non-chromatin bound HMGB proteins induce cell death, and determine if these processes contribute to cancer and aging.

2.    Define the role of TORC1 signaling in sirtuin-dependent metabolic functions.  We have determined that TORC1 actively suppresses the activity of a class of histone deacetylases called sirtuins to promote global histone acetylation, and possibly non-histone protein acetylation as well.  TORC1 does so by signaling through a highly conserved phosphatase complex to modulate the cellular localization and protein stability of a subset of these enzymes.  We are defining how TORC1 signaling coordinates chromatin metabolism with the cell’s overall metabolic state to control cell growth and proliferation.  These pathways are conserved in human cells so our long term goal will be to expand our studies into human cancer cell models and delineate their function in tumorigenesis.

Long-term vision statement.  Our laboratory utilizes yeast to address mechanistic questions regarding the control of chromatin structure and function via environmentally-regulated signaling pathways.  The utilization of a simple genetic and biochemical model is essential to probe these scientific questions since they are both complex in nature and difficult to experimentally address.  However, our long term goals are to expand these studies into human cell lines to understand how these processes function in development of diseases such as cancer.  Each pathway and/or process we study in yeast is highly conserved in human cells so the information generated by our yeast model will inform our studies in human cells.

Publications

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Fuchs, SM, Laribee, RN, Strahl, BD. Protein modifications in transcription elongation. Biochim Biophys Acta, 1789 (1), 26-36, 2009.
  8. 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.
  9. Laribee, RN, Fuchs, SM, Strahl, BD. H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev, 21 (7), 737-43, 2007.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. Laribee, RN, Klemsz, MJ. Loss of PU.1 expression following inhibition of histone deacetylases. J Immunol, 167 (9), 5160-6, 2001.
  16. 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.