The particular amount of long RNA transcripts that aid as precursors for small RNA species is still undefined. Recent research using array-based approaches on human cell lines has shown that a prominent percentage of small RNAs arises from longer RNA precursors. However, only a small proportion of these long RNAs actually coincide with small RNAs (Borel et al. 2008; Kapranov et al. 2007a). Regardless of this, many of the identified RNAs show important changes in reaction to retinoic acid treatment, with a large percentage (26–43%) being exact to certain cell lines (Borel et al. 2008).
The purpose restrictions of array-based ways mean that these studies may not arrest in all cases where long RNAs are treated into small RNAs. Additional newly, deep-sequencing studies have exposed that many small RNAs with controlling functions are created from stem-loop structures and double-stranded RNAs in various organisms, including mice, insects, and plants (Chung et al. 2008; Czech et al. 2008; Ghildiyal et al. 2008; Kawaji et al. 2008; Kawamura et al. 2008; Okamura et al. 2008; Tam et al. 2008; Watanabe et al. 2008; Lister et al. 2008; Meins et al. 2005; Vaucheret 2006). For example, in mouse oocytes, double-stranded RNAs shaped by sense-antisense transcripts from inverted repeats, retrotransposons, and protein-coding genes are managed into small interfering RNAs (siRNAs) that help control the levels of these transcripts. If the enzymes Dicer or Ago2, which are involved in processing these small RNAs, are missing, the levels of expression of the target RNAs increase (Tam et al. 2008; Watanabe et al. 2008).
Maximum of these small RNAs originate from repetitive sequences, but remarkably, pseudogenes—previously considered “junk” DNA—also produce siRNAs that control related protein-coding genes (Tam et al. 2008; Watanabe et al. 2008). The connections between sense and antisense RNA expressions are difficult (Katayama et al. 2005). Given the huge number of these RNA sets in eukaryotes, there is an option of extensive links of endogenous siRNAs that regulate gene expression in animals, which could have important consequences for development. For example, in zebrafish, a pair of coexpressed sense-antisense RNAs from the Slc34a2a gene, which is preserved in mammals, yields short RNAs of about 23 nucleotides that are controlled differently during development (Carlile et al. 2008). Inserting these RNA pairs into Xenopus oocytes effects in specific treatment and degradation of target RNAs, a process that is also understood once RNA from zebrafish embryos is inserted. Alike controlling mechanisms have been detected in plants (Borsani et al. 2005; Jin et al. 2008). Though the genomes of unicellular eukaryotes are naturally dense and mainly consist of sequences that code for proteins (Taft et al. 2007), long non-coding RNA molecules are involved in a diversity of mechanisms that rule the expression of genes and the diversity of cells in these organisms. One of the most outstanding examples can be witnessed in the life cycle of ciliates belonging to the Oxytricha genus. These ciliated protozoans have a transcriptionally energetic somatic macronucleus that is detached after fertilization during sexual reproduction, and an inactive germline micronucleus. It has long been uncertain how the germline genome is used to renovate the somatic genome in the progeny, even if the germline nucleus is passed down to the progeny (Yao 2008).