User:Anthony Salvagno/Notebook/Research/2009/02/19/Bidirectional promoters generate pervasive transcription in yeast, Zhenyu Xu

For all you new comers to my notebook (anyone who reads this publicly) I have a unique style of reading papers. For me, the only way I understand and remember anything is if I take notes on it as I read it. I also interject my note taking with random thoughts and some experimental ideas. I ask lots of questions too. What you will see on here is my entire thought process laid out on screen.

Intro
Well this starts kinda roughly. They talk about pervasive transcription. What the hell is that? Pervasive means spread throughout, so I guess they mean genome-wide transcription. Next they talk about non-coding RNAs as part of the organizational method. There are: To determine and understand function of these transcripts, the author performs an analysis of the location of these molecules. They show that these new transcripts originate in nucleosome free regions (NFRs) from promoters of other transcripts or from the 3' end of protein-coding genes. They then say how bidirectionality of promoters is an important piece of the puzzle. Also they say the coding of these transcripts could be a way of transcriptional regulation.
 * SUTs - stable unannotated transcripts
 * CUTs - cryptic unstable transcripts

Methods
They characterized yeast samples in YPE (ethanol), YPD, and YPGal (galactose). They used a segmentation algorithm to map transcript start and end positions. They measured profiles of a deletion mutant of RRP6 which codes for a nuclear exosome. This is involved in the degredation of CUTs, so this is how they identified CUTs. They do a lot more stuff, but I'm lost in the jargon and since they reference the supplemental materials and the methods a lot I will just skim it.

As I read their techniques I realize this study involves a lot of sequence mapping, which may be an avenue our research could be very helpful in. As of now its a lot of RNA stuff, but who knows how we could map that with a couple more years of other people's studies under our belts.

Results and Comments
They say there could be a distinction between CUTs and SUTs and that in some cases it is condition dependent.
 * for example, the CUT on the antisense strand of PHO84, which is stabilized in old cells11.

They also state that the median CUT length is 4xx bases and for SUTs it's 7xx bases.

They found that there are nucleosome free regions upstream of the transcipt start site. They concluded that there were bidirectional promoters because they found that a large number of non-overlapping divergent pairs that had a nucleosome free region at their start site.

Of all the transcripts that shared a 5' nucleosome free region (NFR), the average distance between two transcipt start site was 180bp and the distance of the NFR was 130bp.

I'm kinda loosing steam on this paper. I'll come back to it at some later date.