microRNA transcription start site prediction

Question

[paulamic]

Hi there

I am interested in promoter analysis of microRNAs (miRs). I collected the 2 KB upstream sequences of pre-miRs from http://genome.ucsc.edu/cgi-bin/hgTables. Now I need to find out the Transcription start sites of these miRs. I was wondering is there any way to predict the Transcription Start Sites of miRs through UCSC genome Browser. I am new in this field. That's why it will be really helpful if you can provide me any clue.

Thanks in advance.

Paulami

Answer 1

[Martombo]

are you working with the human genome? if so, you can have a look at this web service described in this paper and this table from this paper.

the kind of information they take into account are: histone metilation, CpG islands, TSS libraries, CAGE experiments, TFBS. if you're not working with human, you can try to exploit this data on your own. also, be aware that if a miRNA is inside a gene, it is usually believed that its pri-miRNA is the gene itself [ http://www.ncbi.nlm.nih.gov/pubmed/19038026 ].

[Martombo]

I should add that the latter concept is being disputed http://rnajournal.cshlp.org/content/16/3/495.short

Answer 2

[paulamic]

Thank you for the answer. Yes I am working with human genome. I have consulted miRStart earlier, but there I came across with some difficulties.

For instance take the microRNA hsa-miR-34a. Now, I have collected the 2kb upstream sequence from UCSC. It ranges from chr1:9211727-9213836 (its pre-miR genomic location denoted in miRBase is chr1: 9211727-9211836 [-]).

Now in miRstart I am getting its TSS= 9259025(47189) with the same genomic location (Chr1:9211836[-]). Does that mean the TSS of this miR is far ahead of the pre-miR? Generally TSS lies within 2kb upstream. But in this case it is about 4kb distance. I am confused. Am I making some wrong interpretation? Can you please guide me in this?

Sincerely
Paulami

[ancient_learner]

For mirna the case is different there are many instances where Tss is present far from mature mirna. taking 2kb upstream will apply for normal genes not for mirna. read some papers by typing mirna promoters in pubmed

[paulamic]

Thank you for the answer.

[paulamic]

I found that you are also working on microRNA TFBS. I am doing similar kind of study in human genome. I have collected TSS of a list of human miRs. Now I want to study the promoter regions. Can you please tell me how to obtain the upstream sequences of these particular TSS? It will be really helpful.
Can I use DNA methylation study in this respect? Do you have any reference on that?

Thanks & Regards

Paulami

[ancient_learner]

You can use the combination of computational, experimental data for getting the precise promoter regions for mirna. refer mirbase genomics site for computational prediction. Don't focus on obtaining upstream regions. use bedtools (closest bed) option to find closest methylation marks (H3k4me3 as well as h3k9/14ac marks) for you pre-mirna (the positions for all you can get from mirbase itself). then compare those regions with your output obtained from mirbase genomics. Hope this helps

[paulamic]

Thank you again for your guidance. Since I am new in this field I am afraid I am going to ask you some silly questions. I have no idea about these bedtools, can you please clarify a little on how to obtain the methylation marks using bedtools? Besides, can you please clarify the role of CpG islands in promoter regions of microRNA?

Regards

Paulami

[ancient_learner]

celltype specific methylation patterns (chip-seq data) which indicate the presence of promoters (me3,k9/14ac) can be obtained through geo database. cpg islands are also one of the markers for predicting the possible promoter regions for mirna. you can get them through ucsc genome browser. you need to refer the previously published papers for understanding more better way. regd bedtools google it there is lot of information available.