The School of Molecular and Cellular Biology at the University of Illinois at Urbana-Champaign

Summary of Research Interests and Current Projects

I was dually trained in mouse genetics and genomics and have an abiding interest in both fields. My group combines genetics and genomic approaches to explore the functional content of the vertebrate genome, focusing especially on the evolution of cis- and trans-acting components of vertebrate regulatory machinery. Our interests include aspects of regulatory biology that are deeply conserved but we are particularly interested in those components 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.

KRAB-Zinc finger genes and the evolution of vertebrate gene regulatory networks

Group members: Katja Nowick, Tim Gernat, Nadya Kholina

Collaborators: Michael Zhang, Andrew Smith (Cold Spring Harbor Lab.); Eivind Almaas (Lawrence Livermore National Laboratory), Joomyeong Kim (Louisiana State University)

Past labmates and collaborators include: Aaron Hamilton, Stuart Huntley, Laurie Gordon, N. Alice Yamada, Ivan Ovcharenko, Dan Baggott, Anne Bergmann, Mary Tran-Gyamfi, Meiye Wu, Shalini Mabery, Sha Coleman

Our group has long been interested in the mechanisms and consequences of genome evolution, especially the functional impact of genome rearrangements, gene duplication and gene loss. Tandemly clustered gene families are especially fertile sources of genomic change, giving rise to new functional genes through segmental duplications and serving as hotspots for changes in genome architecture. Gene duplication and loss in tandem families is a major source of genomic divergence in vertebrates, creating species-specific repertoires of protein-coding genes and even differences between individuals of the same species. These novel genes have significant potential to define species-specific and individual traits.

We have focused one of the largest and most dynamic vertebrate gene families, members of which encode Kruppel-type zinc finger (KZNF) transcription factors. The human genome contains 423 protein-coding KZNF genes, and at least one-third of these arose recently enough to encode primate-specific proteins. Our studies have shown that the duplicated genes diverge rapidly in ways that predict altered DNA binding properties, suggesting a selection for functional novelty. KZNFs are the only family of transcription factors that vary extensively in gene number, sequence and function between different evolutionary lineages, and even between species as closely related as humans and chimpanzees. Because each KZNF transcription factor potentially influences the expression patterns of hundreds of target genes, their inter- and intraspecies variation is likely to have had significant and wide-ranging biological impact. However, regulatory functions have been determined for only a handful of mammalian KZNF proteins, leaving us with a significant challenge and exciting opportunities for scientific discovery.

We are developing methods to trace genes and pathways that are regulated by these lineage-specific transcription factors to identify the basis for species-specific functions, individual variation, and mechanisms of evolutionary divergence. To begin these studies we have chosen subgroups of KZNFs with unusual evolutionary histories and expression patterns that suggest roles in important biological processes. Of special current focus are (1) a cluster of ZNF genes that are subject to genomic imprinting, and are active in placenta and embryonic tissues; (2) genes that have evolved very recently in the primate lineage, encoding transcription factors that are unique to old world monkeys, apes and hominids. Other subgroups of KZNFs with potential roles brain development, reproduction, and immune function are also being targeted. Using a combination of methods including transgenic expression, creation of dominant negative mutations, siRNA knockdown, chromatin immunoprecipation and bioinformatics we are identifying target genes, binding sites and regulatory networks that are impacted by gain and loss of specific ZNF genes. We are also developing new insights to the correlations between ZNF sequence divergence and DNA target choice, with the aim of developing models to understand the impact of KZNF gene gain, loss and sequence divergence on mammalian evolution and human health.

Mouse mutants as tools for understanding human disease and the genome’s regulatory architecture

Group members: Xiaochen Lu, Dina Leiding

Past labmates and collaborators: Colleen Elso, Heather Thompson, Hillary Thurkow, Stephanie Morrison, Laura Chittenden, Cymbeline Culiat, Ethan Carver, Joe Rutledge, Waldy Generoso, Ivan Ovcharenko

In past years, my group worked with collaborators who had generated mouse mutant lines carrying reciprocal translocations, selecting lines that expressed health-related visible phenotypes for further study. We have focused on the genetic, molecular and phenotypic characterization of 20 mutations associated with defects in eye, ear, neural tube, and skeletal development, neurological disorders, obesity or susceptibility to cancer. Because the mutations affect chromosome structure in a visible way, we have been able to map all mutations to single bacterial artificial chromosome (BAC) clones using fluorescent in situ hybridization (FISH). We have mapped and sequenced mutation breakpoints and identified obvious candidate genes for most mutations. The sequenced mutations reveal simple chromosome breakage and reunion events with molecular signatures of non-homologous end-joining, a repair mechanism also associated with translocations occurring in somatic tissues.

Many of the translocations disrupt genes by breaking within the transcription unit, providing obvious “knockout” mutations. However, several mutations break outside of the coding sequence of the affected genes defining locations of distant regulatory elements; these mutations are especially valuable since the existence, functions and locations of such elements difficult are difficult to identify by other means. While most of the mutations identify new links between disease-related phenotypes and genes of unknown function, others have defined novel functions and regulatory structures for well-studied genes. These include a novel mutation in the Pax6 gene, which separates alternative promoters and disturbs specific aspects of eye, pancreas and pituitary development (C. Elso et al., in preparation); a novel mutation of Tbx18 that breaks >50 kb from the gene but produces a null mutation in somites; and mutations associated with obesity, neurological defects, neural tube or ear development by ablating or altering the expression and function of novel genes.

We are especially in translocations that produce full or tissue-specific null mutations by separating genes from key regulatory elements, some of which are located at great distances from protein-coding sequences. Because of our long-term interest in genome architecture, regulation and genome evolution, we have been involved in development of several computational tools for comparative genome analysis. We combine these computational approaches with experimental methods including chromatin immunoprecipitation (ChIP) and transgenic mouse technology, to locate key tissue-specific elements whose functions are disturbed in our mutant mice.