4557

Classically, miRs are regarded as negative regulators of gene expression that inhibit translation and/or promote mRNA degradation by base pairing to complementary sequences within the 3′-untranslated region (3′-UTR) of protein-coding mRNA transcripts [ 27 , 28 ]—mRNA degradation accounts for the majority of miR activity [ 29 ]. By altering levels of key regulators within complex genetic pathways, miRs provide a posttranscriptional level of control of homeostatic and developmental events [ 30 – 32 ]. Specifi c structural aspects of miRs are discussed in detail in Chap. 2 of this book. Briefl y, maturation of miRs involves a multi-step process [ 33 – 35 ] that starts from the transcription (mainly operated by RNA polymerase II) of single-stranded nonproteincoding RNAs, which are either transcribed as stand-alone transcripts ( intergenic miRs), often encoding various miRs, or generated by the processing of introns of protein-coding genes ( intragenic or intronic miRs). Transcription of intergenic miRs leads to the formation of primary miRs (pri-miRs) with a characteristic hairpin or stem–loop structure [ 36 ], which are subsequently processed by the nuclear RNase III, Drosha [ 37 ], and its partner proteins, including the DiGeorge Syndrome Critical Region 8 (DGCR8, known as Pasha in invertebrates), named for its association with DiGeorge Syndrome [ 38 , 39 ], to become precursor miRs (pre- miRs). On the other hand, intronic miRs are obtained by the regular transcription of their host genes and then spliced to form looped pre-miRs, bypassing thereby the Drosha pathway [ 33 , 40 ]. Recently, Claudio Alarcón and colleagues discovered that the addition of an m6A mark to primary miRs by methyltransferase-like 3 (METTL3) is required for their recognition by DGCR8 [ 41 ]. They also proved that METTL3 is suffi cient to enhance Table 1.1 (continued) Abbreviation Complete name Main functions Length (nt) Ref. RNase MRP Mitochondrial RNA processing ribonuclease Mitochondrial DNA replication and rRNA maturation (ribozyme) 265–340 [ 111 , 112 ] SINE Short interspersed repetitive elements Transcriptional suppressor (e.g. Alu element) <500 [ 113 , 114 ] TERC Telomerase RNA component Telomere synthesis 451 [ 115 , 116 ] T-UCR Transcribed ultra-conserved region Transcriptional enhancer >200 [ 117 , 118 ] vlincRNAs Very long intergenic RNA Transcriptional and posttranscriptional regulation >50 kb [ 119 , 120 ] 1 A Fleeting Glimpse Inside microRNA, Epigenetics, and Micropeptidomics 4 miR maturation in a global and non-cell-type-specifi c manner, acting as a strategic posttranscriptional modifi cation that promotes the initiation of miR biogenesis. Pre-miRs are exported from the nucleus in the cytoplasm in a process involving the Ran-GTP-dependent shuttle Exportin-5 [ 42 ]. Once in the cytosol, the pre-miR hairpin is cleaved by the RNase III enzyme Dicer [ 43 , 44 ], yielding a mature miR:miR* duplex about 22 nucleotides in length, which is subsequently incorporated into the protein complex called RNA-induced silencing complex (RISC) to form miRISC [ 45 , 46 ]. At this point, one of the double strands, the guide strand, is selected by the argonaute protein [ 47 ], the catalytically active RNase in the RISC complex, on the basis of the thermodynamic stability of the 5′ end. In particular, the strand with a less thermodynamically stable 5′ end is commonly chosen and loaded into the RISC complex [ 48 ], serving as a guide for mRISC to fi nd its complementary motifs in the 3′-UTR of the target mRNA(s). Although either strand of the mature duplex may potentially act as a functional miR, only one strand is usually incorporated into the RISC where the miR and its mRNA target interact [ 49 , 50 ]. Such a binding inhibits the translation of the protein that the target mRNA encodes or promotes gene silencing via mRNA degradation [ 51 , 52 ]. Nearly 2000 miR sequences have been heretofore identifi ed in the human genome, with over 50,000 miR-target interactions. Several algorithms and bioinformatics websites, including TargetScan and miRWalk [ 53 , 54 ], have been developed to predict specifi c mRNA/miR interactions. However, miR binding rules are quite complex and not fully understood, resulting in a lack of consensus in the literature. Given all these crucial features, miRs could represent an important way for the cell to establish intercellular (with other cells, via secreted miRs) and intracellular (among its own genes) communication. Determining direct cause-and-effect links between miRs and mRNA targets is essential to understanding the molecular mechanisms underlying disease and the subsequent development of targeted therapies [ 55 , 56 ].