Brenner Group Undergraduate Research Projects
About the group
We develop computational methods for the analysis and integration of molecular sequence and structure. Our aim is to understand organismal biology by interpreting the information encoded in complete genomes. This work is presently focused on the areas of structural and functional genomics. Here are further details about our research interests.
Notes about all projects
Projects are available in several of the group's areas of interest and will be tailored to the abilities and interests of the student apprentice and current membership of the group. Students should expect to spend at least 12 hours per week on the project. The ideal student will have a strong molecular biology background and considerable programming experience. Students with < 3.6 GPA will only be considered in exceptional circumstances.
Specific projects
The correct splicing of a pre-mRNA is an important level of gene regulation, much like gene regulation at the transcriptional and translational levels. Cis-acting regulatory sequences are located along the pre-mRNA and recruit trans-acting factors that influence splicing decisions. This project will use computational methods to identify splicing regulatory sequences.
Experimental and genomic data will be used to identify these regulatory sequences. Upon knockdown of ~100 trans-acting splicing factors, sequence motifs enriched near co-regulated splicing events will be identified. Microarray and new high-throughput sequencing technologies will be used to detect these co-regulated splicing events. In addition, genomic sequences from D. melanogaster and 11 other fly species will be used to look for conservation of these regulatory sequences and will be used to implement statistical methods to discover splicing regulatory sequences.
This project is part of a collaboration with multiple institutions with the common goal of finding all functional sequence elements in the D. melanogaster genome.
The role of splicing and alternative splicing in human gene expression remains enigmatic. Recent work in our lab has shown that some alternate isoforms may have dramatically different fates than others. Current goals include development of tools for classifying alternate isoforms and extending recent results. The ideal applicant is a competent coder and has knowledge of modern molecular biology.
Proteins often fold into compact structural units, called domains. Protein domains are basic units of protein function and evolution. Delineating domain boundaries is a prerequisite for further analyses of protein structures. However, this process is largely a manual process and the accuracy of these computer programs is still not satisfactory. This project will include two parts: critical assessment of current protein domain identification programs, and development of approaches to improve the accuracy by combining existing computer programs. The ideal candidate is willing to learn and knows how to write programs (in any language); knowledge of protein structures is a plus.
Experimental research on Nonsense-Mediated mRNA decay (NMD) in Human
Supervisor: Dan Liang
As a new addition to the computational biology research in the Brenner lab, we are conducting experimental research to validate computation predictions of NMD targets in Human. Our goals are to better understand NMD and to identify genes whose expression are "regulated [by] unproductive splicing and translation" (RUST). Currently, we are focusing on the SR protein family, whose unproductive splicing is associate with highly- and ultraconserved DNA elements. We are testing their mRNA abundance under control and NMD inhibited conditions with traditional realtime PCR and the advanced Fluidigm dynamic array technology. The NMD inhibition condition is generated by knockdown of the key protein (Upf1) involved in NMD by RNAi. The experimental methods we are using include: cloning, reporter enzyme assay, Western Blot, total RNA extraction and quantitation by RT-PCR and real time PCR.
How to apply
Applicants should send a cover letter (with description of interests) and transcript to:
Brenner Laboratory Jobs
111P Koshland Hall # 3102
University of California
Berkeley, CA 94720-3102
jobs@compbio.berkeley.edu
You can also apply through the URAP, URO, Guidant, or other undergraduate research programs in order to get credit (and possibly money) for your work.