A novel non-coding DNA family in Caenorhabditis elegans

Yasuo Takashima, Tetsuya Bando, Hiroaki Kagawa

Research output: Contribution to journalArticle

Abstract

Many repetitive elements, for example, SINEs, LINEs, LTR-retrotransposons and other SSRs are dispersed throughout eukaryotic genomes. To understand the biological function of these repetitive elements is of great current research interest. In this study, we report on the identification of a novel non-coding DNA family, designated CE1 family, in the nematode C. elegans genome. Some CE1 elements constituted a large palindrome sequence. The CE1 elements were interspersed at 95 sites in the C. elegans genome. Most of the CE1 elements were associated with, or were within, protein-coding genes. The sequence of the CE1 elements indicated that some could form a hairpin structure. One of the CE1 family, CE1(bs258), is located in the first intron of a novel gene, C46H11.6 which encodes a PDZ/DHR/GLGF domain protein. In gfp and lacZ reporter gene assays the CE1(bs258) element appeared to behave as an enhancer element for the expression of C46H11.6 but no effect on the expression of the opposite direction gene, pat-10 which encodes the body-wall muscle troponin C. The CE1(bs258) RNA transcript was detected by RT-PCR even when CE1(bs258) was located in an intron. We conclude that CE1 elements are involved in the expression of adjacent genes and are therefore selectively retained in the C. elegans genome. We discussed a biological function of the CE1(bs258) having many transcription factor-binding sites.

Original languageEnglish
Pages (from-to)61-73
Number of pages13
JournalGene
Volume388
Issue number1-2
DOIs
Publication statusPublished - Feb 15 2007

Fingerprint

Caenorhabditis elegans
Genome
DNA
Introns
Short Interspersed Nucleotide Elements
Inverted Repeat Sequences
Troponin C
PDZ Domains
Retroelements
Lac Operon
Reporter Genes
Genes
Proteins
Transcription Factors
Binding Sites
RNA
Gene Expression
Muscles
Polymerase Chain Reaction
Research

Keywords

  • Enhancer
  • Gene/element association
  • Genome organization
  • Palindrome
  • Repetitive element

ASJC Scopus subject areas

  • Genetics

Cite this

A novel non-coding DNA family in Caenorhabditis elegans. / Takashima, Yasuo; Bando, Tetsuya; Kagawa, Hiroaki.

In: Gene, Vol. 388, No. 1-2, 15.02.2007, p. 61-73.

Research output: Contribution to journalArticle

Takashima, Yasuo ; Bando, Tetsuya ; Kagawa, Hiroaki. / A novel non-coding DNA family in Caenorhabditis elegans. In: Gene. 2007 ; Vol. 388, No. 1-2. pp. 61-73.
@article{717a93fc83834d989dd903a8d9224c28,
title = "A novel non-coding DNA family in Caenorhabditis elegans",
abstract = "Many repetitive elements, for example, SINEs, LINEs, LTR-retrotransposons and other SSRs are dispersed throughout eukaryotic genomes. To understand the biological function of these repetitive elements is of great current research interest. In this study, we report on the identification of a novel non-coding DNA family, designated CE1 family, in the nematode C. elegans genome. Some CE1 elements constituted a large palindrome sequence. The CE1 elements were interspersed at 95 sites in the C. elegans genome. Most of the CE1 elements were associated with, or were within, protein-coding genes. The sequence of the CE1 elements indicated that some could form a hairpin structure. One of the CE1 family, CE1(bs258), is located in the first intron of a novel gene, C46H11.6 which encodes a PDZ/DHR/GLGF domain protein. In gfp and lacZ reporter gene assays the CE1(bs258) element appeared to behave as an enhancer element for the expression of C46H11.6 but no effect on the expression of the opposite direction gene, pat-10 which encodes the body-wall muscle troponin C. The CE1(bs258) RNA transcript was detected by RT-PCR even when CE1(bs258) was located in an intron. We conclude that CE1 elements are involved in the expression of adjacent genes and are therefore selectively retained in the C. elegans genome. We discussed a biological function of the CE1(bs258) having many transcription factor-binding sites.",
keywords = "Enhancer, Gene/element association, Genome organization, Palindrome, Repetitive element",
author = "Yasuo Takashima and Tetsuya Bando and Hiroaki Kagawa",
year = "2007",
month = "2",
day = "15",
doi = "10.1016/j.gene.2006.10.002",
language = "English",
volume = "388",
pages = "61--73",
journal = "Gene",
issn = "0378-1119",
publisher = "Elsevier",
number = "1-2",

}

TY - JOUR

T1 - A novel non-coding DNA family in Caenorhabditis elegans

AU - Takashima, Yasuo

AU - Bando, Tetsuya

AU - Kagawa, Hiroaki

PY - 2007/2/15

Y1 - 2007/2/15

N2 - Many repetitive elements, for example, SINEs, LINEs, LTR-retrotransposons and other SSRs are dispersed throughout eukaryotic genomes. To understand the biological function of these repetitive elements is of great current research interest. In this study, we report on the identification of a novel non-coding DNA family, designated CE1 family, in the nematode C. elegans genome. Some CE1 elements constituted a large palindrome sequence. The CE1 elements were interspersed at 95 sites in the C. elegans genome. Most of the CE1 elements were associated with, or were within, protein-coding genes. The sequence of the CE1 elements indicated that some could form a hairpin structure. One of the CE1 family, CE1(bs258), is located in the first intron of a novel gene, C46H11.6 which encodes a PDZ/DHR/GLGF domain protein. In gfp and lacZ reporter gene assays the CE1(bs258) element appeared to behave as an enhancer element for the expression of C46H11.6 but no effect on the expression of the opposite direction gene, pat-10 which encodes the body-wall muscle troponin C. The CE1(bs258) RNA transcript was detected by RT-PCR even when CE1(bs258) was located in an intron. We conclude that CE1 elements are involved in the expression of adjacent genes and are therefore selectively retained in the C. elegans genome. We discussed a biological function of the CE1(bs258) having many transcription factor-binding sites.

AB - Many repetitive elements, for example, SINEs, LINEs, LTR-retrotransposons and other SSRs are dispersed throughout eukaryotic genomes. To understand the biological function of these repetitive elements is of great current research interest. In this study, we report on the identification of a novel non-coding DNA family, designated CE1 family, in the nematode C. elegans genome. Some CE1 elements constituted a large palindrome sequence. The CE1 elements were interspersed at 95 sites in the C. elegans genome. Most of the CE1 elements were associated with, or were within, protein-coding genes. The sequence of the CE1 elements indicated that some could form a hairpin structure. One of the CE1 family, CE1(bs258), is located in the first intron of a novel gene, C46H11.6 which encodes a PDZ/DHR/GLGF domain protein. In gfp and lacZ reporter gene assays the CE1(bs258) element appeared to behave as an enhancer element for the expression of C46H11.6 but no effect on the expression of the opposite direction gene, pat-10 which encodes the body-wall muscle troponin C. The CE1(bs258) RNA transcript was detected by RT-PCR even when CE1(bs258) was located in an intron. We conclude that CE1 elements are involved in the expression of adjacent genes and are therefore selectively retained in the C. elegans genome. We discussed a biological function of the CE1(bs258) having many transcription factor-binding sites.

KW - Enhancer

KW - Gene/element association

KW - Genome organization

KW - Palindrome

KW - Repetitive element

UR - http://www.scopus.com/inward/record.url?scp=33845766239&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33845766239&partnerID=8YFLogxK

U2 - 10.1016/j.gene.2006.10.002

DO - 10.1016/j.gene.2006.10.002

M3 - Article

VL - 388

SP - 61

EP - 73

JO - Gene

JF - Gene

SN - 0378-1119

IS - 1-2

ER -