Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends

Mojca Tajnik; Alessandra Vigilante; Simon Braun; Heike Hänel; Nicholas M. Luscombe; Jernej Ule; Kathi Zarnack; Julian König

doi:10.1093/nar/gkv956

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends

Mojca Tajnik, Alessandra Vigilante, Simon Braun, Heike Hänel, Nicholas M. Luscombe, Jernej Ule, Kathi Zarnack^*, Julian König

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

27 Citations (Scopus)

Abstract

The 3′ untranslated regions (3′ UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3′ UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3′ UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3′ UTRs.

Original language	English
Pages (from-to)	10492-10505
Number of pages	14
Journal	Nucleic Acids Research
Volume	43
Issue number	21
DOIs	https://doi.org/10.1093/nar/gkv956
Publication status	Published - 22 Sept 2015

Access to Document

10.1093/nar/gkv956

Cite this

@article{0981bc499a534227967958767b182520,

title = "Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends",

abstract = "The 3′ untranslated regions (3′ UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3′ UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3′ UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3′ UTRs.",

author = "Mojca Tajnik and Alessandra Vigilante and Simon Braun and Heike H{\"a}nel and Luscombe, {Nicholas M.} and Jernej Ule and Kathi Zarnack and Julian K{\"o}nig",

note = "Funding Information: LOEWE programme Ubiquitin Networks (Ub-Net) of the State of Hesse (Germany) [K.Z.]; EMBO Short-Term Fellowship [M.T]. Funding for open access charge: Institute of Molecular Biology (IMB). Publisher Copyright: {\textcopyright} The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2015",

month = sep,

day = "22",

doi = "10.1093/nar/gkv956",

language = "English",

volume = "43",

pages = "10492--10505",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford Univerity Press; Oxford",

number = "21",

}

TY - JOUR

T1 - Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends

AU - Tajnik, Mojca

AU - Vigilante, Alessandra

AU - Braun, Simon

AU - Hänel, Heike

AU - Luscombe, Nicholas M.

AU - Ule, Jernej

AU - Zarnack, Kathi

AU - König, Julian

N1 - Funding Information: LOEWE programme Ubiquitin Networks (Ub-Net) of the State of Hesse (Germany) [K.Z.]; EMBO Short-Term Fellowship [M.T]. Funding for open access charge: Institute of Molecular Biology (IMB). Publisher Copyright: © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2015/9/22

Y1 - 2015/9/22

N2 - The 3′ untranslated regions (3′ UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3′ UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3′ UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3′ UTRs.

AB - The 3′ untranslated regions (3′ UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3′ UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3′ UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3′ UTRs.

UR - http://www.scopus.com/inward/record.url?scp=84975074328&partnerID=8YFLogxK

U2 - 10.1093/nar/gkv956

DO - 10.1093/nar/gkv956

M3 - Article

C2 - 26400176

AN - SCOPUS:84975074328

SN - 0305-1048

VL - 43

SP - 10492

EP - 10505

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 21

ER -

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends

Abstract

Access to Document

Other files and links

Fingerprint

Cite this