Associate Professor of Biological Sciences
ResearchThe research interests and experience within the Hinman lab fall into the area broadly defined as evolution of developmental mechanisms. Our particular approach for understanding conserved and divergent properties of animal development is to compare architectural organization of gene regulatory networks (GRNs). GRN models consider not only the expression domains and function of many regulatory genes (mostly transcription factors), but importantly their inter-relationships. The construction of GRNs involves the use of cutting edge embryological and molecular biological technologies to study gene expression and to undertake gene perturbation, gene transfer and cis -regulatory analyses. Since our work is comparative these techniques must often be adapted for use in non-model organisms. The relationships between regulatory genes are portrayed as a network diagrams.
We use a variety of marine invertebrates, particularly echinoderms, for our research. This is due largely to the fact that the most extensive GRN currently exists for the sea urchin embryo (see http://sugp.caltech.edu/endomes/) and the starfish has been shown to be an excellent comparative model. Also marine invertebrates represent the largest morphological diversity on the planet and present a wealth of opportunity to explore the association between development, phenotype and evolution.
We use a comparative GRN method to answer questions such as:
- What are conserved features of GRNs? These may be particular relationships of orthologous genes that can explain the preservation of phylotypic characters or may even represent developmental phenomena more widespread among the metazoa that are thus crucial for understanding animal development.
- How does the architecture of GRNs diverge with morphological differences in development and how did these architectural changes arise in evolution?
- What are the similarities and differences that underlie the GRN of two independently evolving taxa that converge upon the same morphological outcome?
- What is the cis -regulatory organization that underlies GRN structure and how has the cis regulatory logic evolved in conjunction with network architecture evolution?
McCauley, B.S.; Akyar, E.; Filliger, L.Z.; Hinman, V.F. Expression of Wnt and Frizzled genes in the embryos of the sea star Patiria miniata. (in press).
Yankura, K.A.; Koechlein, C.S.; Cryan, A.F.; Cheatle, A.; Hinman, V.F. Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning. Proc Natl Acad Sci U S A. 2013.
Le, H.S.; Schulz, M.; McCauley, B.M.; Hinman, V.F.; Bar-Joseph, Z. Probabilistic error correction for RNA sequencing. Nucleic Acids Research 2013.
McCauley, B.S.; Wright, E.P.; Exner, C; Kitazawa, C; Hinman, V.F. Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms. Evodevo 2012, 3(1):17. doi: 10.1186/2041-9139-3-17.
Kadri, S.; Hinman, V.F.; Benos, P.V. RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS One 2011, 6(12):e29217. doi: 10.1371/journal.pone.0029217. Epub 2011 Dec 28.
Yankura, K.A.; Martik, M.L.; Jennings, C.K.; Hinman, V.F. Uncoupling of complex regulatory patterning during evolution of larval development in echinoderms. BMC Biol. 2010 8:143. See commentary:BMC Biology 2011, 9:6;F1000 review.
McCauley, B.S.; Weideman, E.P.; Hinman, V.F. A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos. Dev Biol. 2009, 340(2):200-8, 2010 Apr 15. Epub 2009 Nov 23.
Kadri, S.; Hinman, V.; Benos, P.V. HHMMiR: Efficient de novo prediction of microRNAs using hierarchical hidden Markov models. BMC Bioinformatics 2009, 10 Suppl 1:S35.
Hinman, V.F.; Yankura, K.A.; McCauley, B.S. Evolution of gene regulatory network architectures: Examples of subcircuit conservation and plasticity between classes of echinoderms. Biochim Biophys Acta.2009, 1789(4):326-32.
Hinman, V.F.; Davidson, E.H. Evolutionary plasticity of developmental gene regulatory network architecture. Proceedings National Academy of Sciences (USA) 2007, 104(49):19404-9.