VI. RNAi
A. General Information
ChromDB was established through funding from the Plant Genome Research Program of the National Science Foundation (NSF award #9975930; Functional Genomics of Chromatin: Global Control of Plant Gene Expression; PI: R.A. Jorgensen). A broad goal of this project was to identify and functionally characterize the complement of genes in maize and Arabidopsis that contribute to chromatin-based control of gene expression. A more narrow focus of the project was to produce RNAi lines for a set of Arabidopsis and maize chromatin-associated genes. With renewed funding from the Plant Genome Research Program (NSF award #DBI-0421679; SChromDB: Integrating Information on Plant Chromatin Proteins and Complexes; PI: C.A. Napoli). The grant does not fund additional RNAi line work; although the Maize Chromatin Consortium is continuing this work for maize. As a service to the community and a goal of the previous funding, ChromDB will continue to display RNAi information generated from the previous grant. Please note that ChromDB staff members do not distribute the Arabidopsis RNAi lines. These are distributed through ABRC/TAIR. The maize lines are distributed through the Maize Stock Center and information on the lines, including ordering information, is available at MaizeGDB. Please use the Arabidopsis and maize links shown below to access order information.
B. Vector Information
This document describes a set of binary vectors for producing dominant negative RNAi mutants using a target sequence cloning strategy that is based on the inclusion of two restriction enzyme cleavage sites in each of two primers used to amplify gene-specific fragments from cDNA. This design minimizes the number of PCR primers and results in the placement of unique restriction enzyme recognition sites to allow for flexibility in future manipulations of the plasmid, e.g., moving the inverted repeat target sequence to a different vector. ChromDB's RNAi vectors are based on pCAMBIA binary vectors, a set of plasmids developed by the Center for Application of Molecular Biology to International Agriculture (CAMBIA). Importantly, CAMBIA vectors contain two origins of replication, a wide-host-range origin for plasmid replication in Agrobacterium tumefaciens and the pBR322 origin for replication in Escherichia coli, following the design of the Maliga lab (Plant Mol Biol 1994; 25(6):989-94). Detailed descriptions of pCAMBIA vectors, including conditions for use and distribution, can be obtained at the CAMBIA web site.
Please do not request plasmids from ChromDB. The RNAi vectors are distributed by ABRC/TAIR. The "Order Vectors" link provides a list of available vectors in Table 1 and includes the ABRC stock number (direct link to the vector page at the TAIR database), brief information about each vector and links to bring up plasmid maps and FASTA sequence files. For those researchers using Gene Construction Kit software, a GCK file for each sequence is included as a link
C. Order Vectors
The RNAi vectors have been deposited at ABRC; they are not available through the ChromDB database. Please use the Order Vectors link for instructions on how to submit an order to ABRC.
D. RNAi Lines
TAs a service to the community and a goal of the previous funding, ChromDB will continue to display RNAi information generated from the previous grant. But, please note that ChromDB staff members do not distribute the Arabidopsis RNAi lines. These are distributed through ABRC/TAIR. The maize lines are distributed through the Maize Stock Center and information on the lines, including ordering information, is available at MaizeGDB . Please use the Arabidopsis and maize links shown below to access order information. The RNAi Lines link brings up two further links, one to Arabidopsis lines and one to Maize line.
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