My research program investigates the regulation of gene expression.
The anthocyanin biosynthetic pathway in maize is the focus of our
work, as it provides an exceptionally tractable system for genetic,
biochemical and molecular approaches. A major emphasis in our research
is to investigate how the regulatory genes of this pathway are controlled.
These regulatory genes, which encode transcription factors that
activate the anthocyanin biosynthetic genes, have multiple alleles
that produce distinct developmental and tissue-specific patterns
of anthocyanin pigments. In addition, we have identified negatively
acting modifier genes that reduce the expression of the biosynthetic
and regulatory genes. Identifying the cis-acting sequences regulating
differential expression, and factors that interact with these sequences
should provide important information on mechanisms of gene regulation,
applicable to numerous plant systems. In addition, the availability
of regulatory sequences that can control expression in distinct
tissues and developmental stages will greatly enhance the potential
of genetic engineering.
We are also using this system to investigate mechanisms of gene
silencing, which has a fundamental role in development and has recently
become a major problem with genetic engineering approaches to crop
improvement. We use both forward and reverse genetic approaches
to study paramutation, the regulation of transposable elements and
transgene silencing. Paramutation is a mitotically and meiotically
heritable change in gene expression that is induced by allele interactions.
We have demonstrated that the heritable change is accompanied by
a ten- to twenty-fold reduction in transcription.
Recently we have used a combination of classical genetics, genomics,
and molecular methods to identify and characterize the minimal sequences
required for paramutation, which map within 95-102 kbp upstream
of the transcription initiation site. We have also identified multiple
mutations in other genes required for the establishment and maintenance
of paramutation. We have shown that these mutants also activate
previously silent transposable elements and transgenes, indicating
that the wild type proteins are required for multiple gene-silencing
processes. Experiments are in progress to clone the genes represented
by these mutations and determine their role in gene silencing. As
heritable changes in chromatin structure are clearly involved in
the establishment and maintenance of distinct transcription states
we are also pursuing a functional genomics approach to understand
chromatin-level control of gene expression in both maize and Arabidopsis.
Any link on the below references will take you off
of the BMCB site and to an abstract of that particular paper.
Alleman, M., L. Sidorenko, K. McGinnis, V. Seshadri, J.E. Dorweiler,
J. White, K. Sikkink, and V.L. Chandler. 2006. An RNA-dependent
RNA polymerase is required for paramutation in maize. Nature 442: 295-298.
McGinnis, K.M., C. Springer, Y. Lin, C.C. Carey, and V. Chandler.
2006. Transcriptionally silenced transgenes in maize are activated
by three mutations defective in paramutation. Genetics 173: 1637-1647.
McGinnis, K., V. Chandler, K. Cone, H. Kaeppler, S. Kaeppler, A.
Kerschen, C. Pikaard, E. Richards, L. Sidorenko, T. Smith, N. Springer,
and T. Wulan. 2005. Transgene-induced RNA interference as a tool
for plant functional genomics. Methods in Enzymology 392:
1-24.
Chandler, V.L., and M. Stam. 2004. Chromatin conversations: mechanisms
and implications of paramutation. Nature
Reviews. Genetics 5: 532-544.
Carey, C.C., J.T. Strahle, D.A. Selinger, and V.L. Chandler. 2004.
Mutations in the pale aleurone color1 regulatory gene of the Zea
mays anthocyanin pathway have distinct phenotypes relative to the
functionally similar TRANSPARENT TESTA GLABRA1 gene in Arabidopsis
thaliana. The
Plant Cell 16: 450-464.
Chandler, V.L. 2004. Poetry of b1 paramutation: cis- and trans-chromatin
communication. Cold Spring Harbor Symposia on Quantative Biology 69: 355-361.
Stam, M., C. Belele, W. Ramakrishna, J.E. Dorweiler, J.L. Bennetzen,
and V.L. Chandler. 2002. The regulatory regions required for B'
paramutation and expression are located far upstream of the maize
b1 transcribed sequences. Genetics 162: 917-930.
Stam, M., C. Belele, J.E. Dorweiler, and V.L. Chandler. 2002. Differential
chromatin structure within a tandem array 100 kb upstream of the
maize b1 locus is associated with paramutation. Genes
and Development 16: 1906-1918.
Lisch, D., C.C. Carey, J.E. Dorweiler, and V.L. Chandler. 2002.
A mutation that prevents paramutation in maize also reverses Mutator
transposon methylation and silencing. Proceedings
of the National Academy of Sciences U.S.A. 99: 6130-6135.
Chandler, V.L., M. Stam, and L.V. Sidorenko. 2002. Long-distance
cis and trans interactions mediate paramutation. Advances
in Genetics 46: 215-234.
Selinger, D.A., and V.L. Chandler. 2001. B-Bolivia, an allele of
the maize b1 gene with variable expression, contains a high copy
retrotransposon-related sequence immediately upstream. Plant
Physiology 125: 1363-1379.
Chandler, V.L., and H. Vaucheret. 2001. Gene activation and gene
silencing. Plant
Physiology 125: 145-148.
Dorweiler, J.E., C.C. Carey, K.M. Kubo, J.B. Hollick, J.L. Kermicle,
and V.L. Chandler. 2000. Mediator of paramutation1 is required for
establishment and maintenance of paramutation at multiple maize
loci. The
Plant Cell 12: 2101-2118.
Chandler, V.L., W.B. Eggleston, and J.E. Dorweiler. 2000. Paramutation
in maize. Plant
Molecular Biology 43: 121-145.
