**5.2 rRNA (ribosomal RNA)**

It is one of the longest and most stable RNA molecules which form a major constituent of protein-synthesizing organelle comprising nearly 60% of ribosome's mass. Ribosomes of both prokaryotes and eukaryotes are made of smaller and larger subunits and they form a complex during translation. The smaller subunit of prokaryotes constitutes an RNA molecule with a Svedberg coefficient of 16S and its sedimentation rate is 30S after combining with other proteins. The larger subunit has two RNA molecules (5S and 23S) and they form a 50S subunit by binding with other proteins. On the contrary, the eukaryotic ribosome consists of 60S and 40S subunits with the larger subunit containing two long RNA molecules (18S and 28S) and the smaller subunit containing two short RNAs molecules (5S and 5.8S). A unique rRNA component, such as an undescribed helical structure, was found in the small subunit near the mRNA exit channel of 80S ribosome of *Trypanosoma cruzi*, a protozoan that causes Chagas disease. This structure was most likely involved in the binding of the ribosome to the 5'end of the mRNA facilitating translation [29].

### **5.3 snRNA (small nuclear RNA)**

One of the most important post-transcriptional modifications is the splicing of pre-mRNA which is carried out by an RNA-protein complex known as spliceosome. Small nuclear RNAs form a part of this spliceosome and catalyze splicing [30]. On account of their sub-nuclear localization, snRNAs are grouped into spliceosomal uridylate snRNA, which is the most conserved among eukaryotes, small nucleolar RNA (snoRNA), and small Cajal-body-specific RNA (scaRNA) [31]. UsnRNA comprises U1–U6 being the most abundant and U7–U14 being the low abundant ones. The five major types U1, U2, U4, U5, and U6 are involved in the splicing of mRNA, whereas U3, U8, U13, and U14 are involved in the processing of mRNA [32]. Small nuclear ribonucleoprotein complexes (snRNPs) are formed by the association of each snRNA with one or more proteins.

#### **5.4 snoRNA (small nucleolar RNA)**

snoRNAs are functional non-coding RNAs with a length of 60–300 nucleotides, which are usually found near nucleoli and are prevalent in all eukaryotic organisms. Like snRNPs, they also form snoRNPs in association with a set of proteins [33]. snoRNA are majorly categorized into C/D box, snoRNAs which contain two conserved sequences box C (RUGAUGA and box D (CUGA) and direct 2′-*O*-ribose methylation, whereas H(ANANNA)/ACA box snoRNAs directs pseudouridylation. This classification is based on conserved sequence motifs [34]. The binding of fibrillarin, Nop56p, Nop58p, and 15.5 kDa/Snu13p snoRNP proteins are directed by the box C/D motif and form a kink turn, which is the most prevalent motif found in various RNAs. Proteins like dyskerin/Cbf5p, Gar1p, Nhp2p, and Nop10p are associated with the box H/ACA snoRNAs [35].

#### **5.5 Other small non-coding RNA**

Many types of small non-coding RNA have emerged in the last decade, but it is mainly classified into si (short interfering RNA), miRNA (microRNA), and piRNA (piwi-interacting RNAs). These are small non-coding RNAs with a length of about 20–30 nucleotides and form a protein complex with the Argonaute protein family and are present only in eukaryotes [36, 37].

#### *5.5.1 miRNA and siRNA*

Both miRNA and siRNA are initially part of a double-stranded RNA molecule with a guided strand and passenger strand. Their size is around 20–24 nucleotides only. A unique feature of siRNA is the occurrence of di-nucleotide overhang at the 3'OH. Phased siRNAs, trans-acting siRNAs, epigenetically activated siRNAs, and natsiRNAs are some of the types of siRNAs that play a role in regulating gene expression. A similar type of small non-coding RNA is the miRNA which is a small single-stranded RNA transcribed from DNA sequences into primary miRNA and processed into precursor miRNAs and finally becomes a mature miRNA [38]. Both siRNA and miRNA are almost similar in their biogenesis where an enzyme of the RNAse III family cleaves dsRNA into siRNA and miRNA. Respective RNA-induced silencing complexes are formed with the association of siRNA and miRNA termed siRSC and miRSC and are involved in gene regulation [39].

*Non-Coding RNA and Its Prospective Utilization in Plant Breeding DOI: http://dx.doi.org/10.5772/intechopen.106429*

#### *5.5.2 piRNA*

piRNAs are also single-stranded with a length of 23–36 nucleotides and are more prevalent in animals. They bind to PIWI proteins that belong to the Argonaute protein family. The binding to PIWI and the independence from Dicer distinguished piRNA from siRNA and miRNA. piRNA is grouped into transposon-derived piRNA, miRNAderived piRNA, lnc-derived piRNA, and *Caenorhabditis-*specific piRNA [40].

#### **5.6 lncRNA (long non-coding RNA)**

As previously said, non-coding RNA is of two types, small and long. lncRNA due to its length of more than 200 nucleotides develops complicated secondary and tertiary structures. They are prevalent either in the nucleus or in the cytoplasm of the cell. To sustain their function, structural conservation is more common than nucleotide sequence conservation. Furthermore, when compared to other non-coding RNAs the conservation is found to be less and low prevalence adds to the challenge of identifying and understanding the mode of action. Long non-coding RNA contains linear and circular lncRNA. They are synthesized from pre-mRNA by alternate splicing, which consists of a 5′ cap and 3′ tail. In circular ncRNA, the 5'end and 3′ end are linked forming a circle-like structure [41]. It was found that the level of expression varies between different types of lncRNA, some are organ and tissue-specific and the rest are expressed after encountering different external or internal stresses [42, 43].
