Synthetic signaling systems: half-life control as a determinant of dynamic properties. Cellular stress responses often rely on underlying regulatory processes that are highly dynamic. In the context of interconnected gene-regulatory and signaling networks, the lifetime of mRNA and protein molecules has a large effect on the overall behavior of the cell. This effect often manifests itself in the underlying network dynamics, as degradation rates can play a central role in determining the crucial timing of events. In this program, we will examine the role of degradation on signaling networks. To do this, we will utilize tools from computational biophysics and synthetic biology to design and construct novel gene signaling circuits that allow for control over the degradation rates of proteins and mRNA.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Specialized Center (P50)
Project #
5P50GM085764-03
Application #
8380339
Study Section
Special Emphasis Panel (ZGM1-CBCB-2)
Project Start
Project End
Budget Start
2012-09-01
Budget End
2013-08-31
Support Year
3
Fiscal Year
2012
Total Cost
$414,922
Indirect Cost
$145,531
Name
University of California San Diego
Department
Type
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Didovyk, Andriy; Tsimring, Lev S (2017) Synthetic Gene Circuits Learn to Classify. Cell Syst 4:151-153
Xiong, Xiong; Zhang, Yanxiao; Yan, Jian et al. (2017) A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. ACS Synth Biol 6:1034-1042
Diao, Yarui; Fang, Rongxin; Li, Bin et al. (2017) A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells. Nat Methods 14:629-635
Spahn, Philipp N; Bath, Tyler; Weiss, Ryan J et al. (2017) PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens. Sci Rep 7:15854
Soonthornvacharin, Stephen; Rodriguez-Frandsen, Ariel; Zhou, Yingyao et al. (2017) Systems-based analysis of RIG-I-dependent signalling identifies KHSRP as an inhibitor of RIG-I receptor activation. Nat Microbiol 2:17022
Scott, Spencer R; Din, M Omar; Bittihn, Philip et al. (2017) A stabilized microbial ecosystem of self-limiting bacteria using synthetic quorum-regulated lysis. Nat Microbiol 2:17083
Shen, John Paul; Zhao, Dongxin; Sasik, Roman et al. (2017) Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nat Methods 14:573-576
Attali, Ilan; Tobelaim, William Sam; Persaud, Avinash et al. (2017) Ubiquitylation-dependent oligomerization regulates activity of Nedd4 ligases. EMBO J 36:425-440
Sundaramoorthy, Elayanambi; Leonard, Marilyn; Mak, Raymond et al. (2017) ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. Mol Cell 65:751-760.e4
Humphries, Jacqueline; Xiong, Liyang; Liu, Jintao et al. (2017) Species-Independent Attraction to Biofilms through Electrical Signaling. Cell 168:200-209.e12

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