TY - JOUR
T1 - A novel non-coding DNA family in Caenorhabditis elegans
AU - Takashima, Yasuo
AU - Bando, Tetsuya
AU - Kagawa, Hiroaki
N1 - Funding Information:
We would express our sincere gratitude to Dr. Naruya Saitou (National Institute of Genetics) and Dr. Norihiro Okada (Tokyo Institute of Technology) for their invaluable discussion, Dr. Donald G. Moerman (University of British Columbia) for proofreading and critical comments. We thank Dr. Andrew Fire (Stanford University) for providing the pPD vector series for gfp expression analysis and lacZ enhancer assay. C. elegans strains were provided by the Caenorhabditis Genetic Center (CGC) which is funded by the NIH National Center for Research Resources (NCRR). This study was supported by a grant from the Ministry of Education, Culture, Sports and Technology of Japan to H.K.
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
C2 - 17134856
AN - SCOPUS:33845766239
SN - 0378-1119
VL - 388
SP - 61
EP - 73
JO - Gene
JF - Gene
IS - 1-2
ER -