Our laboratory studies all aspects of the cell nucleus, with particular emphasis on the structure of chromosomes, the transcription and processing of RNA, and the role of nuclear bodies, especially the Cajal body (CB) and the histone locus body (HLB).
Much of our work makes use of the giant oocyte of amphibians and the equally giant nucleus or germinal vesicle (GV) found in it.
An oocyte of the frog Xenopus tropicalis and the GV (nucleus) that was isolated from it.
The GV contains the largest known chromosomes, the so-called lampbrush chromosomes, named after their fuzzy appearance at low magnification.
A pair of homologous lampbrush chromosomes in prophase of the first meiotic division. Phase contrast image of unfixed chromosomes isolated from a GV of the American newt Notophthalmus.
Even at moderate magnification this fuzziness is clearly resolved into paired loops of chromatin that extend laterally from the main axis of the chromosome, each pair of loops (sister chromatids in cytological terminology) corresponding to one or a few actively transcribing genes. Thus, it is possible to study transcription at the single gene level using a variety of immunofluorescent and fluorescent in situ hybridization probes.
Paired transcription loops (sister chromatids) on a
lampbrush chromosome of the newt, immunostained
with antibodiesagainst RNA polymerase II (green)
and an RNA-binding protein (red).
This protein is found on only a few loop pairs.
Currently we are using super-resolution microscopy to analyze nascent transcripts on the lampbrush chromosome loops in even greater detail.
Super-resolution image of a pair of transcription
loops, immunostained for RNA polymerase II (green)
and an RNA-binding protein (red).
Complementing our structural studies of the lampbrush chromosomes, we use deep sequencing technology to analyze the RNA made by the oocyte. Because the GV is easy to isolate manually, amphibian oocytes provide a unique opportunity to study cytoplasmic and nuclear transcripts in pure form. We find that the cytoplasm contains spliced messenger RNA, as expected. However, much of the nuclear RNA consists of stable molecules derived from the introns of transcribed genes, a novel population that we have named stable intronic sequence RNA (sisRNA).
Genome browser view of nuclear RNA (GV, top) and cytoplasmic RNA (bottom) transcribed from thenasp gene of Xenopus tropicalis.
Even more surprising, we find specific sisRNA molecules in the cytoplasm. These cytoplasmic sisRNAs exist as circles (lariats without tails). Both nuclear and cytoplasmic sisRNAs are transmitted to the egg at fertilization and persist intact until at least the blastula stage of the embryo. A major focus of our research is to determine the function(s) of sisRNAs in the oocyte and embryo.
We study the Cajal body (CB) and histone locus body (HLB) in tissue culture cells, in amphibian oocytes, and in the fly Drosophila. Studies from our lab and many others suggest that CBs and HLBs are involved in assembly of the RNA splicing machinery and histone pre-mRNA processing machinery respectively. AlthoughDrosophila cells are much smaller than frog cells, flies have the great advantage that they permit genetic studies on nuclear body components. In Drosophila one can manipulate the genes that encode proteins and RNAs of the CB and HLB, and follow the consequences in various embryonic, larval, and adult tissues.
Drosophila egg chamber showing Cajal bodies (green) and histone locus bodies (red) in giant nuclei of the nurse cells. DNA is blue (DAPI stain). Arrow points to the single Cajal body in the oocyte nucleus.