Table 1.

Glossary of terms used in the microRNA world.

ASO: An antisense oligonucleotide is a single-stranded, chemically modified DNA-like molecule that is 17 to 22 nt in length and designed to be complementary to a selected messenger RNA or ncRNA and thereby specifically inhibit expression of that gene.

Exome sequencing (targeted exome capture) is an efficient strategy to selectively sequence the coding regions of the genome.

Messenger RNA (mRNA): The form of RNA that mediates the transfer of genetic information from the DNA in the cell nucleus to ribosomes in the cytoplasm, where it serves as a template for protein synthesis.

MicroRNAome: the full complement of known (cloned) microRNAs present in a genome. Due to the multiple cloning efforts this is growing constantly and by May 2014 contains 2578 mature human miRNAs (release 20 of miRBase at http://www.mirbase.org/index.shtml)

Noncoding RNAs (ncRNAs): Any RNA molecule that is not translated into a protein.

Oncogenic microRNA: a microRNA that when expressed at higher levels as normally, initiate or favor the development of a tumor.

Open Reading Frame (ORF): A section of a mRNA that begins with an initiation (methionine ATG) codon and ends with a nonsense codon. ORFs all have the potential to encode a protein or polypeptide, however many may not actually do so.

Pol II: RNApolymerase II (also called RNAP II) catalyzes the transcription of DNA to synthesize precursors of mRNA and most small nuclear RNA.

Pol III: RNA polymerase III (also called RNAP III) transcribes DNA to synthesize ribosomals RNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of “housekeeping” genes whose expression is required in all cell types and most environmental conditions.

Pseudogene: A copy of a gene that usually lacks introns and other essential DNA sequences necessary for function. A pseudogene has been mutated into an inactive form over the course of evolution, but contains the majority of interactor sites with microRNAs as the original functional gene.

Sense/Antisense: Referring to the strand of a nucleic acid that directly specifies the product or referring to the strand of a double-stranded molecule that does not directly encode the product but is complementary to it.

The Cancer Genome Atlas (TCGA): a project started in 2005, to catalogue genetic mutations responsible for cancer, using gene expression profiling, copy number variation profiling, SNP genotyping, genome wide DNA methylation profiling, microRNA profiling, and exome sequencing.

Transcription: The process whereby RNA is synthesized from a DNA template.

Translation: The process of ribosome-mediated production of a protein whereby the primary structure of the protein is determined by the codon nucleotide sequence in mRNA.

Tumor suppressor microRNA: a microRNA that when expressed normally block the initiation or development of a tumor; at lower levels of expression this braking effect disappear and the tumor can develop. The same miRNA can behave as an oncogene in one type of tissue and as tumor suppressor in another type.

Untranslated Region (UTR): 5′UTR is the portion of an mRNA from the 5′end to the position of the first codon used in translation. The 3′ UTR is the portion of an mRNA from the 3′end of the mRNA to the position of the last codon used in translation.