I would like to get some key articles and/or presentations to help understand the underlying mechanism responsible that is responsible for transcription and their function.
Try skimming through the following papers, are actually very good resources.
http://compbio.mit.edu/publications/79_Washietl_WileyRNA_12.pdf
http://www.genetics.org/content/193/3/651.full.pdf+html
http://www.nature.com/nrg/journal/v10/n3/abs/nrg2521.html
http://www.nature.com/nrg/journal/v12/n12/pdf/nrg3074.pdf
http://jcs.biologists.org/content/123/11/1825.full.pdf
And ofcourse, you can always find the basics on wikipedia. This pageactually also gives links to quite a few interesting reads.
http://en.wikipedia.org/wiki/Non-coding_RNA
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