My laboratory
is interested in DNA structure, especially that which
is found associated with various repetitive elements
of DNA. Although repetitive DNA is often irreverently
referred to as "junk" DNA by genome aficionados, it
apparently plays an important structural role in the
genomes of higher eucaryotes. Perturbing the structure
of such DNA repeats appears to have detrimental
effects on the cell. For instance, the expansion of
certain repetitive DNA sequences has been linked with
a number of human diseases. My previous work has
studying the packaging of such repeats into chromatin,
where DNA is wrapped around spools of protein in order
to be packaged into the nucleus.
Two classes of research projects are
ongoing in my lab which enable us to elucidate the
function of repetitive DNA:
1) “Wet lab” experiments using the thermophilic
bacteria, Thermus thermophilus, to better
characterize these repeats.
2) “In silico” experiments using computers to search
for repetitive elements.
The former approach is currently being used to
isolate large plasmids from the bacteria (megaplasmids)
which contain CRISPR (Clustered Regularly
Interspaced Short Palindromic Repeats) and to
compare the sequences from different strains. In the
future, I would like to isolate our own strains of
the bacteria to continue this analysis.
Other projects in my laboratory
involve computer-based analysis of genomic
sequences, or bioinformatics. People who study this
field of science are usually called "data miners"
since they take large amounts of data and extract
important sequences from them. Since I’m more
concerned with junk DNA, my students are more akin
to "data junk collectors", or if you prefer, "bioinfomaniacs".
Focus here centers on the identification and
analysis of repetitive sequences in a wide range of
eucaryotic genomes and the prediction of the "bendability"
of DNA in these repetitive regions, with the hopes
of someday being able to predict their ability to
assume structural roles in the genome.
Godde, J. S. (in
press) “Biotechnology” in
Encyclopedia of
Global Warming,
Salem Press: Pasadena, CA.
Godde, J. S. & Ura, K. (in
press)
Dynamic alterations of linker histone variants during development., Int. J.
Dev. Biol.
Godde, J. S. (in
press) “Chromosomes
and cancer” in Salem
Encyclopedia of Health and Medicine: Cancer,
Salem Press: Pasadena, CA.
Godde, J. S. (in
press) “STR
(short tandem repeat) analysis”
in Encyclopedia of Forensic Science, Salem Press: Pasadena, CA.
Godde, J. S. & Ura, K. (2008)
Cracking the enigmatic linker histone code., J. Biochem.
143:287-293.
Godde, J. S. (2007) “Last human
chromosome sequenced” in Magill’s Medical Encyclopedia, 4th
rev. ed., Vol. 2, 1122, Salem Press: Pasadena, CA.
Godde, J.
S. & Bickerton, A.
J. (2006) The repetitive DNA elements called CRISPRs and
their associated genes: evidence of horizontal transfer among
prokaryotes.,
J.
Molec. Evol.,
62, 718-729.
Godde, J. S. (2005) “Genomics” in
Magill’s Medical Encyclopedia, 3rd rev. ed., 1066-1070,
Salem Press: Pasadena, CA.
Godde, J. S. (2004) “Telomere Length
in Clones” in Encyclopedia of Genetics, rev. ed., 730, Salem Press:
Pasadena, CA.
Feig, J.,
Hussein, Y., & Godde, J. S. (2001) Combinatorial libraries of porphyrin derivatives: finding G-quadruplex interactive agents with
a high specificity for human telomeric repeats., J Biomol. Struct.
Dyn., 18, 967.
Goldman, K., Lembeck, M., & Godde, J. S. (1999) Probing the structure of (CGG)n
triplet repeats in the human FMR1 gene via interstrand crosslinking.,
J Biomol. Struct. Dyn., 16, 1274-1275.
Goldman, K., Donaire, M., & Godde, J. S. (1998) Mapping mitomycin crosslink sites
in the human Fragile X gene., National Minority Research Symposium
Proceedings., 88.
Godde, J. S.,
Kas, S.U., Hirst, M. & Wolffe, A.P. (1996) Nucleosome assembly on
methylated CGG triplet repeats in the Fragile X Mental Retardation
Gene 1 promoter., J. Biol. Chem., 271, 24325-24329.
Godde, J. S.,
& Wolffe, A.P. (1996) Nucleosome assembly on CTG triplet repeats.,
J. Biol. Chem., 271, 15222-15229.
Godde, J. S.,
Nakatani, Y., & Wolffe, A.P. (1995) The amino-terminal tails of the
core histones and the translational position of the TATA box
determine TBP/TFIIA association with nucleosomal DNA., Nucleic Acids
Research., 23, 4557-4564.
Godde, J. S.,
& Wolffe, A.P. (1995) Disruption of reconstituted nucleosomes: the
effect of particle concentration, MgCl2 and KCl
concentration, the histone tails and temperature., J. Biol. Chem.,
270, 27399-27402.
