transcription start sites (TSS)

[altodor]

Hi all!

I'm new to ChIPseq analysis and have a question regarding TSS.

I need to compare my ChIPseq regions against transcription start sites, human. Can I download TSS from Ensembl? Is transcription start site the same as transcript start (like first nucleotide of the first exon)?

When I tried to get them in ChIPPeakAnno package using
EnsemblTSS<-getAnnotation(mart, featureType=c("TSS")))
I got the same table with
EnsemblAnnotation<-as.data.frame(getAnnotation(mart, featureType=c("TSS","miRNA", "Exon", "5utr", "3utr", "ExonPlusUtr")))
How can it be the same?

Thank you!

[biznatch]

I'm not very familiar with getting data from Ensembl, but you can get transcription start sites for all genes in the human genome from the UCSC Table Browser.

Group: Genes and Gene Prediction Tracks
track: UCSC Genes
table: known genes
output format: selected fields...

Then click "get output" and select the fields you want, including "Transcription Start Position".

[kwatts59]

Originally Posted by altodor

Is transcription start site the same as transcript start (like first nucleotide of the first exon)?

No, the first codon of the first exon is the start codon "ATG" which also codes for methionine. This is called the translation start site.

The transcription start site is where the RNA polymerase binds to in the 5' UTR upstream of the start codon. IMHO

Maybe someone else can elaborate more. I dont want to give you the incorrect info.

[idonaldson]

I have done this sort of thing using the ensembl BioMart. However, the UCSC table browser for RefSeq gene annotations is my current favourite.

[altodor]

So, from Ensembl or RefSeq we get translation start sites, don't we?

And a lot of bioconductor packages, when refering to TSS, actually give us translation start site, not transcription start site (first of all, ChiPpeakAnno)

Does anyone use a database for TSS=transcription start sites?

I found this discussion about TSS:
http://www.protocol-online.org/biolo...osts/6050.html

[Jelena]

Originally Posted by kwatts59

No, the first codon of the first exon is the start codon "ATG" which also codes for methionine. This is called the translation start site.

The transcription start site is where the RNA polymerase binds to in the 5' UTR upstream of the start codon. IMHO

Maybe someone else can elaborate more. I dont want to give you the incorrect info.

This is incorrect.

The first codon of the first exon is approximately the transcription start site. The translation start site (i.e. the start of the CDS) is located somewhere within the transcript, but doesn't necessarily have to be in the first exon at all.

The first nucleotide of the first exon is a good approximation. The main issue with it is that the exact TSS can shift around a bit depending on tissue and condition, so the genome annotations are only so accurate. But they're a good start.