Jon Houseley
Genomes produce vast amounts of non-protein coding RNA
Although only a tiny fraction of a eukaryotic genome encodes proteins, eukaryotes from yeast to humans transcribe almost their entire genomes into RNA. This creates a large gap in our understanding, since although some functional non-protein coding RNAs such as ribosomal RNAs, telomerase, etc. are well characterised, the RNA produced from most of the genome has no known function. Non-protein coding RNAs come in many forms – abundant and rare; stable and unstable; nuclear and cytoplasmic, suggesting that there are a huge range of forms and functions amongst these uncharacterised RNAs.
A handful of non-protein coding RNAs have been characterised, of which the best known is Xist, an RNA that coats the inactive X chromosome. Most have been found to play roles in modulating gene expression, either by recruiting chromatin remodelling factors to particular loci, altering DNA methylation patterns or interfering directly with the transcription of a protein coding gene. In a few cases, however, non-coding RNAs affect the actual structure and sequence of the genome. This is seen most dramatically in the protist Oxytricha, which fragments and restructures its entire genome during development using non-coding RNAs as templates, but in the yeast ribosomal DNA non-coding RNAs have also been shown to alter DNA recombination rates.
Cryptic unstable transcripts
Cryptic unstable transcripts (CUTs) are a particularly unusual class of RNA; they are transcribed at reasonably high levels from many places in eukaryotic genomes, but the RNA is degraded so fast after transcription that under normal circumstances these RNAs cannot be detected. It is unknown whether many CUTs result simply from transcriptional noise producing unwanted RNA that must be degraded, or if the transcription of these RNAs serves some purpose.
That the latter may be true is suggested by the fact that a few CUTs are clearly involved in gene regulation, but these may be the exception rather than the rule. We recently searched for CUTs in heterochromatin, previously thought transcriptionally silent, and found them at all the yeast heterochromatic regions. Since there are no verified protein coding genes in these regions, it is likely that these CUTs are involved in the function of the heterochromatic DNA.
Indeed, we were able to show that one CUT in the yeast ribosomal DNA recruits a specific RNA degradation protein (Trf4) to its transcription site, and that Trf4 is important for the stability of the ribosomal DNA. Based on this data we have theorised that an important role for CUTs is to specify genomic locations for the recruitment of DNA and chromatin modifying enzymes (see figure for a simplified model of how this could happen).
Aims of the lab
The aim of the current research in my lab is to find and functionally characterise novel non-coding RNAs involved both in chromatin remodelling and DNA stability. We are particularly concentrating on CUT transcripts and the function of the RNA degradation protein Trf4, since Trf4 has known roles in genome stability. Loss of Trf4 stabilises CUT transcripts sufficiently to allow their detection, and also destabilises the genome in a number of ways. We theorise that this destabilisation may reflect the loss of a Trf4-based mechanism for recruitment of chromatin remodelling factors to sites of CUT transcription.
Recent selected publications
Houseley JM, Tollervey D (2009) The many pathways of RNA degradation.
Cell 136 763-776
http://dx.doi.org/10.1016/j.cell.2009.01.019
Houseley JM, Rubbi L, Grunstein M, Tollervey D, Vogelauer M (2008) A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster.
Molecular Cell 32 685-695
http://dx.doi.org/10.1016/j.molcel.2008.09.027
Houseley JM, Tollervey D (2008) The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast?.
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1779 239-246
http://dx.doi.org/10.1016/j.bbagrm.2007.12.008
Houseley JM, Kotovic K, El Hage A, Tollervey D (2007) Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control.
EMBO Journal 26 4996-5006
http://dx.doi.org/10.1038/sj.emboj.7601921
Houseley JM, LaCava J, Tollervey D (2006) RNA-quality control by the exosome.
Nature Reviews Molecular Cell Biology 7 529-539
http://dx.doi.org/10.1038/nrm1964
Houseley JM, Tollervey D (2006) Yeast Trf5p is a nuclear poly(A) polymerase.
EMBO Reports 7 205-211
http://dx.doi.org/10.1038/sj.embor.7400612
LaCava J, Houseley JM, Saveanu C, Petfalski E, Thompson E, Jacquier A, Tollervey D (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex.
Cell 121 713-724
http://dx.doi.org/10.1016/j.cell.2005.04.029
