Transcription elongation involves the synthesis of an mRNA transcript and occurs on the DNA while in a highly condensed chromatin state.  The nucleosomes in the chromatin form a barrier to the main transcription enzyme RNA polymerase II (RNAPII), thus the enzyme depends on a large number of accessory factors to promote efficient transcription through the nucleosome.  One such factor is the protein complex Spt4/5.  This protein complex is the only known RNAPII associated factor that has been conserved across all three domains of life indicating its importance in transcription elongation.  Spt4/5 can both inhibit and promote the processivity of RNAPII during transcription elongation; however, the mechanism of these roles remains elusive. 

Spt4 is a small zinc finger protein, which binds through hydrophobic interactions to a conserved region of Spt5 (NGN domain).  Apart from this conserved regions, another important feature of Spt5 is the presence of five RNA binding (KOW) domains.  An Spt4/5 construct encompassing the full length Spt4 and the Spt5 NGN domain has been shown to bind to RNAPII in the middle of the RNAPII claw acting to completely encircle the DNA in the binding channel during transcription^1 2 . It has been hypothesised that the first KOW domain of Spt5 stabilises the upstream DNA as it emerges from the transcription bubble, and that the second to fifth KOW domain contacts the nascent RNA as it emerges from RNAPII ¹. 

In order to better understand the function of the multiple KOW domains of Spt4/5 we have carried out biophysical studies and nucleic acid binding assays on constructs of the protein containing different numbers of KOW domains.  These results characterise the RNA binding specificity of the protein, and provide insight into the structure and function of Spt4/5.