Protein encoding by both DNA strands

Labrador, Mariano; Mongélard, Fabien; Plata-Rengifo, Piedad; Baxter, Ellen M.; Corcés, Victor G.; Gerasimova, T. I.

doi:10.1038/35059000

Cited by 65 publications

(69 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA transcription of protein-coding mRNAs observed from both strands of a locus (Labrador et al 2001), intron-containing genes (Levinson et al 1992;Conrad et al 2002), and transcripts with elongated or shortened exons coding for proteins with different functions (Rahman et al 2002) have all been previously observed. Consistent with these examples, the observed novel transcription found proximal to annotations may represent alternative exon isoforms (novel exons, extension of exons, or extensions of 5Ј-or 3Ј-UTRs) or distinct transcriptional units encoded on either the same strand or antisense strand to the characterized annotation.…”

Section: Transcriptome Of Chromosomes 21 and 22mentioning

confidence: 87%

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Kampa¹,

Cheng²,

Kapranov³

et al. 2004

Genome Res.

474

377

View full text Add to dashboard Cite

In this report, we have achieved a richer view of the transcriptome for Chromosomes 21 and 22 by using high-density oligonucleotide arrays on cytosolic poly(A) + RNA. Conservatively, only 31.4% of the observed transcribed nucleotides correspond to well-annotated genes, whereas an additional 4.8% and 14.7% correspond to mRNAs and ESTs, respectively. Approximately 85% of the known exons were detected, and up to 21% of known genes have only a single isoform based on exon-skipping alternative expression. Overall, the expression of the well-characterized exons falls predominately into two categories, uniquely or ubiquitously expressed with an identifiable proportion of antisense transcripts. The remaining observed transcription (49.0%) was outside of any known annotation. These novel transcripts appear to be more cell-line-specific and have lower and less variation in expression than the well-characterized genes. Novel transcripts were further characterized based on their distance to annotations, transcript size, coding capacity, and identification as antisense to intronic sequences. By RT-PCR, 126 novel transcripts were independently verified, resulting in a 65% verification rate. These observations strongly support the argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome.

show abstract

Section: Transcriptome Of Chromosomes 21 and 22mentioning

confidence: 87%

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Kampa¹,

Cheng²,

Kapranov³

et al. 2004

Genome Res.

474

377

View full text Add to dashboard Cite

show abstract

“…In mod(mdg4), alternative 3 ′ exons from multiple loci on both DNA strands are trans-spliced to a 5 ′ transcript containing four common exons (Fig. 1A) and result in at least 31 isoforms (Labrador et al 2001;Dorn and Krauss 2003;Gabler et al 2005;McManus et al 2010). Trans-splicing of mod(mdg4) is conserved in insects, including silkworms (Shao et al 2012), mosquitos (Krauss and Dorn 2004), and cotton bollworms (Cai et al 2012).…”

mentioning

confidence: 99%

A conserved intronic U1 snRNP-binding sequence promotestrans-splicing inDrosophila

et al. 2015

View full text Add to dashboard Cite

Unlike typical cis-splicing, trans-splicing joins exons from two separate transcripts to produce chimeric mRNA and has been detected in most eukaryotes. Trans-splicing in trypanosomes and nematodes has been characterized as a spliced leader RNA-facilitated reaction; in contrast, its mechanism in higher eukaryotes remains unclear. Here we investigate mod(mdg4), a classic trans-spliced gene in Drosophila, and report that two critical RNA sequences in the middle of the last 5 ′ intron, TSA and TSB, promote trans-splicing of mod(mdg4). In TSA, a 13-nucleotide (nt) core motif is conserved across Drosophila species and is essential and sufficient for trans-splicing, which binds U1 small nuclear RNP (snRNP) through strong base-pairing with U1 snRNA. In TSB, a conserved secondary structure acts as an enhancer. Deletions of TSA and TSB using the CRISPR/Cas9 system result in developmental defects in flies. Although it is not clear how the 5 ′ intron finds the 3 ′ introns, compensatory changes in U1 snRNA rescue trans-splicing of TSA mutants, demonstrating that U1 recruitment is critical to promote trans-splicing in vivo. Furthermore, TSA core-like motifs are found in many other trans-spliced Drosophila genes, including lola. These findings represent a novel mechanism of trans-splicing, in which RNA motifs in the 5 ′ intron are sufficient to bring separate transcripts into close proximity to promote trans-splicing.

show abstract

“…Recently, Labrador et al (7) have shown that the mod(mdg4)-67.2 isoform in Drosophila is encoded on both DNA strands and suggested formation of the mature mRNA by trans-splicing of two independent transcripts.…”

mentioning

confidence: 99%

Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila

Dorn

Reuter

Loewendorf

2001

Proc. Natl. Acad. Sci. U.S.A.

122

View full text Add to dashboard Cite

The Drosophila BTB domain containing gene mod(mdg4) produces a large number of protein isoforms combining a common Nterminal region of 402 aa with different C termini. We have deduced the genomic structure of this complex locus and found that at least seven of the mod(mdg4) isoforms are encoded on both of its antiparallel DNA strands, suggesting the generation of mature mRNAs by trans-splicing. In transgenic assays, we demonstrate the ability of Drosophila to produce mod(mdg4) mRNAs by trans-splicing of pre-mRNAs generated from transgenes inserted at distant chromosomal positions. Furthermore, evidence is presented for occurring of trans-splicing of mod(mdg4)-specific exons encoded by the parallel DNA strand. The mod(mdg4) locus represents a new type of comlpex gene structure in which genetic complexity is resolved by extensive trans-splicing, giving important implications for genome sequencing projects. Demonstration of naturally occurring trans-splicing in the model organism Drosophila opens new experimental approaches toward an analysis of the underlying mechanisms.T rans-splicing is a process that produces mature transcripts by combining exons of independent pre-mRNA molecules and was first reported in trypanosomes (1-3). The capability of mammalian cells for mRNA trans-splicing was first shown by Eul et al. (4). Recently, additional reports demonstrated transsplicing in higher eukaryotes. Li et al. (5) identified a splice variant of the human acyltransferase ACAT-1 that contains a 5Ј-untranslated exon encoded from chromosome 7 connected with exons 1-16 encoded from chromosome 1. In rat liver cells, carnitine octanoyltransferase mRNA variants with duplications of coding exons 2 and 3 not present in the genomic complement have been identified (6). In this case, different proteins are encoded by the splice variants. However, the physiological significance of these trans-splicing events remains largely unknown.So far no experimental proof for naturally occurring transsplicing in insects has been documented. Recently, Labrador et al. (7) have shown that the mod(mdg4)-67.2 isoform in Drosophila is encoded on both DNA strands and suggested formation of the mature mRNA by trans-splicing of two independent transcripts.Sequence analysis of a large number of mod(mdg4) cDNA clones (8-12) and the available genomic sequence of the mod-(mdg4) locus (13) indicated that usage of both DNA strands as coding strands is a general property of the mod(mdg4) locus. The common exons 1-4, which are found in all identified transcripts, are located at the 5Ј end of the locus whereas the alternatively spliced 3Ј-specific exons are organized in five groups on both DNA strands. In transgenic assays, we provide evidence that trans-splicing is the basic mechanism responsible for production of multiple mod(mdg4) isoforms. (14) in both orientations. The construct was partially sequenced and used for germline mediated transformation. However, by sequencing the transgene specific reverse transcription (RT)-PCR product, we found a frame shift...

show abstract

Protein encoding by both DNA strands

Cited by 65 publications

References 9 publications

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

A conserved intronic U1 snRNP-binding sequence promotestrans-splicing inDrosophila

Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila

Contact Info

Product

Resources

About