Our laboratory studies several aspects of gene expression in animal cells. These include transcription initiation of mRNA encoding genes, mRNA splicing, and mRNA polyadenylation. All three of these processes occur in the cell nucleus and require numerous protein (and in the case of splicing, RNA) factors that assemble into massive multi-subunit complexes. It is our goal to identify and isolate these factors, to understand how the complexes assemble and function on the DNA template or pre-mRNA substrate, and to learn how these important molecules function to regulate gene expression and how they themselves are controlled. These studies involve a large number of experimental approaches, including a variety of in vitro assays, biochemical fractionation and protein purification, cDNA and genomic DNA cloning, production of recombinant proteins and antibodies, in vitro mutagenesis, and genetic analyses of cultured cells using a novel gene targeting approach.
With respect to transcription, we are studying a variety of factors that function in gene control. Projects range from understanding how the activity of an important regulatory protein in the early Drosophila embryo, called Dorsal, is itself regulated by a complex signal transduction pathway that controls the subcellular localization and activity of the protein; to elucidating the molecular mechanism by which a homeodomain protein, Even-skipped, functions to repress transcription; to analyzing genetically how general transcription factors, especially components of TFIID, function and interact with regulators in vertebrate cells.
Our studies on mRNA processing involve principally mammalian systems. We study the mechanism of pre-mRNA splicing by examining the role that small nuclear RNAs (snRNAs) play in the catalysis of splicing. We are also very interested in regulation of alternative splicing, and are concentrating on understanding how members of the SR protein family, characterized by a human protein we co-discovered called ASF/SF2, function to modulate the selection of splice sites in alternatively spliced pre-mRNAs; how these proteins are regulated by phosphorylation; and how they interact with other regulatory proteins. Addition of the poly(A) tail to an mRNA is the last step in the synthesis of mRNA, and it, too, requires numerous protein factors. The polyadenylation factors, including the poly(A) polymerase itself, constitute an interesting family of proteins that interact with each other and with the pre-mRNA in novel ways, and which play important regulatory roles in different cell types and at different stages of the cell cycle.
Recently we made the discovery that these three processes, transcription, splicing and polyadenylation, are all linked in an unexpected way: RNA polymerase II, long known to be responsible for synthesis of mRNA precursors, also functions directly in both splicing and polyadenylation. We are currently studying how this occurs, and how these interactions contribute to gene control.
Calvo, O. and Manley, J.L. (2001). Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation and termination. Mol. Cell 7, 1013-1023. Abstract
Kleiman, F.E. and Manley, J.L. (2001). The Bard1-CstF-50 interaction links mRNA 3' end formation to DNA damage and tumor suppression. Cell 104, 743-753. Abstract
Chen, Z. and Manley, J.L. (2000). Robust mRNA transcription in chicken DT40 cells depleted of TAFII31 suggests both functional degeneracy and evolutionary divergence. Mol. Cell. Biol. 20, 5064-5076. Abstract
Hirose, Y., Tacke, R. and Manley, J.L. (1999). Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13, 1234-39. Abstract
Tacke, R., Tohyama, M., Ogawa, S. and Manley, J.L. (1998). Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing. Cell 93, 139-148. Abstract