Rice University
BioSciences at Rice

James Chappell

Assistant Professor

The goal of the Chappell lab is to forward our ability to understand and engineer the bacteria domain of life. Central to this is our ability to control how cells express their genetic code. Our lab focuses on understanding how the biomolecule RNA can be designed to create synthetic regulators of gene expression—allowing for the manipulation of natural cellular processes to elicit deeper biological understanding and for the engineering of new synthetic cellular functions. As such our lab focuses both on the creation of new gene regulatory tools and their application.

Chappell's Research

Central to our approach is the philosophy that RNA is a powerful molecule for cellular engineering. Firstly, RNA regulators are highly designable, as they exert regulation by the formation of specific structures within mRNAs that are determined largely by the simple rules of Watson-Crick base pairing. Secondly, RNA regulators can be used to create gene regulatory networks capable of performing complex signal processing. Such synthetic networks are highly valuable to many Synthetic Biology applications, such as metabolic engineering and creation of biological diagnostics. Finally, RNA regulators are potentially highly transferable across bacterial species because they depend on universal base pairing interactions between nucleotides and require minimal cellular machinery. Therefore, RNA is potentially a powerful molecule for harnessing the diversity of the bacteria domain of life.

The main areas of research focus are currently: (1) Creation of synthetic RNA regulators of gene expression. (2) Deciphering the portability of RNA regulators across the bacteria domain of life. (3) Creation of synthetic genetic circuits capable of performing signal processing. (4) Applying RNA-based tools for functional genomics

Select Publications

Wen, Ke Yan; Cameron, Loren; Chappell, James; Jensen, Kirsten; Bell, David J; Kelwick, Richard; Kopniczky, Margarita; Davies, Jane C; Filloux, Alain; Freemont, Paul S; A Cell-Free Biosensor for Detecting Quorum Sensing Molecules in P. aeruginosa-Infected Respiratory Samples.  ACS synthetic biology 2017

Chappell, James; Westbrook, Alexandra; Verosloff, Matthew; Lucks, Julius B; Computational design of small transcription activating RNAs for versatile and dynamic gene regulation.  Nature communications, 8 2017: 1051

Meyer, Sarai; Chappell, James; Sankar, Sitara; Chew, Rebecca; Lucks, Julius B; Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies.  Biotechnology and bioengineering, 113 2016: 216-225

Chappell, James; Lucks, Julius B; Turning It Up to 11: Modular Proteins Amplify RNA Sensors for Sophisticated Circuitry.  Cell systems, 3 2016: 509-511

Chappell, James; Watters, Kyle E; Takahashi, Melissa K; Lucks, Julius B; A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future.  Current opinion in chemical biology, 28 2015: 47-56

Takahashi, Melissa K; Hayes, Clarmyra A; Chappell, James; Sun, Zachary Z; Murray, Richard M; Noireaux, Vincent; Lucks, Julius B; Characterizing and prototyping genetic networks with cell-free transcription�ranslation reactions.  Methods, 86 2015: 60-72

Chappell, James; Takahashi, Melissa K; Lucks, Julius B; Creating small transcription activating RNAs.  Nature chemical biology, 11 2015: 214-220

Takahashi, Melissa K; Chappell, James; Hayes, Clarmyra A; Sun, Zachary Z; Kim, Jongmin; Singhal, Vipul; Spring, Kevin J; Al-Khabouri, Shaima; Fall, Christopher P; Noireaux, Vincent; Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription�ranslation (TX-TL) systems.  ACS synthetic biology, 4 2014: 503-515

Chappell, James; Takahashi, Melissa K; Meyer, Sarai; Loughrey, David; Watters, Kyle E; Lucks, Julius; The centrality of RNA for engineering gene expression.  Biotechnology journal, 8 2013: 1379-1395

Chappell, James; Jensen, Kirsten; Freemont, Paul S; Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology.  Nucleic acids research, 41 2013: 3471-3481

Chappell, J. and Freemont, P.S Synthetic biology – A new generation of biofilm biosensors.  The Science and Applications of Synthetic and Systems Biology,, 8 2011: 159–178

Group website

  • B.Sc Biochemistry (2008) Imperial College London
  • Ph.D. Molecular Biosciences (2013) Imperial College London
  • Department of BioSciences
Research Areas
  • Synthetic biology
  • RNA gene control
  • Functional genomics
Professional Experience
  • Postdoctoral Research
    Northwestern University
    2016-2017
  • Postdoctoral Research
    Cornell University
    2013-2016
Contact Information
Email: jc125@rice.edu
Phone: 713-348-3781
Office: Keck Hall , 332