Sequencing and expression of the second allele of the interleukin-1β1 gene in rainbow trout (Oncorhynchus mykiss)

identification of a novel SINE in the third intron

Tiehui Wang, Niel Johnson, Jun Zou, Niels Bols, Christopher J Secombes

Research output: Contribution to journalArticle

28 Citations (Scopus)

Abstract

A lambda clone containing a rainbow trout IL-1beta1 gene was isolated by a PCR screening strategy from a genomic library cloned in lambda GEM-11, and an EcoRI fragment from this clone was fully sequenced, and contained 1680 bp 5'-flanking sequence, the whole IL-1beta1 gene open reading frame, and the 3'-flanking region with two potential poly A signals and poly A sites. This clone encoded a protein that shared 99.8% identity to the previously published trout IL-1beta1 cDNA sequence, with only three base substitutions. The main difference was that this clone had an additional complete HpaI SINE insertion in the 3rd intron making intron III 211 bp larger (834 bp via 623 bp). Thus this sequence was designated as allele B (Big intron III) of IL-1beta1 and the previously reported sequence as allele S (Short intron III). Three lines of evidence (allele specific PCR, cloning and sequencing, and direct sequencing of PCR products) revealed that allele B was constitutively expressed and could respond to stimulation with lipopolysaccharide or trout recombinant IL-1beta. Searching of the GenBank database with the HpaI SINE sequence resulted in three additional HpaI loci being identified in rainbow trout. Another SINE retroposition was also identified in the same intron of both alleles of IL-1beta1 by comparison with the trout IL-1beta2 gene. This novel SINE sequence, sharing high homology with the HpaI SINE at the 3'-end region, is present in EST databases of several species including human, mouse and fish. The consensus of this novel SINE shares 57 to 61% identities to tRNA-Leu from different species. Another older retroposition event in the same intron of IL-1beta1 has also been hypothesised, recognised as six adenines, that may function as a RNA polIII terminator. A model for the IL-1beta1 allele formation is proposed. Following the earliest retroposition into one of the two IL-1beta genes that resulted from a genome duplication in salmonids, the proper environment for successive PV SINE retroposition was created. A recent retroposition of the HpaI SINE in IL-1beta1 resulted in the formation of the two alleles of IL-1beta1. Examination of the SINEs insertion and their host gene microenvironments revealed that the SINE retroposition does not appear random, both in the site selection and the direction of insertion. The mechanism governing this outcome is discussed.
Original languageEnglish
Pages (from-to)335-358
Number of pages24
JournalFish & Shellfish Immunology
Volume16
Issue number3
Early online date3 Oct 2003
DOIs
Publication statusPublished - Mar 2004

Keywords

  • rainbow trout
  • interleukin-1 beta 1
  • allele B
  • SINE
  • allele formation
  • retroposition
  • nitric-oxide synthase
  • short interspersed elements
  • polymerase-chain-reaction
  • receptor antagonist
  • molecular-cloning
  • ancestral tetraploidy
  • IL-1-BETA gene
  • messenger-RNA
  • salmonid fish
  • tandem repeat
  • animals
  • alleles
  • animals
  • base sequence
  • DNA primers
  • gene expression
  • interleukin-1
  • introns
  • models
  • genetic
  • molecular sequence data
  • ncorhynchus mykiss
  • reverse transcriptase polymerase chain reaction
  • sequence alignment
  • sequence analysis
  • DNA
  • sequence homology
  • short interspersed nucleotide elements

Cite this

@article{a35b8242ee99415288f52277924c11f4,
title = "Sequencing and expression of the second allele of the interleukin-1β1 gene in rainbow trout (Oncorhynchus mykiss): identification of a novel SINE in the third intron",
abstract = "A lambda clone containing a rainbow trout IL-1beta1 gene was isolated by a PCR screening strategy from a genomic library cloned in lambda GEM-11, and an EcoRI fragment from this clone was fully sequenced, and contained 1680 bp 5'-flanking sequence, the whole IL-1beta1 gene open reading frame, and the 3'-flanking region with two potential poly A signals and poly A sites. This clone encoded a protein that shared 99.8{\%} identity to the previously published trout IL-1beta1 cDNA sequence, with only three base substitutions. The main difference was that this clone had an additional complete HpaI SINE insertion in the 3rd intron making intron III 211 bp larger (834 bp via 623 bp). Thus this sequence was designated as allele B (Big intron III) of IL-1beta1 and the previously reported sequence as allele S (Short intron III). Three lines of evidence (allele specific PCR, cloning and sequencing, and direct sequencing of PCR products) revealed that allele B was constitutively expressed and could respond to stimulation with lipopolysaccharide or trout recombinant IL-1beta. Searching of the GenBank database with the HpaI SINE sequence resulted in three additional HpaI loci being identified in rainbow trout. Another SINE retroposition was also identified in the same intron of both alleles of IL-1beta1 by comparison with the trout IL-1beta2 gene. This novel SINE sequence, sharing high homology with the HpaI SINE at the 3'-end region, is present in EST databases of several species including human, mouse and fish. The consensus of this novel SINE shares 57 to 61{\%} identities to tRNA-Leu from different species. Another older retroposition event in the same intron of IL-1beta1 has also been hypothesised, recognised as six adenines, that may function as a RNA polIII terminator. A model for the IL-1beta1 allele formation is proposed. Following the earliest retroposition into one of the two IL-1beta genes that resulted from a genome duplication in salmonids, the proper environment for successive PV SINE retroposition was created. A recent retroposition of the HpaI SINE in IL-1beta1 resulted in the formation of the two alleles of IL-1beta1. Examination of the SINEs insertion and their host gene microenvironments revealed that the SINE retroposition does not appear random, both in the site selection and the direction of insertion. The mechanism governing this outcome is discussed.",
keywords = "rainbow trout, interleukin-1 beta 1, allele B, SINE, allele formation, retroposition, nitric-oxide synthase, short interspersed elements, polymerase-chain-reaction, receptor antagonist, molecular-cloning, ancestral tetraploidy, IL-1-BETA gene, messenger-RNA, salmonid fish, tandem repeat, animals , alleles, animals, base sequence, DNA primers, gene expression, interleukin-1, introns, models, genetic, molecular sequence data, ncorhynchus mykiss , reverse transcriptase polymerase chain reaction, sequence alignment, sequence analysis, DNA, sequence homology, short interspersed nucleotide elements",
author = "Tiehui Wang and Niel Johnson and Jun Zou and Niels Bols and Secombes, {Christopher J}",
year = "2004",
month = "3",
doi = "10.1016/S1050-4648(03)00114-1",
language = "English",
volume = "16",
pages = "335--358",
journal = "Fish & Shellfish Immunology",
issn = "1050-4648",
publisher = "ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD",
number = "3",

}

TY - JOUR

T1 - Sequencing and expression of the second allele of the interleukin-1β1 gene in rainbow trout (Oncorhynchus mykiss)

T2 - identification of a novel SINE in the third intron

AU - Wang, Tiehui

AU - Johnson, Niel

AU - Zou, Jun

AU - Bols, Niels

AU - Secombes, Christopher J

PY - 2004/3

Y1 - 2004/3

N2 - A lambda clone containing a rainbow trout IL-1beta1 gene was isolated by a PCR screening strategy from a genomic library cloned in lambda GEM-11, and an EcoRI fragment from this clone was fully sequenced, and contained 1680 bp 5'-flanking sequence, the whole IL-1beta1 gene open reading frame, and the 3'-flanking region with two potential poly A signals and poly A sites. This clone encoded a protein that shared 99.8% identity to the previously published trout IL-1beta1 cDNA sequence, with only three base substitutions. The main difference was that this clone had an additional complete HpaI SINE insertion in the 3rd intron making intron III 211 bp larger (834 bp via 623 bp). Thus this sequence was designated as allele B (Big intron III) of IL-1beta1 and the previously reported sequence as allele S (Short intron III). Three lines of evidence (allele specific PCR, cloning and sequencing, and direct sequencing of PCR products) revealed that allele B was constitutively expressed and could respond to stimulation with lipopolysaccharide or trout recombinant IL-1beta. Searching of the GenBank database with the HpaI SINE sequence resulted in three additional HpaI loci being identified in rainbow trout. Another SINE retroposition was also identified in the same intron of both alleles of IL-1beta1 by comparison with the trout IL-1beta2 gene. This novel SINE sequence, sharing high homology with the HpaI SINE at the 3'-end region, is present in EST databases of several species including human, mouse and fish. The consensus of this novel SINE shares 57 to 61% identities to tRNA-Leu from different species. Another older retroposition event in the same intron of IL-1beta1 has also been hypothesised, recognised as six adenines, that may function as a RNA polIII terminator. A model for the IL-1beta1 allele formation is proposed. Following the earliest retroposition into one of the two IL-1beta genes that resulted from a genome duplication in salmonids, the proper environment for successive PV SINE retroposition was created. A recent retroposition of the HpaI SINE in IL-1beta1 resulted in the formation of the two alleles of IL-1beta1. Examination of the SINEs insertion and their host gene microenvironments revealed that the SINE retroposition does not appear random, both in the site selection and the direction of insertion. The mechanism governing this outcome is discussed.

AB - A lambda clone containing a rainbow trout IL-1beta1 gene was isolated by a PCR screening strategy from a genomic library cloned in lambda GEM-11, and an EcoRI fragment from this clone was fully sequenced, and contained 1680 bp 5'-flanking sequence, the whole IL-1beta1 gene open reading frame, and the 3'-flanking region with two potential poly A signals and poly A sites. This clone encoded a protein that shared 99.8% identity to the previously published trout IL-1beta1 cDNA sequence, with only three base substitutions. The main difference was that this clone had an additional complete HpaI SINE insertion in the 3rd intron making intron III 211 bp larger (834 bp via 623 bp). Thus this sequence was designated as allele B (Big intron III) of IL-1beta1 and the previously reported sequence as allele S (Short intron III). Three lines of evidence (allele specific PCR, cloning and sequencing, and direct sequencing of PCR products) revealed that allele B was constitutively expressed and could respond to stimulation with lipopolysaccharide or trout recombinant IL-1beta. Searching of the GenBank database with the HpaI SINE sequence resulted in three additional HpaI loci being identified in rainbow trout. Another SINE retroposition was also identified in the same intron of both alleles of IL-1beta1 by comparison with the trout IL-1beta2 gene. This novel SINE sequence, sharing high homology with the HpaI SINE at the 3'-end region, is present in EST databases of several species including human, mouse and fish. The consensus of this novel SINE shares 57 to 61% identities to tRNA-Leu from different species. Another older retroposition event in the same intron of IL-1beta1 has also been hypothesised, recognised as six adenines, that may function as a RNA polIII terminator. A model for the IL-1beta1 allele formation is proposed. Following the earliest retroposition into one of the two IL-1beta genes that resulted from a genome duplication in salmonids, the proper environment for successive PV SINE retroposition was created. A recent retroposition of the HpaI SINE in IL-1beta1 resulted in the formation of the two alleles of IL-1beta1. Examination of the SINEs insertion and their host gene microenvironments revealed that the SINE retroposition does not appear random, both in the site selection and the direction of insertion. The mechanism governing this outcome is discussed.

KW - rainbow trout

KW - interleukin-1 beta 1

KW - allele B

KW - SINE

KW - allele formation

KW - retroposition

KW - nitric-oxide synthase

KW - short interspersed elements

KW - polymerase-chain-reaction

KW - receptor antagonist

KW - molecular-cloning

KW - ancestral tetraploidy

KW - IL-1-BETA gene

KW - messenger-RNA

KW - salmonid fish

KW - tandem repeat

KW - animals

KW - alleles

KW - animals

KW - base sequence

KW - DNA primers

KW - gene expression

KW - interleukin-1

KW - introns

KW - models

KW - genetic

KW - molecular sequence data

KW - ncorhynchus mykiss

KW - reverse transcriptase polymerase chain reaction

KW - sequence alignment

KW - sequence analysis

KW - DNA

KW - sequence homology

KW - short interspersed nucleotide elements

U2 - 10.1016/S1050-4648(03)00114-1

DO - 10.1016/S1050-4648(03)00114-1

M3 - Article

VL - 16

SP - 335

EP - 358

JO - Fish & Shellfish Immunology

JF - Fish & Shellfish Immunology

SN - 1050-4648

IS - 3

ER -