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Unscrambling genetic information at the RNA level

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Abstract Genomics aims at unraveling the blueprint of life; however, DNA sequence alone does not always reveal the proteins and structural RNAs encoded by the genome. The reason is that genetic information is often encrypted. Recognizing the logic of encryption, and understanding how living cells decode hidden information—at the level of DNA, RNA or protein—is challenging. RNA‐level decryption includes topical RNA editing and more ‘macroscopic’ transcript rearrangements. The latter events involve the four types of introns recognized to date, notably spliceosomal, group I, group II, and archaeal/tRNA splicing. Intricate variants, such as alternative splicing and trans‐splicing, have been reported for each intron type, but the biological significance has not always been confirmed. Novel RNA‐level unscrambling processes were recently discovered in mitochondria of dinoflagellates and diplonemids, and potentially euglenids. These processes seem not to rely on known introns, and the corresponding molecular mechanisms remain to be elucidated. WIREs RNA 2012, 3:213–228. doi: 10.1002/wrna.1106 This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > RNA Editing and Modification

Taxonomic distribution of RNA splicing types and variants. The schematic tree (left) shows the major eukaryotic lineages, and archaea and bacteria. For each taxonomic group, the presence of intron types and variants is shown in the right panel. Intron types are spliceosomal, group I, group II, and archaeal/tRNA introns. Variants of the four types are cis‐splicing (Cis), alternative splicing (AS), and trans‐splicing (TS) introns. The subcellular location of the genome that hosts the particular introns and in which the splicing process takes place is specified by letters N (nucleus or in the case of prokaryotes, the cell as a whole), M (mitochondria), and C (chloroplasts, plastids). The absence of mitochondria or plastids is symbolized by a slash. Boxes shown in transparent color indicate that the corresponding intron splicing type has not been reported. The asterisk indicates twintrons and introns by some authors referred to as group III. Within the shown taxonomic groups, representative species with available genome sequences or substantial expressed sequence tag data are: Plantae, Arabidopsis thaliana; Rhodophyta, Porphyra yezoensis; Glaucophyta, Cyanophora paradoxa; Animals, human; Choanoflagellata, Monosiga brevicollis; Ichthyosporea, Spheroforma arctica; Fungi, Rhizopus oryzae; Nuclearidae, Nuclearia simplex; Amoebozoa, Entamoeba histolytica; Cercozoa, Bigelowiella natans; Foraminifera, Reticulomyxa filosa; Alveolates, Tetrahymena thermophila; Stramenopiles, Phytophthora infestans; Malawinonads, Malawimonas jakobiformis; Euglenozoa, Trypanosoma brucei; Heterolobosea, Naegleria gruberi; Jakobida, Reclinomonas americana; Parabasalids, Trichomonas vaginalis; Fornicata, Giardia lamblia; Hacrobia, Guillardia theta; Archaea, Sulfolobus islandicus; Bacteria, Escherichia coli. For references, see text and NCBI nucleotide, complete genome, and BioProject sections.

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Processing of mitochondrial transcripts in diplonemids. Expression of the Diplonema papillatum cox1 gene is shown. This gene is broken up in nine pieces, whereof each is encoded on an individual, small, and circular chromosome. The coding regions (modules) are shown as colored boxes labeled m1 to m9. Non‐coding regions of the chromosomes are shown as black lines. Modules together with flanking non‐coding regions are transcribed as separate RNA species. Subsequently, non‐coding sequence is removed from the transcripts and the most 3′ module is poly‐adenylated. Only in the case of cox1 (shown here), six Us are appended to module 4 prior to joining with module 5. Otherwise, RNA editing is very rare in Diplonema mitochondria. For references, see text.

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Trans‐splicing of cox3 in dinoflagellates. Karlodinium micrum and other dinoflagellates possess a split cox3 gene whose fragments (labeled m1 and m2) are transcribed as separate RNA species that only contain coding regions. Both transcripts are poly‐adenylated and subsequently trans‐spliced to yield a continuous cox3 mRNA. The junction between the two spliced fragments contains non‐encoded adenosine residues, likely originating from the poly‐(A) tail of the upstream fragment. Only cox3 (shown here) is encoded by separate gene fragments and trans‐spliced, the other genes are transcribed from contiguous reading frames. For details and references, see text.

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Trans‐splicing of archaeal/tRNA introns. (a) Regular trans‐splicing of tRNA‐His from the archaean Nanoarchaeum equitans. Representation of exons as in Figure 2. The blue arrows point to the exon/intron boundaries. The exons of trnH are encoded in distant genomic regions. Exon 1 (E1) is flanked at its 3′ by an intron half (I1_a) and exon 2 (E2) is preceded by the second half of intron 1 (I1_b). The exons plus their adjacent intron halves are transcribed separately and the two transcripts fold by intermolecular base pairing into a cloverleaf secondary structure, whose anticodon loop is replaced by the bulge–helix–bulge (BHB) motif. This motif is recognized by the splicing endonuclease, a tetrameric protein complex. Cleavage generates a 5′‐hydroxyl group and a 2′,3′ cyclic phosphate. The splicing RNA ligase joins these two ends to form an uninterrupted anticodon loop and releases the intron. (b) Permutated trans‐splicing of the nucleus‐encoded tRNA‐Gln from the red alga Cyanidioschyzon merolae. Exon 1 (E1) encodes the 3′ and exon 2 (E2) the 5′ half of the tRNA. The pre‐tRNA folds intro the cloverleaf structure that is closed in the acceptor stem region, while the molecule's 5′ and 3′ ends are in the anticodon region which contains the BHB structural motif. After intron splicing, the molecule is circular closed. Finally, cleavage in the acceptor region yields the conventional tRNA 5′ and 3′ ends. For references, see text.

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Trans‐splicing of group II introns. The example is psaA, the chloroplast‐encoded gene specifying the P700 apoprotein A1 of photosystem I from Chlamydomonas reinhardtii. Representation of exons and introns as in Figure 2. D1, D4, D5, D6, conserved secondary structure domains of group II introns. The three exons are encoded in distant regions of the chloroplast genome. Intron 1 is split in three pieces and intron 2 in two. The trans‐splicing process is shown only for the tripartite intron 1. The first intron‐tier (I1_a) is located immediately downstream of exon 1, the second intron‐tier (I1_b; locus designation tscA, see text) is free standing, encoded elsewhere in the genome; and the third intron‐tier (I1_c) flanks exon 2. The intron tiers fold into the canonical group II secondary structure by intermolecular base pairing. An adenosine (A) at the base of domain 6 attacks the 3′ end of exon 1 to detach the latter from I1_a. Subsequently, the 3′ hydroxyl group of exon 1 attacks the 5′ end of exon 2, joins the two exons and releases the intron lariat. For references, see text.

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Trans‐splicing of group I introns. The depicted example is cox1, the mitochondrion‐encoded gene for cytochrome oxidase subunit 1 of Trichoplax adhaerens. Representation of exons and introns as in Figure 2. P8, distinctive paired region of group I introns. The three cox1 exons are located in distant regions of the genome. Exon 1 (E1) is flanked at its 3′ end by an intron half (I1_a); exon 2 (E2) is bounded by two intron halves, intron 1_b (I1_b) at its 5′ and intron 2_a (I2_a) at its 3′ side; and exon 3 (E3) is preceded by the second half of intron 2 (I2_b). The three exons plus their adjacent intron halves are transcribed separately. The trans‐splicing process is shown only for the split intron 2. The two separate intron halves fold into the canonical group I secondary structure by intermolecular base pairing. An exogenous guanosine (G) attacks the 3′ end of exon 2 to detach the latter from the intron half. Subsequently, the 3′ hydroxyl group of exon 2 attacks the 5′ of exon 3, joins the two exons and releases the intron. The uridine (U, shown as T in DNA) at the intron–exon boundary of exon 3, which is highly conserved for group I introns, undergoes U‐to‐C RNA editing. See text for details and references.

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Trans‐splicing of spliceosomal introns. The example shown is spliced leader trans‐splicing of the Variant‐Surface Glycoproteins (VSG) locus in the Trypanosoma brucei nucleus.32 Exons are shown in thick gray and black bars, and intron halves in thinner blue bars. SL, exon coding for the spliced leader [the common 5′ untranslated region (UTR) of all mRNAs]; this is the most 5′ exon (exon 1) of all protein‐coding genes in this genome. Multiple copies of SL exons, each flanked at its 3′ side by an intron half (I1_a), are arranged in tandem in the genome. VSG, exon containing the protein‐coding region. Formally, this is exon 2 of the VSG gene. This exon is flanked at its 5′ side by the ‘other’ intron half (I1_b). After separate transcription of both exons plus intron halves, splicing proceeds according to the canonical steps of spliceosomal splicing. First, the conserved adenosine (A) in intron 1_b attacks the guanosine at the exon 1/intron 1_a boundary to set free the exon. Second, the 3′ hydroxyl group of exon 1 attacks the guanosine (G) at the 5′ of exon 2 and thus joins the two exons. Instead of a lariat produced in cis‐splicing, the excised intron in trans‐splicing has a Y‐shape. For references, see text.

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