Identification of a novel transcript isoform of the TTLL12 gene in human cancers

Wen,Ruiling; Xiao,Yingying; Zhang,Yuhua; Yang,Min; Lin,Yongping; Tang,Jun

doi:10.3892/or.2016.5135

Identification of a novel transcript isoform of the TTLL12 gene in human cancers

Authors:
- Ruiling Wen
- Yingying Xiao
- Yuhua Zhang
- Min Yang
- Yongping Lin
- Jun Tang
View Affiliations

Affiliations: KingMed Diagnostics and KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong 510330, P.R. China, Cytate Institute for Precision Medicine and Innovation, Guangzhou Cytate Biomedical Technologies Inc., Guangzhou, Guangdong 510663, P.R. China, Department of Clinical Laboratory and Research Center of Translational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510120, P.R. China
Published online on: September 28, 2016 https://doi.org/10.3892/or.2016.5135
Pages: 3172-3180
Copyright: © Wen et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Tubulin tyrosine ligase like 12 (TTLL12), a member of the tubulin tyrosine ligase (TTLL) family, has not been completely characterized to date. It is reported that histone methylation, tubulin modifications, mitotic duration and chromosome ploidy play crucial roles in a variety of cancers, and are related to tumorigenesis and cancer progression. A recent study showed that TTLL12 may be a pseudo-enzyme which has a SET-like domain and a TTL-like domain. In the present study, we first used 3'-rapid amplification of cDNA ends (3'-RACE) to amplify the transcripts of the TTLL12 gene from a human lung cancer cell line H1299, and unexpectedly discovered a new transcript isoform characterized with an additional 108-bp nucleotide sequence inserted at the location from 902 to 903 bases of the TTLL12 coding sequence (CDS), where it also locates between exons 5 and 6. Next, utilizing RT-PCR and Sanger sequencing, we further confirmed the existence of such a new transcript isoform of TTLL12 in more human cancer cells including lung cancer cells and other cancer cells. Moreover, several lung cancer cell lines were found to display a much higher proportion of the new isoform compared with TTLL12 wild-type transcript. These results suggest that the new TTLL12 isoform may be of importance for proper maintenance of lung cancer cells. Therefore, the new isoform of TTLL12, with the inserted sequences probably acting as a disordered region, provides a novel perspective regarding TTLL12 functions in human cancers including lung cancer.

View Figures

View References

1	Janke C, Rogowski K, Wloga D, Regnard C, Kajava AV, Strub JM, Temurak N, van Dijk J, Boucher D, van Dorsselaer A, et al: Tubulin polyglutamylase enzymes are members of the TTL domain protein family. Science. 308:1758–1762. 2005. View Article : Google Scholar : PubMed/NCBI
2	Fukushima N, Furuta D, Hidaka Y, Moriyama R and Tsujiuchi T: Post-translational modifications of tubulin in the nervous system. J Neurochem. 109:683–693. 2009. View Article : Google Scholar : PubMed/NCBI
3	Ersfeld K, Wehland J, Plessmann U, Dodemont H, Gerke V and Weber K: Characterization of the tubulin-tyrosine ligase. J Cell Biol. 120:725–732. 1993. View Article : Google Scholar : PubMed/NCBI
4	Brants J, Semenchenko K, Wasylyk C, Robert A, Carles A, Zambrano A, Pradeau-Aubreton K, Birck C, Schalken JA, Poch O, et al: Tubulin tyrosine ligase like 12, a TTLL family member with SET- and TTL-like domains and roles in histone and tubulin modifications and mitosis. PLoS One. 7:e512582012. View Article : Google Scholar : PubMed/NCBI
5	Gurland G and Gundersen GG: Stable, detyrosinated microtubules function to localize vimentin intermediate filaments in fibroblasts. J Cell Biol. 131:1275–1290. 1995. View Article : Google Scholar : PubMed/NCBI
6	Peris L, Thery M, Fauré J, Saoudi Y, Lafanechère L, Chilton JK, Gordon-Weeks P, Galjart N, Bornens M, Wordeman L, et al: Tubulin tyrosination is a major factor affecting the recruitment of CAP-Gly proteins at microtubule plus ends. J Cell Biol. 174:839–849. 2006. View Article : Google Scholar : PubMed/NCBI
7	Dunn S, Morrison EE, Liverpool TB, Molina-París C, Cross RA, Alonso MC and Peckham M: Differential trafficking of Kif5c on tyrosinated and detyrosinated microtubules in live cells. J Cell Sci. 121:1085–1095. 2008. View Article : Google Scholar : PubMed/NCBI
8	Gyoeva FK and Gelfand VI: Coalignment of vimentin intermediate filaments with microtubules depends on kinesin. Nature. 353:445–448. 1991. View Article : Google Scholar : PubMed/NCBI
9	Kato C, Miyazaki K, Nakagawa A, Ohira M, Nakamura Y, Ozaki T, Imai T and Nakagawara A: Low expression of human tubulin tyrosine ligase and suppressed tubulin tyrosination/detyrosination cycle are associated with impaired neuronal differentiation in neuroblastomas with poor prognosis. Int J Cancer. 112:365–375. 2004. View Article : Google Scholar : PubMed/NCBI
10	Lafanechère L, Courtay-Cahen C, Kawakami T, Jacrot M, Rüdiger M, Wehland J, Job D and Margolis RL: Suppression of tubulin tyrosine ligase during tumor growth. J Cell Sci. 111:171–181. 1998.PubMed/NCBI
11	Mialhe A, Lafanechère L, Treilleux I, Peloux N, Dumontet C, Brémond A, Panh MH, Payan R, Wehland J, Margolis RL, et al: Tubulin detyrosination is a frequent occurrence in breast cancers of poor prognosis. Cancer Res. 61:5024–5027. 2001.PubMed/NCBI
12	Wasylyk C, Zambrano A, Zhao C, Brants J, Abecassis J, Schalken JA, Rogatsch H, Schaefer G, Pycha A, Klocker H, et al: Tubulin tyrosine ligase like 12 links to prostate cancer through tubulin posttranslational modification and chromosome ploidy. Int J Cancer. 127:2542–2553. 2010. View Article : Google Scholar : PubMed/NCBI
13	Soucek K, Kamaid A, Phung AD, Kubala L, Bulinski JC, Harper RW and Eiserich JP: Normal and prostate cancer cells display distinct molecular profiles of α-tubulin posttranslational modifications. Prostate. 66:954–965. 2006. View Article : Google Scholar : PubMed/NCBI
14	Szyk A, Deaconescu AM, Piszczek G and Roll-Mecak A: Tubulin tyrosine ligase structure reveals adaptation of an ancient fold to bind and modify tubulin. Nat Struct Mol Biol. 18:1250–1258. 2011. View Article : Google Scholar : PubMed/NCBI
15	Ikegami K and Setou M: TTLL10 can perform tubulin glycylation when co-expressed with TTLL8. FEBS Lett. 583:1957–1963. 2009. View Article : Google Scholar : PubMed/NCBI
16	Wloga D, Webster DM, Rogowski K, Bré MH, Levilliers N, Jerka-Dziadosz M, Janke C, Dougan ST and Gaertig J: TTLL3 is a tubulin glycine ligase that regulates the assembly of cilia. Dev Cell. 16:867–876. 2009. View Article : Google Scholar : PubMed/NCBI
17	Rogowski K, Juge F, van Dijk J, Wloga D, Strub JM, Levilliers N, Thomas D, Bré MH, Van Dorsselaer A, Gaertig J, et al: Evolutionary divergence of enzymatic mechanisms for posttranslational polyglycylation. Cell. 137:1076–1087. 2009. View Article : Google Scholar : PubMed/NCBI
18	Dillon SC, Zhang X, Trievel RC and Cheng X: The SET-domain protein superfamily: Protein lysine methyltransferases. Genome Biol. 6:2272005. View Article : Google Scholar : PubMed/NCBI
19	Cheng X and Zhang X: Structural dynamics of protein lysine methylation and demethylation. Mutat Res. 618:102–115. 2007. View Article : Google Scholar : PubMed/NCBI
20	Xu D, Bai J, Duan Q, Costa M and Dai W: Covalent modifications of histones during mitosis and meiosis. Cell Cycle. 8:3688–3694. 2009. View Article : Google Scholar : PubMed/NCBI
21	Qian C and Zhou MM: SET domain protein lysine methyltransferases: Structure, specificity and catalysis. Cell Mol Life Sci. 63:2755–2763. 2006. View Article : Google Scholar : PubMed/NCBI
22	Aravind L, Abhiman S and Iyer LM: Natural history of the eukaryotic chromatin protein methylation system. Prog Mol Biol Transl Sci. 101:105–176. 2011. View Article : Google Scholar : PubMed/NCBI
23	Garnham CP and Roll-Mecak A: The chemical complexity of cellular microtubules: Tubulin post-translational modification enzymes and their roles in tuning microtubule functions. Cytoskeleton Hoboken. 69:442–463. 2012. View Article : Google Scholar : PubMed/NCBI
24	Wloga D and Gaertig J: Post-translational modifications of microtubules. J Cell Sci. 123:3447–3455. 2010. View Article : Google Scholar : PubMed/NCBI
25	Janke C and Bulinski JC: Post-translational regulation of the microtubule cytoskeleton: Mechanisms and functions. Nat Rev Mol Cell Biol. 12:773–786. 2011. View Article : Google Scholar : PubMed/NCBI
26	Sharp PA: Split genes and RNA splicing. Cell. 77:805–815. 1994. View Article : Google Scholar : PubMed/NCBI
27	Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, et al: Widespread expansion of protein interaction capabilities by alternative splicing. Cell. 164:805–817. 2016. View Article : Google Scholar : PubMed/NCBI
28	Du Q, Li C, Li D and Lu S: Genome-wide analysis, molecular cloning and expression profiling reveal tissue-specifically expressed, feedback-regulated, stress-responsive and alternatively spliced novel genes involved in gibberellin metabolism in Salvia miltiorrhiza. BMC Genomics. 16:10872015. View Article : Google Scholar : PubMed/NCBI
29	Rodríguez SA, Grochová D, McKenna T, Borate B, Trivedi NS, Erdos MR and Eriksson M: Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging. Aging Cell. 15:267–278. 2016. View Article : Google Scholar : PubMed/NCBI
30	Shang J, Fan X, Shangguan L, Liu H and Zhou Y: Global gene expression profiling and alternative splicing events during the chondrogenic differentiation of human cartilage endplate-derived stem cells. BioMed Res Int. 2015:6049722015. View Article : Google Scholar : PubMed/NCBI
31	Stevens M and Oltean S: Alternative splicing in CKD. J Am Soc Nephrol. 27:1596–1603. 2016. View Article : Google Scholar : PubMed/NCBI
32	Sheng Z, Sun Y, Zhu R, Jiao N, Tang K, Cao Z and Ma C: Functional cross-talking between differentially expressed and alternatively spliced genes in human liver cancer cells treated with berberine. PLoS One. 10:e01437422015. View Article : Google Scholar : PubMed/NCBI
33	Adamopoulos PG, Kontos CK, Tsiakanikas P and Scorilas A: Identification of novel alternative splice variants of the BCL2L12 gene in human cancer cells using next-generation sequencing methodology. Cancer Lett. 373:119–129. 2016. View Article : Google Scholar : PubMed/NCBI
34	Faustino NA and Cooper TA: Pre-mRNA splicing and human disease. Genes Dev. 17:419–437. 2003. View Article : Google Scholar : PubMed/NCBI
35	Forman-Kay JD and Mittag T: From sequence and forces to structure, function, and evolution of intrinsically disordered proteins. Structure. 21:1492–1499. 2013. View Article : Google Scholar : PubMed/NCBI
36	Dunker AK, Bondos SE, Huang F and Oldfield CJ: Intrinsically disordered proteins and multicellular organisms. Semin Cell Dev Biol. 37:44–55. 2015. View Article : Google Scholar : PubMed/NCBI
37	Wright PE and Dyson HJ: Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. J Mol Biol. 293:321–331. 1999. View Article : Google Scholar : PubMed/NCBI
38	Chouard T: Structural biology: Breaking the protein rules. Nature. 471:151–153. 2011. View Article : Google Scholar : PubMed/NCBI
39	Kotta-Loizou I, Tsaousis GN and Hamodrakas SJ: Analysis of molecular recognition features (MoRFs) in membrane proteins. Biochim Biophys Acta. 1834:798–807. 2013. View Article : Google Scholar : PubMed/NCBI
40	Tompa P and Fuxreiter M: Fuzzy complexes: Polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci. 33:2–8. 2008. View Article : Google Scholar : PubMed/NCBI
41	Fuxreiter M and Tompa P: Fuzzy complexes: A more stochastic view of protein function. Adv Exp Med Biol. 725:1–14. 2012. View Article : Google Scholar : PubMed/NCBI
42	Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Uversky VN and Obradovic Z: Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res. 6:1882–1898. 2007. View Article : Google Scholar : PubMed/NCBI
43	Yoon MK, Mitrea DM, Ou L and Kriwacki RW: Cell cycle regulation by the intrinsically disordered proteins p21 and p27. Biochem Soc Trans. 40:981–988. 2012. View Article : Google Scholar : PubMed/NCBI
44	Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF and Jones DT: Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol. 337:635–645. 2004. View Article : Google Scholar : PubMed/NCBI
45	Andresen C, Helander S, Lemak A, Farès C, Csizmok V, Carlsson J, Penn LZ, Forman-Kay JD, Arrowsmith CH, Lundström P, et al: Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Res. 40:6353–6366. 2012. View Article : Google Scholar : PubMed/NCBI
46	Harrison MR, Holen KD and Liu G: Beyond taxanes: A review of novel agents that target mitotic tubulin and microtubules, kinases, and kinesins. Clin Adv Hematol Oncol. 7:54–64. 2009.PubMed/NCBI
47	Verhey KJ and Gaertig J: The tubulin code. Cell Cycle. 6:2152–2160. 2007. View Article : Google Scholar : PubMed/NCBI
48	Ghoreschi K, Laurence A and O'Shea JJ: Selectivity and therapeutic inhibition of kinases: To be or not to be? Nat Immunol. 10:356–360. 2009. View Article : Google Scholar : PubMed/NCBI