Four major steps of RNA polymerase II (RNAPII) transcription were heavily described: Initiation, Early Elongation, Productive Elongation, Termination.We know that each of those four steps carry specific markers (i.e chromatin modification or modification of the RNAPII CTD tail) with specific positions along-side genes. RNAPII is known to transcribe both coding genes and long-non-coding RNAs (LncRNAs).
Sometimes, transcription from non-coding RNA regions induce a shift of the positional information and dis-regulate the downstream coding gene. This mechanism is called Transcription Interference (TI).
A new complex regulates Transcription Interference ?
TFIID is a large complex helping to initiate transcription. It binds to the TATA box, recruits transcription factors, RNAPII and initiate transcription. TFIID is conserved in eukaryotes and is composed of TAFs TFIID Associated Factors. In Arabidopsis they are 15 TAFs with several homologs.
We have shown that two TAFs suppress a known TI event. We will investigate further this mechanism and characterize the role of TFIID in the initiation of pervasive transcription in Arabidopsis.
You will follow up the possible role of the TAFs; TAF12B, TAF12 and TAF15, TAF15B in transcription interference (crossings, Northen blots..etc).
You will transform Arabidopsis with constructs of these two TAFs with Agrobacterium for downstream analysis. (i.e ChiP-Seq)
If other homologs suggest more involvement of TFIID in TI suppression, the project could lead to use high-throughput RNA sequencing to find endogenous TI events. And pull-down proteomics experiments to identify TFIID associated factors in TI regulation.
Keywords:Transcription, Non-coding, RNA, Plant
Supervisor(s): Sebastian Marquardt