trans-splicing

{{Short description|Maturation process joining exons from different pre-mRNAs into a mature mRNA}}

Trans-splicing is a special form of RNA processing where exons from two different primary RNA transcripts are joined end to end and ligated. It is usually found in eukaryotes and mediated by the spliceosome, although some bacteria and archaea also have "half-genes" for tRNAs.{{cite journal | vauthors = Lei Q, Li C, Zuo Z, Huang C, Cheng H, Zhou R | title = Evolutionary Insights into RNA trans-Splicing in Vertebrates | journal = Genome Biology and Evolution | volume = 8 | issue = 3 | pages = 562–77 | date = March 2016 | pmid = 26966239 | pmc = 4824033 | doi = 10.1093/gbe/evw025 }}

Genic ''trans''-splicing

Whereas "normal" (cis-)splicing processes a single molecule, trans-splicing generates a single RNA transcript from multiple separate pre-mRNAs. This phenomenon can be exploited for molecular therapy to address mutated gene products.{{cite journal | vauthors = Iwasaki R, Kiuchi H, Ihara M, Mori T, Kawakami M, Ueda H | title = Trans-splicing as a novel method to rapidly produce antibody fusion proteins | journal = Biochemical and Biophysical Research Communications | volume = 384 | issue = 3 | pages = 316–21 | date = July 2009 | pmid = 19409879 | doi = 10.1016/j.bbrc.2009.04.122 | url = https://zenodo.org/record/895586 }} Genic trans-splicing allows variability in RNA diversity and increases proteome complexity.{{Cite journal|last1=Lasda|first1=Erika L.|last2=Blumenthal|first2=Thomas|date=2011|title=Trans-splicing|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/wrna.71|journal=WIREs RNA|language=en|volume=2|issue=3|pages=417–434|doi=10.1002/wrna.71|pmid=21957027|s2cid=209567118|issn=1757-7012}}

= Oncogenesis =

While some fusion transcripts occur via trans-splicing in normal human cells, trans-splicing can also be the mechanism behind certain oncogenic fusion transcripts.{{cite journal | vauthors = Li H, Wang J, Mor G, Sklar J | title = A neoplastic gene fusion mimics trans-splicing of RNAs in normal human cells | journal = Science | volume = 321 | issue = 5894 | pages = 1357–61 | date = September 2008 | pmid = 18772439 | doi = 10.1126/science.1156725 | bibcode = 2008Sci...321.1357L | s2cid = 13605087 }}{{cite journal | vauthors = Rickman DS, Pflueger D, Moss B, VanDoren VE, Chen CX, de la Taille A, Kuefer R, Tewari AK, Setlur SR, Demichelis F, Rubin MA | display-authors = 6 | title = SLC45A3-ELK4 is a novel and frequent erythroblast transformation-specific fusion transcript in prostate cancer | journal = Cancer Research | volume = 69 | issue = 7 | pages = 2734–8 | date = April 2009 | pmid = 19293179 | pmc = 4063441 | doi = 10.1158/0008-5472.CAN-08-4926 }}

SL ''trans''-splicing

Spliced leader (SL) trans-splicing is used by certain microorganisms, notably protists of the Kinetoplastea class to express genes. In these organisms, a capped splice leader RNA is transcribed, and simultaneously, genes are transcribed in long polycistrons.{{cite journal | vauthors = Campbell DA, Sturm NR, Yu MC | title = Transcription of the kinetoplastid spliced leader RNA gene | journal = Parasitology Today | volume = 16 | issue = 2 | pages = 78–82 | date = February 2000 | pmid = 10652494 | doi = 10.1016/s0169-4758(99)01545-8 }} The capped splice leader is trans-spliced onto each gene to generate monocistronic capped and polyadenylated transcripts.{{cite journal | vauthors = Liang XH, Haritan A, Uliel S, Michaeli S | title = trans and cis splicing in trypanosomatids: mechanism, factors, and regulation | journal = Eukaryotic Cell | volume = 2 | issue = 5 | pages = 830–40 | date = October 2003 | pmid = 14555465 | pmc = 219355 | doi = 10.1128/EC.2.5.830-840.2003 }} These early-diverging eukaryotes use few introns, and the spliceosome they possess show some unusual variations in their structure assembly.{{cite journal | vauthors = Günzl A | title = The pre-mRNA splicing machinery of trypanosomes: complex or simplified? | journal = Eukaryotic Cell | volume = 9 | issue = 8 | pages = 1159–70 | date = August 2010 | pmid = 20581293 | pmc = 2918933 | doi = 10.1128/EC.00113-10 }} They also possess multiple eIF4E isoforms with specialized roles in capping.{{cite journal | vauthors = Freire ER, Sturm NR, Campbell DA, de Melo Neto OP | title = The Role of Cytoplasmic mRNA Cap-Binding Protein Complexes in Trypanosoma brucei and Other Trypanosomatids | journal = Pathogens | volume = 6 | issue = 4 | pages = 55 | date = October 2017 | pmid = 29077018 | pmc = 5750579 | doi = 10.3390/pathogens6040055 | doi-access = free }} The spliced leader sequence is highly conserved in lower species that undergo trans-splicing. Such as trypanosomes. While the spliced leader's role is not known in the cell, it's thought to be involved in translation initiation. In C.elegans, the splicing of the sequence leader occurs close to the initiation codon. Some scientists also suggest the sequence is required for cell viability. In Ascaris, the spliced leader sequence is needed to the RNA gene can be transcribed. The Spliced leader sequence may be responsible for initiation, mRNA localization, and translation initiation or inhibition.

Some other eukaryotes, notably among dinoflagellates, sponges, nematodes, cnidarians, ctenophores, flatworms, crustaceans, chaetognaths, rotifers, and tunicates also use more or less frequently the SL trans-splicing.{{cite journal | vauthors = Lasda EL, Blumenthal T | title = Trans-splicing | journal = Wiley Interdisciplinary Reviews: RNA | volume = 2 | issue = 3 | pages = 417–34 | date = 2011-05-01 | pmid = 21957027 | doi = 10.1002/wrna.71 | s2cid = 209567118 }} In the tunicate Ciona intestinalis, the extent of SL trans-splicing is better described by a quantitative view recognising frequently and infrequently trans-spliced genes rather than a binary and conventional categorisation of trans-spliced versus non-trans-spliced genes.{{cite journal | vauthors = Matsumoto J, Dewar K, Wasserscheid J, Wiley GB, Macmil SL, Roe BA, Zeller RW, Satou Y, Hastings KE | display-authors = 6 | title = High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates | journal = Genome Research | volume = 20 | issue = 5 | pages = 636–45 | date = May 2010 | pmid = 20212022 | pmc = 2860165 | doi = 10.1101/gr.100271.109 }}

The SL trans-splicing functions in the resolution of polycistronic transcripts of operons into individual 5'-capped mRNAs. This processing is achieved when the outrons are trans-spliced to unpaired, downstream acceptor sites adjacent to cistron open reading frames.{{Cite journal|last=Clayton|first=Christine E.|date=2002-04-15|title=Life without transcriptional control? From fly to man and back again|journal=The EMBO Journal|language=en|volume=21|issue=8|pages=1881–1888|doi=10.1093/emboj/21.8.1881|issn=1460-2075|pmc=125970|pmid=11953307}}{{Cite journal|last1=Blumenthal|first1=Thomas|last2=Gleason|first2=Kathy Seggerson|date=February 2003|title=Caenorhabditis elegans operons: form and function|journal=Nature Reviews Genetics|language=en|volume=4|issue=2|pages=110–118|doi=10.1038/nrg995|pmid=12560808|s2cid=9864778|issn=1471-0056}}

Mechanism

Trans-splicing is characterized by the joining of two separate exons transcribed RNAs. The signal for this splicing is the outron at the 5’ end of the mRNA, in the absence of a functional 5’ splice site upstream. When the 5’ outron in spliced, the 5’ splice site of the spliced leader RNA is branched to the outron and forms an intermediate.{{Cite journal |last1=Girard |first1=Lisa R. |last2=Fiedler |first2=Tristan J. |last3=Harris |first3=Todd W. |last4=Carvalho |first4=Felicia |last5=Antoshechkin |first5=Igor |last6=Han |first6=Michael |last7=Sternberg |first7=Paul W. |last8=Stein |first8=Lincoln D. |last9=Chalfie |first9=Martin |date=January 2007 |title=WormBook: the online review of Caenorhabditis elegans biology |journal=Nucleic Acids Research |volume=35 |issue=Database issue |pages=D472–475 |doi=10.1093/nar/gkl894 |issn=1362-4962 |pmc=1669767 |pmid=17099225}} This step results in a free spliced leader exon. The exon is then spliced to the first exon on the pre-mRNA and the intermediate is released. Trans-splicing differs from cis-splicing in that there is no 5' splice site on the pre-mRNA. Instead the 5' splice site is provided by the SL sequence.

Trans-splicing between sense and anti-sense strands

As a result of the sense strand undergoing transcription, a pre-mRNA is formed that complements the sense strand. The anti-sense strand is also transcribed resulting in a complementary pre-mRNA strand. The exons from the two transcripts are spliced together to form a chimeric mRNA.{{Cite journal |last1=Lei |first1=Quan |last2=Li |first2=Cong |last3=Zuo |first3=Zhixiang |last4=Huang |first4=Chunhua |last5=Cheng |first5=Hanhua |last6=Zhou |first6=Rongjia |date=March 2016 |title=Evolutionary Insights into RNA trans-Splicing in Vertebrates |journal=Genome Biology and Evolution |language=en |volume=8 |issue=3 |pages=562–577 |doi=10.1093/gbe/evw025 |issn=1759-6653 |pmc=4824033 |pmid=26966239}}

Alternative Trans-splicing

Alternative trans-splicing includes intragenic trans-splicing and intergenic trans-splicing. Intragenic trans-splicing involves duplication of exons in the pre-mRNA. Intergenic trans-splicing is characterized by the splicing together of exons formed form the pre-mRNA of two different genes, resulting in trans-genic mRNA.{{Cite journal |last1=Horiuchi |first1=Takayuki |last2=Aigaki |first2=Toshiro |date=February 2006 |title=Alternative trans-splicing: a novel mode of pre-mRNA processing |journal=Biology of the Cell |volume=98 |issue=2 |pages=135–140 |doi=10.1042/bc20050002 |pmid=16417469 |s2cid=10335534 |issn=0248-4900|doi-access=free }}