Xie Group FOR Genetic Circuit Engineering

Tsinghua National Lab - Bioinformatics Division - Center for Synthetic and Systems Biology

Our research interests are in the broad areas of synthetic biology, systems biology, molecular biology, bioinformatics and biomedical engineering. We seek for synthetic molecular systems to understand design principles of transcriptional and post-transcriptional regulations in mammalian cells. We engineer genetic circuits and agents for manipulation of cell decision-making through synthetic information-processing networks. Our goal is to apply such a synthetic system that integrates multi-input sensing, sophisticated information processing, and precisely regulated actuation in living cells to a variety of biomedical and biotechnology applications. A few of our ongoing projects are briefly described below.

  • Integrative microRNA sensing and processing circuits
MicroRNAs (miRNAs) are endogenous 21-23 nt RNAs that pair to mRNAs to exert post-transcriptional repression mainly in metazoans and plants. MicroRNAs play important roles in nearly every aspect of biology, including development and progression of cancers and a variety of other diseases. Although intensive studies have greatly improved our knowledge of the mechanisms of microRNA-mediated RNA interference, our understanding of how dynamics of multiple microRNA levels determine transitions of cellular states is still limited.

We design and create two types of microRNA sensors. Our microRNA high-sensor produces high output when microRNA input is high, while the low-sensor produces high output when microRNA input is low. We study the characteristics of microRNA high- and low-sensors, including sensitivity, response transfer function, and robustness, by developing mathematical models and testing sensors experimentally in mammalian cells. Applying these design principles, we are able to integrate both high-sensors and low-sensors to engineer complex circuits, triggering a predictable function in response to dynamic changes of multiple microRNA inputs. We have demonstrated a scalable and modular RNAi-based logic circuit that selectively identifies HeLa cells and triggers apoptosis without affecting non-HeLa cell types. We will apply these tools to studying microRNA dynamics during cell-state transition, as well as controlling biological functions of specific cell types in a programmable fashion.

  • Coupled transcriptional and post-transcriptional regulations
Gene expression is fine-tuned by coupled transcriptional and post-transcriptional regulations, which could result in complex temporal and spatial gene expression patterns. However, construction of synthetic gene networks is restricted by the limited amount of available transcriptional and post-transcriptional regulation tool kits. With recent advances in the engineering of DNA binding domains, we are able to design a large number of orthogonal transcriptional regulators for specific DNA binding motifs in a short period of time. We will also evaluate, optimize and expand our existed synthetic microRNA library to meet the need of construction of sophisticated genetic circuits. Quantitative models will be developed to describe and predict the performance of synthetic motifs. This work will help elucidate the underlying design principles of conserved regulatory motifs.