Research Interests
- Roles of chromatin structure and epigenetic controls in eucaryotic gene activation
- Roles of mRNA-protein interactions in control of eucarytic mRNA stability and expression
Key words: Chromatin structure, histone modifications, Growth Hormone gene, pituitary, placenta, transcriptional controls, mRNA expression, αCP RNA binding proteins, mRNA stability, globin mRNA.
Description of Research
Roles of chromatin structure and epigenetic controls in eucaryotic gene activation
In eukaryotic organisms gene regulation is dependent upon developmentally controlled alterations in chromatin structure. Epigenetic modifications in histones and DNA result in selective activation of gene expression profiles. In many cases these modifications in chromatin structure result in long-range control of gene promoters, reaching over hundreds of kbs. Understanding how these epigenetic modifications are themselves controlled and the mechanisms by which they selectively activate and/or silence cohorts of genes is central to our understanding of development and cellular differentiation. We are approaching these questions using as a model the human Growth Hormone gene cluster. The genes in this cluster are robustly expressed, physiologically and developmentally controlled, and highly specific to either pituitary somatotropes or placental syncytiotrophoblasts. These controls are conserved between mouse and human. Thus our studies are heavily dependent on the use of transgenic mouse models and are complemented where appropriate with in vitro chromatin analyses and cell culture models.
Roles of mRNA-protein interactions in control of eucaryotic mRNA stability and expression
At any given level of gene transcription, the final level of expression for a particular gene can be altered over a span of several orders of magnitude by modulation in mRNA stability or translational control. For example the half-lives of specific mammalian mRNAs can be as short as 15 minutes and as long as several days. Such post-transcriptional controls are dependent on sequence specific interactions between RNA binding proteins and target mRNAs. We are using a series of model mRNAs and expression systems to explore the role of a specific and highly abundant family of mRNA binding proteins, the αCPs, in mRNA stabilization and a variety of additional post-translational controls. These studies are based on in vitro RNA-protein interaction assays and cell-based expression models. Comprehensive studies of αCP functions are being carried out using immunoaffinity RNP-isolation, Affymetrix chip expression platforms, artificial tethering of RNA binding proteins to mRNAs, and biochemical analysis of RNP sub-localization. We are testing novel models by which mRNAs are stabilized by alterations in the stability of their 3' polyA tails. These analyses of mRNA decay are also revealing novel pathways of mRNA surveillance pathways and mRNA structural modification that impact on the expression of both wild-type and mutant gene expression.
Activation of placental hormone gene expression.
The hGH multigene locus contains a subset of GH-related genes expressed robustly and exclusively in the placenta. We are able to model this expression in transgenic mice carrying the intact hGH gene cluster with remote regulatory elements. Our current studies are aimed at identifying the cis-acting chromatin-based determinants of this highly restricted and developmentally controlled pattern of expression. These studies are carried out in transgenic mice and in ES and trophoblast stem (TS) cells derived from our various mouse lines carrying the hGH locus and addtional site-directed mutations. These studies, in conjunction with our studies of the hGH locus in the pituitary comprise an integrated approach to a chromatin locus with multiple developmental expression profiles and potentials.
Rotation Projects
Lab rotations are available in the areas of chromatin structure/gene activation and in the area of mRNA-protein interactions/mRNA stability control. Studies making extensive use of mouse transgenic models, stem cell cultures, and a variety of in vitro approaches can be explored. Students are encouraged to contact Dr. Liebhaber directly to discuss potential projects for rotation studies.
Lab personnel:
Please see our
lab web-site for this information. Our laboratory has a steady state of approximately 10 doctoral and postdoctoral scientists.
Selected Publications
Ho, Y., Elefant, F., Cooke, N., Liebhaber, S.: A defined locus control region determinant links chromatin domain acetylation with long-range gene activation. Mol Cell 9(2): 291-302, 2002.
Shewchuk, B. M., Liebhaber, S. A., Cooke, N. E.: Specification of unique Pit-1 activity in the hGH locus control region. Proc Natl Acad Sci U S A 99(18): 11784-9, 2002.
Makeyev, A. V., Eastmond, D. L., Liebhaber, S. A.: Targeting a KH-domain protein with RNA decoys. RNA 8(9): 1160-73, 2002.
Ji, X., Kong, J., Liebhaber, S. A.: In vivo association of the stability control protein alphaCP with actively translating mRNAs. Mol Cell Biol 23(3): 899-907, 2003.
Waggoner, S. A., Liebhaber, S. A.: Identification of mRNAs associated with alphaCP2-containing RNP complexes. Mol Cell Biol 23(19): 7055-67, 2003.
Kong, J., Ji, X., Liebhaber, S. A.: The KH-domain protein alpha CP has a direct role in mRNA stabilization independent of its cognate binding site. Mol Cell Biol 23(4): 1125-34, 2003.
Chkheidze, A. N., Liebhaber, S. A.: A novel set of nuclear localization signals determine distributions of the alphaCP RNA-binding proteins. Mol Cell Biol 23(23): 8405-15, 2003.
Cajiao, I., Zhang, A., Yoo, E. J., Cooke, N. E., Liebhaber, S. A.: Bystander gene activation by a locus control region. Embo J 23(19): 3854-63, 2004.
Su, Y., Balice-Gordon, R. J., Hess, D. M., Landsman, D. S., Minarcik, J., Golden, J., Hurwitz, I., Liebhaber, S. A., Cooke, N. E.: Neurobeachin is essential for neuromuscular synaptic transmission. J Neurosci 24(14): 3627-36, 2004.
Kimura, A. P., Liebhaber, S. A., Cooke, N. E.: Epigenetic modifications at the human growth hormone locus predict distinct roles for histone acetylation and methylation in placental gene activation. Mol Endocrinol 18(4): 1018-32, 2004.
Inacio, A., Silva, A. L., Pinto, J., Ji, X., Morgado, A., Almeida, F., Faustino, P., Lavinha, J., Liebhaber, S. A., Romao, L.: Nonsense mutations in close proximity to the initiation codon fail to trigger full nonsense-mediated mRNA decay. J Biol Chem 279(31): 32170-80, 2004.
Weinberg, R. S., Ji, X., Sutton, M., Perrine, S., Galperin, Y., Li, Q., Liebhaber, S. A., Stamatoyannopoulos, G., Atweh, G. F.: Butyrate increases the efficiency of translation of gamma-globin mRNA. Blood 105(4): 1807-9, 2005.
Hiroki, T., Song, Y. H., Liebhaber, S. A., Cooke, N. E.: The human vitamin D-binding protein gene contains locus control determinants sufficient for autonomous activation in hepatic chromatin. Nucleic Acids Res 34(8): 2154-65, 2006.
Shewchuk, B. M., Ho, Y., Liebhaber, S. A., Cooke, N. E.: A single base difference between Pit-1 binding sites at the hGH promoter and locus control region specifies distinct Pit-1 conformations and functions. Mol Cell Biol 26(17): 6535-46, 2006.
Ho, Y., Elefant, F., Liebhaber, S. A., Cooke, N. E.: Locus control region transcription plays an active role in long-range gene activation. Mol Cell 23(3): 365-75, 2006.
Kong, J., Sumaroka, M., Eastmond, D. L., Liebhaber, S. A.: Shared stabilization functions of pyrimidine-rich determinants in the erythroid 15-lipoxygenase and alpha-globin mRNAs. Mol Cell Biol 26(15): 5603-14, 2006.
Silva, A. L., Pereira, F. J., Morgado, A., Kong, J., Martins, R., Faustino, P., Liebhaber, S. A., Romao, L.: The canonical UPF1-dependent nonsense-mediated mRNA decay is inhibited in transcripts carrying a short open reading frame independent of sequence context. Rna 12(12): 2160-70, 2006.
Yoo, E. J., Cajiao, I., Kim, J. S., Kimura, A. P., Zhang, A., Cooke, N. E., Liebhaber, S. A.: Tissue-specific chromatin modifications at a multigene locus generate asymmetric transcriptional interactions. Mol Cell Biol 26(15): 5569-79, 2006.
Chendrimada, T. P., Finn, K. J., Ji, X., Baillat, D., Gregory, R. I., Liebhaber, S. A., Pasquinelli, A. E., Shiekhattar, R.: MicroRNA silencing through RISC recruitment of eIF6. Nature 447(7146): 823-8, 2007.
Kong J and Liebhaber SA: A cell type-restricted mRNA surveillance pathway triggered by ribosome extension into the 3' untranslated region. Nat Struct Mol Biol 14: 670-6, 2007.
Cajiao, I., Sargent, R., Elstrom, R., Cooke, N. E., Bagg, A., Liebhaber, S. A.: Igbeta(CD79b) mRNA expression in chronic lymphocytic leukaemia cells correlates with immunoglobulin heavy chain gene mutational status but does not serve as an independent predictor of clinical severity. Am J Hematol 82(8): 712-20, 2007.
Kimura, A. P., Sizova, D., Handwerger, S., Cooke, N. E., Liebhaber, S. A.: Epigenetic activation of the human growth hormone gene cluster during placental cytotrophoblast differentiation. Mol Cell Biol 27(18): 6555-68, 2007.
Hiroki, T., Liebhaber, S. A., Cooke, N. E.: An intronic locus control region plays an essential role in the establishment of an autonomous hepatic chromatin domain for the human vitamin D-binding protein gene. Mol Cell Biol 27(21): 7365-80, 2007.
Ji X, Kong J, Carstens RP and Liebhaber SA: The 3' untranslated region complex involved in stabilization of human alpha-globin mRNA assembles in the nucleus and serves an independent role as a splice enhancer. Mol Cell Biol 27: 3290-302, 2007.
Silva, A. L., Ribeiro, P., Inacio, A., Liebhaber, S. A., Romao, L.: Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense mediated mRNA decay. RNA 2008.
Waggoner, S. A., Johannes, G. J., Liebhaber, S. A.: Depletion of the poly(C)-binding proteins alphaCP1 and alphaCP2 from K562 cells leads to p53-independent induction of cyclin-dependent kinase inhibitor (CDKN1A) and G1 arrest. J Biol Chem 284(14): 9039-49, 2009.
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Last updated: 09/23/2009
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