Alternative Splicing Regulation of Cancer-Related Pathways in Caenorhabditis elegans: An In Vivo ...

Alternative Splicing Regulation of Cancer-Related Pathways in Caenorhabditis elegans: An In Vivo ...

11 Pages · 2015 · 1.36 MB · English

2 Department of Molecular, Cell and Developmental Biology, The Center for .. elt-6 mpk-1/sur-1. √ eor-1 par-1. √ eor-2. √ ptp-2 gap-1 rom-1 gap-2. √ sem-4 .. [61] M. W. Pastok, M. C. Prescott, C. Dart et al., “Structural diversity.

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Hindawi Publishing Corporation International Journal of Cell Biology Volume 2013, Article ID 636050,10pages http://dxdoiorg/101155/2013/636050 Review Article Alternative Splicing Regulation of CancerRelated Pathways inCaenorhabditis elegans:AnInVivoModel System with a Powerful Reverse Genetics Toolbox Sergio BarberánSoler 1and James Matthew Ragle 2 1SomaGenics, Inc, Santa Cruz, CA 95060, USA2Department of Molecular, Cell and Developmental Biology, The Center for Molecular Biology of RNA, UniversityofCalifornia,SantaCruz,SantaCruz,CA95064,USA Correspondence should be addressed to Sergio Barber´ anSoler; [email protected] Received 17 June 2013; Accepted 29 July 2013 Academic Editor: Claudio Sette Copyright © 2013 S Barber´ anSoler and J M Ragle This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited Alternative splicing allows for the generation of protein diversity and finetunes gene expression Several model systems have been used for the in vivo study of alternative splicing Here we review the use of the nematodeCaenorhabditis elegansto study splicing regulation in vivo Recent studies have shown that close to 25% of genes in the worm genome undergo alternative splicing A big proportion of these events are functional, conserved, and under strict regulation either across development or other conditions Several techniques like genomewide RNAi screens and bichromatic reporters are available for the study of alternative splicing in worms In this review, we focus, first, on the main studies that have been performed to dissect alternative splicing in this system and later on examples from genes that have human homologs that are implicated in cancer The significant advancement towards understanding the regulation of alternative splicing and cancer that theC eleganssystem has offered is discussed 1 Introduction Since the early 1960s with the efforts of Sydney Brenner, the nematodeCaenorhabditis eleganshas been established as a popular model organism in developmental biology and neu robiology There are many biological advantages that make it an attractive system for several fields of research The adult worm contains 959 somatic cells, making its anatomy rela tively simple Experiments in the late 1970s showed that it has an invariant cell lineage during establishment of the somatic tissues [1] It has two sexes, a selffertilizing hermaphrodite and males, allowing genetic crosses to be performedC eleganshas a short life cycle of less than three days and each hermaphrodite produces about 300 progeny by self fertilization or up to 1000 progeny from cross progeny with males The gonad is a relatively large organ in this animal, allowing for studies of organogenesis, cell proliferation, meio sis, and embryogenesis During its development, the her maphrodite worms produce sperm at one stage of their life cycle before switching to produce oocytes The molecularpathwaysofthisspermtooocytetransitionhavebeenstudied extensively [2] Its complete genome, sequenced in 1998, was the first sequenced genome from a multicellular organism It has a genome size of 97 megabases containing close to 19,000 protein coding genes [3] Genomewide alignments with other five related nematodes are now available for any com parative genomics approach [4] The modENCODE project systematically generated genomewide data from transcrip tome profiling, transcription factorbinging sites, and maps ofchromatinorganizationtoimprovegenomeannotation[5] When comparing theC elegansgenome to higher eukaryotes, it was found that close to 40% of the genes that have been associated with diseases in humans have worm orthologues, and cancer is not the exception [6] 2 Alternative Splicing Prevalence In 1990, the first report of an alternative splicing event in theC elegansgenome was published Interestingly the event corresponds to the PKA mRNA, a kinase implicated in the 2International Journal of Cell Biology 25% of genes are alternatively spliced 40% of genes with alternative splicing are regulated during development 35% of genes with alternative splicing are putative targets of NMD C elegans genome 19,000 genes (a) hg19 APAF1 APAF1 APAF1 APAF1 APAF1 1 kb ce6 ced4 ced4 Human APAF1, median intron size 2746 bp, median exon size 132 bp C elegans ced4, median intron size 50 bp, median exon size 181 bp20 kb chrIII:chr12:Scale Scale 4,854,500 4,854,000 4,853,500 4,853,000 4,852,500 RefSeq genes RefSeq genes 99,045,000 99,050,000 99,055,000 99,060,000 99,065,000 99,070,000 99,075,000 99,080,000 99,085,000 99,090,000 99,095,000 99,100,000 99,105,000 99,110,00099,115,000 99,120,000 99,125,000 (b) 10 kb ce6 Y48C3A5 Intron 4 size 19,927 bp C elegans Y48C3A5 chrII: RefSeq genes 13,275,00013,305,000 Scale 13,300,000 13,295,000 13,290,000 13,285,000 13,280,000 (c) ce6 unc52

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