Institute for Integrative Genome Biology

Grants and Programs

Current Interdisciplinary IIGB Grants/Programs

IIGB Pilot Interdisciplinary Research Projects (2007-08)

In an effort to foster innovative interdisciplinary collaborations within the Institute and develop promising technologies enabling private sector development by licensing or the establishment of start-up companies, the Institute offered limited project support in 2007 to groups of at least two IIGB members. At least one investigator was to have background and training in biology with at least one from a different discipline. An odd-numbered review committee was appointed by the IIGB Director and proposals evaluated on the basis of:

  • the quality of science,
  • the multi- and inter-disciplinary nature of the proposed work,
  • the combination of basic and translational science,
  • the possibility of translating the innovation to an application within a reasonable timeframe

The Request for Proposals was emailed in March 2007 to all IIGB investigators with a due date of July 2, 2007.

Listed below are the three proposals were funded by IIGB at the level of $50K each for the project period of 11/1/07 to 10/31/08.

 #1 Project —

Principal Investigators:
Wenwab Zhong (Assistant Professor, Chemistry)
Hailing Jin (Assistant Professor, Plant Pathology)

Title of Project: 
High-throughput Screening of siRNA Expression Using Rolling Circle Amplification

Integrating analytical chemistry with bioscience can result in new methods and technologies to solve complex biological problems. This interdisciplinary project is aimed at developing novel methods for rapid and sensitive detection of small interfering RNAs (siRNA) in plants, which employ the RNA-DNA hybridization to recognize specific siRNA sequences and rely on the isothermal rolling circle amplification (RCA) to achieve high detection sensitivity.

Specific Aims

  • The first approach will use capillary array electrophoresis to obtain relative siRNA expression levels by detecting RCA products generated from the target siRNA and the internal standard simultaneously. This method will be applied to screen for siRNAs with specific functions in a high throughput manner.
  • The second approach will amplify a DNAzyme with the rolling circle replication to form a colorimetric sensor that could be used for on-site monitoring of the specific siRNA discovered with the first approach.

#2 Project —

Principal Investigators:
Sean Cutler (Assistant Professor , Botany and Plant Science)
Michael Pirrung (Professor, Chemistry)

Title of Project:
Enlightening Chemical Genetics with Libraries of Fluorescently Tagged Small Molecules

We will synthesize a large (16,590-member) library of fluorescently-labeled small molecules for use in chemical genetic screens and use this library to identify new inhibitors of Arabidopsis cell expansion. Our library design incorporates fluorescence and affinity tagging sites such that hit molecules can both be visualized in vivo and used directly for purification of target proteins in vitro. Our collaborative strategy for realizing this goal is based on simple and robust Click chemistry and will create an enabling technology available to all IIGB members.

Specific Aims

  • Synthesize 6 tri-functional fluorescent building blocks.
  • Synthesize ~17K library using Click-mediated ligation of building blocks to 2765 diversification elements.
  • Investigate library’s utility for chemical genetics and target identification using a test screen in Arabidopsis.

#3 Project —

Principal Investigators:
Frances Sladek (Professor, Cell Biology and Neuroscience)
Tao Jiang (Professor, Computer Science & Engineering)

Title of Project:
Development of a High Throughput Assay for Transcription Factor Binding

There is an incredible amount of information stored in DNA response elements – DNA sequences in regulatory regions of genes to which transcription factors (TFs) bind. It is the binding of TFs to these binding sites (TFBS) that initiates a cascade of co-factor recruitment that determines the final transcriptional output of a gene. This information is thought to drive tissue-specific and temporal gene expression and to fine tune the transcription response to internal and external signals. However, that information has not been thoroughly mined, and hence we still have an inadequate understanding of gene expression despite all the genomic sequence available. Whereas methods to identify TFBS, such as position weight matrices (PWM), are useful to provide the first level of analysis, they are just that – a preliminary and incomplete analysis. With recent advances in robotics, microarrays and imaging, we now have the technical ability to more thoroughly define the entire complement of sites to which TFs bind, and hence unlock the mysteries of gene regulation. For a TF binding a DNA sequence 13 nucleotides long, there are 413 (>67 million) different sequences to which it can bind. Even though a TF may bind only a fraction of those sites (say 0.1% or 67,000), typically fewer than 100 such sites have been experimentally verified for most TFs. Therefore, in order to fully utilize data from genome-wide assays, it is imperative to expand the repertoire of sites to which a given TF binds. Here, we propose to combine biochemical, computational, statistical and bioengineering expertise with a powerful new technology – protein binding matrices (PBM) – to address the issue of TF binding specificity in a high throughput fashion. The development of this technology at UCR will be of use to any one of the number of UCR investigators investigating the regulation of gene expression, regardless of the organism they use. It will greatly facilitate systems biology research and the advances we propose with sequence-specific co-regulator recruitment will be a first in the field of regulation of gene expression. Finally, since the “golden goose” of drug design is the development of highly specific drugs tailored to a very specific set of genes, our efforts will attract considerable interest from industry and make us competitive for federal funding.

Specific Aims
The goal of this project is to develop a high throughput system to identify TF binding sites (TFBS) and analyze sequence-specific interactions between TFs and co-regulators, and to use bioinformatics and statistical tools to generate new models of transcription regulation.

  • Establish a high throughput assay to identify TF binding sites -- PBMs. Develop a protein binding matrix (PBM) system to systematically screen 1000’s of potential DNA response elements for a given TF, taking advantages of recent advances in robotics, high throughout assays and array technology.
  • Adapt PBMs to assess promoter-selective recruitment of co-regulators. Modify the PBM system to assess TF-co-regulator interaction on 1000’s of unique response elements, taking advantage of recent advances in imaging and our understanding of DNA-protein-protein
  • Develop novel computational and statistical tools to analyze transcription regulation. Use the data generated in Aims 1 and 2 to develop new computational and statistical tools to analyze the regulation of gene expression.

More Information

General Campus Information

University of California, Riverside
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Riverside, CA 92521
Tel: (951) 827-1012

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Genomics Information

Institute of Integrative Genome Biology
2150 Batchelor Hall

Tel: (951) 827-7177
E-mail: Aurelia Espinoza, Managing Director