Wednesday, January 23, 2008

Ribosomal RNA Genes in Eukaryotes

The "genes" for ribosomal RNAs in eukaryotic genomes are found in separate clusters. One cluster consists of hundreds of copies of the 5S gene. These genes are transcribed by RNA polymerase III [Eukaryotic RNA Polymerases].

The other ribosomal RNA genes are found in an "operon"-like structure that's similar to the bacerial operons [Ribosomal RNA Genes in Bacteria]. Unlike bacterial transcription units, these ones are found in large tandem arrays on eukaryotic chromosomes. There can be hundreds of individual transcription units in a cluster and there can be several clusters. In humans, for example there are five clusters on five different chromosomes and each one has between 50 and 100 transcription units. The large eukaryotic ribosomal RNA genes are transcribed by RNA polymerase I.

There is considerable variation in the size of a transcription unit from one species to the next. This variation occurs in the length of the external transcribed sequences (ETS) that are found at either end of a cluster (open rectangles). There can also be substantial variation in the length of the internal transcribed sequences (ITS)—the ones that will be removed when the precursor is processed. The distance between transcription units can also vary. This region is referred to as the non-transcribed spacer (NTS).

Note that the order of the small (18S) and large (28S) RNAs is the same as in bacteria. Note also that the 5.8S eukaryotic ribosomal RNA is found at the 5′ end of the large RNA. The homologous part of the bacterial RNA is found at the end of the 23S RNA. What's happened in eukaryotes is that a new cleavage site has evolved so that the largest RNA is now expressed in two pieces.

RNA precursors derived from typical transcription units like the one shown above are processed by cutting the RNA at various points to release the mature 18S, 5.8S, and 28S RNAs. The processing steps are well understood. In bacteria, some of the cleavages occur before transcription is terminated but eukaryotic nuclei usually accumulate long precursors that are only processed when transcription terminates. In those species that have nucleoli the nucleolus represents the location of ribosomal RNA genes that are being transcribed.

The electron micrograph shows clusters of ribosomal RNA transcription units being transcribed a high rates in nucleoli. The RNA molecules are splayed out from the DNA like the branches of a Christmas tree. RNAs near the beginning of the gene are short and as transcription proceeds the RNAs get longer and longer until the complete precursor is released at the termination site.

In some species the 28S ribosomal RNA gene contains an intron near the 3′ end. In this case the intron sequence is removed and the two ends of the 28S RNA are joined together to produce the mature ribosomal RNA. The remarkable thing about this splicing event is that it is often autocatalytic. In other words, the precursor RNA folds up all by itself, cuts itself in two places, and rejoins its own ends. No proteins or other molecules are needed for this reaction to occur.

The classic example is the ribosomal RNA transcription unit from the protozoan Tetrahymena thermophilus shown above [Monday's Molecule #59]. The self splicing reaction was characterized by Tom Cech who received the Nobel Prize in 1989 along with Sydney Altman for discovering catalytic RNAs. This particular type of intron is called a group I intron and the mechanism of self-splicing requires a guanosine cofactor. Remarkably, the excised fragment of RNA also has catalytic activity; it can act as an endonuclease cleaving other RNAs.

RNA genes in most species do not have introns.


  1. High-fidelity gene arrays like these clusters present special challenges for genome sequencing efforts, since shotgun assembly of such highly repetitive sequences is difficult or impossible. The human genome project for instance doesn't have any information on the larger rDNA arrays, and is greatly abbreviated (read: incorrect) with respect to the 5S arrays.

    This sequence assembly difficulty is unfortunate because lack of genome project representation tends to hide the really tremendous human genomic variation at these loci.

    See for example:
    Stults DM, Killen MW, Pierce HH, Pierce AJ.
    Genomic architecture and inheritance of human ribosomal RNA gene clusters.
    Genome Res. 2008 Jan;18(1):13-8. Epub 2007 Nov 19.

  2. Thank-you very much for the reference. I'm about to post an article on the human ribosomal RNA gene arrays and that reference is crucial.

  3. Love the electron micrograph. Classic. But why are the mRNAs splayed out on a 2-D plane? ie Why is the Christmas tree flat?

  4. The flatness is just an artifact resulting from the way the complexes are prepared for the electron microscope. The first step is to dry them out on a flat grid.

    BTW, in the olden days (late 1960's) we used to call these "Oscar Miller" pictures after the man who first published them.

  5. Looking at the electron micrograph, I'm trying to imagine all that transcriptional activity in a three-dimensional ball-and- stick model. I'm then trying to visualise all the various precursors, enzymes and small molecules zipping around while those strands of RNA flail. It's amazing that anything Nature actually works.

  6. Intragenomic variation in ribosomal RNA gene of the sea urchin Lytechinus variegatus. Molec Biol Rep. Volume 32, Number 1. 61 – 65(2005).N.K.Mishra