ljstubbs@illinois.edu
R2402 Institute for Genomic Biology
Office: (217) 244-4000
Fax: (217) 244-1781
Mail to: Dept of Cell and Developmental Biology University of Illinois B107 601 S. Goodwin Avenue Urbana, IL 61801
Lisa J Stubbs
Professor of Cell and Developmental Biology
Research Topics
Bioinformatics, Chromatin Structure, Development, Genomics, Molecular Evolution, Regulation of Gene Expression
Education
B.S. University of Puget Sound (Biology)
Ph.D. University of California, San Diego (Biology)
Postdoc. California Institute of Technology, Pasadena CA; European Molecular Biology Laboratory, Heidelberg, Germany
Evolution of gene regulatory networks; Long-range regulatory mechanisms; Mouse models for human disease
Summary of Research Interests
Our research combines mouse genetics, bioinformatics and genomic methods to explore cis- and trans-acting components of mammalian gene regulatory machinery. We are particularly interested in those components of the regulatory machinery that have changed over evolutionary time. Working against a background of deep conservation, these changing components hold potential to explain biological differences between species, but also between different individuals in the same populations.
I have long been interested in the mechanisms of genome evolution, especially the functional impact of genome rearrangements, gene duplication and gene loss on species-specific biology. My group’s current work is focused in two areas: (1) Determining the functions of human genes encoding Kruppel-type zinc finger (KZNF) transcription factors; and (2) Investigating mechanisms of long-distance gene regulation, using a unique collection of translocation mutant mice.
The KRAB zinc finger transcription factor family
While most vertebrate transcription factor (TF) genes are deeply conserved, one family of genes, encoding proteins with multiple zinc-fingers, stands our for its evolutionary diversity. The KRAB-ZNF subfamily is both the most numerous and the most diverse. For example, the human and mouse genomes each contain more than 400 protein-coding genes of the KRAB-ZNF type, but only about 100 of these genes are true functional "orthologs". KRAB-ZNFs are the only family of transcription factors that vary so extensively between different evolutionary lineages; these genes also vary in copy number and structure between individuals, including individual humans.
We are developing methods to trace genes and biological pathways that are regulated by these lineage-specific transcription factors, in order to understand their impact on species-specific and individual traits. We combine transgenic expression, siRNA knockdown, chromatin immunoprecipation and bioinformatics to identify target genes, binding sites and the regulatory networks for these ZNF proteins. Our aim is to understand the impact of ZNF gene gain, loss and sequence divergence on vertebrate evolution, primate-specific traits, and human health.
Mouse mutants as tools to dissect the genome’s regulatory architecture
We are working with a unique set of mouse mutant lines that carry reciprocal translocations, and as a result of these mutations express a range of health-related developmental phenotypes. We have mapped all the mutations to small regions using fluorescent in situ hybridization (FISH),and have cloned and sequenced the mutations in several strains of mice. The sequenced translocation breakpoints reveal simple DNA "breakage and reunion" events with molecular signatures of non-homologous end-joining, a repair mechanism also associated with translocations occurring in somatic tissues.
| 12Gso, a reciprocal translocation involving chromosomes 4 and 9, is associated with recessive skeletal development, kidney, and reproductive defects (left). The mutation produces a tissue-specific "knockout" of Tbx18 by separating the gene from long-distance enhancers. Because translocations involve obvious changes in chromosome structure, they can be visualized and mapped with fluorescent in situ hybridization, or FISH (right). |
Several of the translocations disrupt genes by breaking within specific genes, providing obvious “knockout” mutations. However, a number of the mutations break outside of coding sequences and define locations of distant regulatory elements that are critical to expression in one or more tissues. An example is the 12Gso mutation, which is located more than 80 kb downstream of the Tbx18 transcription factor gene; mice inheriting this mutation display a tissue-specific "knockout" of Tbx18 in somites and urogenital tissues (figure, left). Other mutant lines provide insight into regulation of genes linked to deafness, blindness, behavioral abnormalities, seizure disorders, hydrocephalus and other phenotypes. These novel, conserved regulatory elements provide a new window to the genetic and epigenetic causes of related human disease. We are combining experimental methods such as chromatin immunoprecipitation (ChIP), together with mouse genetics, transgenic technologies, and bioinformatics approaches to locate and functionally characterize the long-distance elements to understand their functions and interactions with other chromatin elements throughout development.
Representative Publications
Nowick K, Hamilton AT, Zhang H, and Stubbs L. Rapid sequence and expression divergence suggests selection for novel function in primate-specific KRAB-ZNF genes. Mol Biol Evol 27:2606-2617, 2010.
Nowick, K. Fields, C., Gernat, T., Caetano-Anolles, D., Kholina, N., and Stubbs, L. Gain, loss and divergence in primate zinc-finger genes: a rich resource for the evolution of regulatory differences between species. PLoS One 6:e21553, 2011.
Stubbs L, Caetano-Anolles D, Sun Y. Function and Evolution of C2H2 Zinc Finger Arrays. Subcell Biochem 52:75-94, 2011.
Nowick K and Stubbs L. Lineage-specific transcription factors and the evolution of gene regulatory networks. Briefings in Functional Genomics and Proteomics 9:65-78, 2010.
Nowick, K. and Stubbs, L. Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain. Proc Natl Acad Sci USA 106: 22358-22363, 2009.
Elso C., Lu X., Morrison S., Tarver A., Thompson H., Thurkow H., Yamada N.A., and Stubbs L. Germline translocations in mice: unique tools for analyzing gene function and long-distance regulatory mechanisms. J National Cancer Inst Monographs 39: 91-95, 2008.
Hamilton A.T., Huntley S., Tran-Gyamfi M., Baggott D.M., Gordon L., and Stubbs L. Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes. Genome Research, 16:584-594, 2006.
Huntley S., Baggott D.M., Hamilton A.T., Tran-Gyamfi M., Yang S., Kim J., Gordon L., Branscomb E., and Stubbs L. A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Research 16:669-677, 2006.
Kim., J., Kollhoff, A., Bergmann, A., and Stubbs, L. Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, PEG3. Hum Molec Genet 12: 233-245, 2003.
Ovcharenko I, Loots GG, Nobrega MA, Hardison RC, Miller W and Stubbs L. Evolution and functional classification of vertebrate gene deserts. Genome Res, 15, 137-145, 2005.
Elso CE, Lu X, Culiat CT, Rutledge J, Cacheiro NLA, Generoso WM, and Stubbs LJ. Heightened susceptibility to gastric infection, chronic gastritis, and metaplasia in Kcnq1 mutant mice. Hum Mol Genet 13: 2813-2821, 2004.
Chittenden, L., Lu, X., Cacheiro, N.L.C., Cain, K.T., Generoso, W.M., Bryda, E.C. and Stubbs, L. A New Murine Model for Autosomal Recessive Polycystic Kidney Disease. Genomics 79:499-504, 2002.
Stubbs, L., Carver, E.A., Cachiero, N.L.A., Shelby, M., Generoso, W.M. Generation and characterization of heritable reciprocal translocations in mice. Methods: companion to Methods Enzymol 13, 397-408, 1997.
Related links: ZNF catalog: http://znf.igb.uiuc.edu