Project description:ChIP-seq database identifies genes with promoter regions bound by VgrR in X. campestris pv. campestris grown under osmostress conditions
Project description:Cuscuta campestris is an obligate parasitic plant that attaches to the stems of host plants to obtain water and nutrients. C. campestris produces a specialized set of microRNAs specifically at the host-parasite interface. Many of these interface-induced microRNAs target mRNAs from the host. This experiment was designed to capture full-length primary transcripts that give rise to C. campestris interface-induced microRNAs. C. campestris shoot tips were stimulated to produce haustoria, then harvested to extract total RNA. RNA was then treated with various enzymes to modify 5' ends. Libraries were then made and sequenced. Importantly the library method only captures RNAs with a 5'-monophosphate. Therefore the specific enzymatic treatments can reveal the native 5' ends of the sequenced RNAs. Data were used to identify the primary transcripts for many of the known C. campestris primary microRNA transcripts. The data were also interrogated to tally specific snRNAs (U1, U2, U4, and U5) that are known to have a 2,2,7mGppp cap, and the tally pre-tRNAs, which are known to have a ppp 5' end. The analyzed results indicated that C. campestris interface-induced microRNA primary transcripts likely have a 5' ppp, not a cap, consistent with transcription by RNA polymerase III. The analysis also demonstrated that C. campestris interface-induced microRNA primary transcripts mostly terminate within stretches of polyT and lack polyA tails, also features consistent with Pol III transcription. Finally, the analysis indicated that the transcriptional start sites were located ~ 55 bp downstream of a common ten-base pair promoter element (the upstream sequence element). The 55bp spacing is also consistent with Pol III transcription.
