Next Steps

Though the workshop has performed some novel analyses, this is a preliminary work. It's clear the estimate of transcript initiation has a tremendous amount of uncertainty associated with it. Microarray probe sets are not distinctly comparable with each other as the specific sequences of the probes vary in their target affinity.

An abundance of cell processes can affect the actual amount of protein produced compared to the mRNA reported by a microarray. Just a few of these may include nonsense mediated decay, inhibitory RNA, post-translational editing, protein sorting amongst cellular compartments, secondary structure in the mRNA.

Still for the largest and smallest \(\Theta\) values, the values determined might give some correlation with strong and weak translation. We will next test the leader sequences the largest Transcription Initiation Power in vivo in collaboration with the glowing plant project. To this end we'll be taking the motifs for the 10 largest and some smaller \(\Theta\) motifs and installing the sequence into a plasmid that can be validated in a plant cell by quantitation of florescence from a GFP vs a control construct with its current constitutive motif sequence. When their relative strengths have been determined, the parts themselves will be placed in the golden Braid public repository \cite{olo_Blanca_Granell_Orzaez_2013}.

The collection of motifs will also enable us to examine chloroplast Shine-Delgarno sequences and their relative effects on translation.