Eukaryotic Gene Structure:


The number of genes per genome in eukaryotes is large and they vary in their structure and function.  There is division of labor among the RNAPs that transcribe them.  There are three basic types of RNAPs and they are associated with specific transcription factors and often found to be regulated by activators/Coactivators, enhancers and repressors/corepressor.


Promoter Structure for RNA Pol-I


Genes, whether they are prokaryotic or eukaryotic, have same structural features such as coding regions, promoter elements and terminal sequences. 

·         However the detailed organizations vary in terms sequence blocks and their positions.  The major difference from prokaryotes is that the coding region is split into coding and noncoding regions. 

Promoter regions and the ends of genes show different structural features, because eukaryotic genes, depending upon the kind of gene, they are transcribed by three different enzymes, where as in prokaryotic systems all types of genes are transcribed by only one type of RNA polymerase, of course with different sigma factors for different set of genes.

·         It clearly means, eukaryotic gene structure, especially promoter regions, including their regulatory regions and their structure are different and more complicated. 

So far except for few simple genes, understanding of others is nebulous; this is in spite of great strides made in gene cloning, sequencing and expressions of genes in different cell types. 

·         Genes transcribed by different enzymes have different structural features and different functions.




A.   Promoter Structure: For RNA pol-I:


Genes for ribosomal RNA are exclusively transcribed by RNA polymerase-I.  

·         In eukaryotic system most active and highly productive genes, which are transcribed most of the time, are ribosomal RNA genes. 

More than 90 % of the total RNA found in any eukaryotic cell is rRNA. 



This illustrative diagram represents the assembly of Transcriptional complex on specific promoter elements.




·         Its synthesis is triggered, when cells are activated for cell proliferation, in such situations tremendous increase of rRNA takes place, ex. rRNA synthesis during oogenesis is a par excellent example.

The rRNA genes themselves, at least in some cases get amplified by rolling circle mode of replication.  The demand for rRNA is very high in developing Oocyte for once the eggs are formed; rRNA is not synthesized for at least 6-7 cell cycles after fertilization, which means there should be high concentration of stored rRNA in the Oocyte.

·         In almost all eukaryotic systems, rRNA genes are organized as clusters of tandemly repeated genes in secondary constriction region of chromosomes. 

The number of genes found in the region range from 200 to 600 per genome.  These clusters are distributed to few other chromosomes of the genome.  For example Homo sapiens, have secondary constrictions for rRNA genes in five pairs of homologous chromosomes.



·         Most complicated organization of rRNA genes is, one of the rRNA components called 5s RNA.  This rRNA gene is not located with major rRNA gene segments but found elsewhere. 

The 5sRRNA genes are distributed all over the genomic chromosomes, some are found near the tips of certain chromosome just behind telomeres, and others are located elsewhere.

·         In real terms, though the rRNA genes are clustered as tandem repeats, each of the ribosomal genes show their own structural features. 

The tandemly repeated genes have spacers in between them, which is not transcribed.  The spacer regions can be as large as 2000 to 40,000bps long. 

·         And the spacer regions themselves are organized into blocks, each of which have their own sequence elements that promote transcriptional initiation, perhaps they act as enhancers.  Basically they all have what is an essential structural elemental of a promoter.

The consensus promoter elemental feature of all rRNA is presence of core structure encompassing about 40 bp from the start site. 

·         A consensus sequence that has been established from several rRNA genes is the presence of a sequence from start site of transcription.

It is important to note the rRNA genes don’t have TATA boxes in their promoters.   But they contain an 11 base pair elements surrounding the start site called INR sequences;  (py) 2-C- [A]-(py) 5.  This is to some extent true for protein coding genes.  At start site the sequence invariably starts with A and some times it is G. 

·         It has, what is termed as core promoter region between (-) 10 and (-) 45 and an upstream control elements (UCE), it is the region to which upstream element binding factors bind.

Between –110 and –142 regions a GC rich sequence is present.

·         At the start region it has --3(py) - A – 3-4 (py).

·         The core region attracts selectivity factor SL-I, 3 TAFs (TBP associated factors) and TBP (TATA binding factors).  Positioning of the TBP is assisted and determined by the SL-I and then TAFs bring TBP.

·         It is now known that two histone like proteins are also associated with this complex.

This assembly ultimately brings RNA pol-I to the site.  But the activation depends on upstream control element binding factors UBF 1; they bind not only to the core but also to UCE. 

·         UBFI binding results in protein-protein interaction in such a way two units of UBFs join with one another with a DNA loop, and activate the RNA pol-I complex.




Promoter of rRNA genes:


--142                      -- 110                                             >

---------I----I----------I----I----------I-promoter core—I---------ter-

             GC rich                         --45-----I>


            [---CTCCGAGTCG (N) 5TGGGCCGCCGG—]



Transcription Terminator regions:


Transcription termination takes far beyond the coding region of rRNA, and the region contains a (T)n sequences recognized by a set of protein-factors called ancillary factors (TTERF)/TTFs, which make the RNAP I to dissociate from the rRNA and the DNA template.