Takashima Y et al. (2007) Gene "A novel non-coding DNA family in Caenorhabditis elegans."

Takashima Y, Bando T, Kagawa H

[Gene, 2007]

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.

Yasuo Takashima et al. (2003) International Worm Meeting "GENOME ANALYSIS OF THE NOVEL REPETITIVE SEQUENCES IN C. ELEGANS"

Yasuo Takashima, Hiromi Terami, Hiroaki Kagawa, Tetsuya Bando

[International Worm Meeting, 2003]

Genome analysis of many model living organisms suggests that the rate of the non-coding to the coding regions in the genome relates to the complexity of living organisms. This means that the evolution of living organisms may be derived from the increment of non-coding regions. Although the genome sequence of the nematode C. elegans is completed, functional analysis of non-coding regions leaves unsolved and is one of the important subjects in the post genome era. In this study, the bs258 sequence that located at the 1kb upstream of the body-wall muscle troponin C gene pat-10 was analyzed by computational and experimental approaches. The bs258 sequence consisted of a long inverted repeat and formed a stem-loop structure. The bs258 sequence interspersed at the intron and the non-coding region in C. elegans genome and was also well conserved in C. briggsae genome. This sequence was also found in the genomes of other model organisms at the different homology. The bs258 binding factors were isolated by the method of yeast one-hybrid screening. These proteins were transcription factors and chromatin recognition proteins. The expression of gfp reporter gene with the bs258 sequence was stronger than that without the bs258 sequence. By the reason of the distribution in the genome and the function as an enhancer, the bs258 sequence could be a nematode SINE (short interspersed repetitive element). We also found the rt1640 sequence at the 700bp upstream of the pharyngeal muscle troponin C gene tnc-2. Its homologous sequences encoded a reverse transcriptase or a pseudogene and interspersed in the genome. The rt1640 sequence may be a nematode LINE (long interspersed repetitive element) or a trace of transposon. These computational and experimental analysis are useful not only to identify the function of these intronic or non-coding specific sequences of the animal but also to know how genomes were constructed from the simple to the complex.

Yasuo Takashima et al. (2004) East Asia Worm Meeting "Functional analysis of a novel SINE family in C. elegans"

Yasuo Takashima, Tetsuya Bando, Hiroaki Kagawa

[East Asia Worm Meeting, 2004]

Many genomes of model organisms are sequenced and we got so many data on transcriptome, proteome, protein interactome, and SNPs. These results show that introns and intergenic regions in the genome are increasing the complexity of organisms. This means that non-coding regions are involved in a genome evolution. The nematode C. elegans has been studied as a model organism, but the data about retrotransposon or non-coding regions is few. In this study, we found that the CE1 element, a novel SINE ( S hort IN terspersed E lement) derived from tRNA, locates at the 1 kb upstream of the body wall muscle troponin C gene, pat-10 . The CE1 elements were exclusively composed of type 2 Pol III promoters, A box and B box, and formed single/tandem array of tRNA-related regions. The CE1 elements contained transcription factor binding sites, and were interspersed in all chromosomes, but most of the CE1 elements associated with some genes. The CE1 elements associated genes encoded various proteins; transcription factor, DNA repair related, RNA polymerase, reverse transcriptase, and 7TM chemoreceptor. We performed yeast one-hybrid screening for isolating the CE1 element binding proteins, and the GFP reporter assay of the CE1 element associated gene, C46H11.6. These results suggest that the CE1 element is involved in a gene expression by its enhancer activity and a chromatin maintenance. The CE1 element could contain miRNA, which was suported by two approaches. First, stem-loop structure of the CE1 elements was calculated by the computer program. Second, the transcript of the CE1 element was detected by RT-PCR. It is well known that SINE elements are interspersed at non-coding regions only. We got some evidences that the nematode SINE CE1 family are involved in transcriptional functions. SINE analysis on the database of C. elegans allow us to reveal the biological significance of non-coding regions.

Yasuo Takashima et al. (2002) Japanese Worm Meeting "Molecular analysis of the repetitive palindrome sequence bs258 in the Caenorhabditis elegans genome"

Hiroaki Kagawa, Tetsuya Bando, Yasuo Takashima, Hiromi Terami

[Japanese Worm Meeting, 2002]

The human genome and the C. elegans genome encode 35,000 genes in 3,000Mb and 19,000 genes in 99.3Mb, respectively. The average size per gene of the both animals is estimated 85.7kbp and 5.2kbp, respectively. This means that a non-coding region of the human genome is a relatively bigger size. Elucidations of the biological meaning of introns and non-coding regions are important to understand how function of each gene in eukaryote. In this study, we found 197 sequences having 58-83% homology to the bs258 sequence that located at the 1kb upstream of the body-wall muscle troponin C gene, pat-10/tnc-1 . We also found 522 sequences having 66-98% homology to the rt1640 sequence that located at the 700 bp upstream of the pharyngeal muscle troponin C gene, tnc-2 in the genome. The later sequence was a trace of the transposon and was not studied more details. The former sequence was also existed in the genomes of bacteria, yeast, fly, and human. This sequence had palindrome sequence and formed a stem loop or a hairpin structure. Moreover, many transcription factors binding sequences were in it. This sequence may function as histone binding, DNA recombination, insulator (gene partition) and a trace of the transposon. To identify the factors binding to the bs258 sequence, we screened a library by yeast one-hybrid system. Consequently, we identified many factors as novel proteins, transcription factors including homeodomain, zinc finger and leucine zipper families, chromatin recognition proteins and others. Since the bs258 sequence is well conserved in the genome of many species, we propose that this sequence traps transcription factors temporarily and keeps them to the correct time. This approach helps to solve the biological functions of non-coding sequence in the accumulating genome date.

Yasuo Takashima et al. (2005) International Worm Meeting "A novel SINE family derived from tRNA is closely associated with genes in the C. elegans genome"

Tetsuya Bando, Hiroaki Kagawa, Yasuo Takashima

[International Worm Meeting, 2005]

Short interspersed elements (SINEs) of approximately ~500 bp length are abundant components of the eukaryotic genome that contain internal promoters for type 2 RNA polymerase III. SINEs have a great significance in constituting higher organism genomes during their evolution. SINEs as well as LINEs have been described in many multicellular organisms, whereas the nematode SINEs have not been reported.Here we report a novel SINE family, designated CE1 family, in the nematode C. elegans genome. A novel repetitive element composed of 258 bp and designated CE1(bs258) was found in the genome. The CE1(bs258) locates at the 1 kb upstream of pat-10, the body-wall troponin C gene, and also present into the first intron of C46H11.6, a novel gene encodes PDZ protein-binding domain. A novel repetitive family standardized by the CE1(bs258) was constituted of 293 elements in the genome. Distribution of 58 copies of the CE1 ortholog in the C. briggsae genome suggests that the CE1 family is the ancient element appeared since 80-110 MYA. The CE1 family was heterodimeric tRNA-derived SINEs with A and B boxes, internal promoters of RNA polymerase III. Most of the CE1 family was closely associated with protein-coding genes, and the one-third was exclusively located into introns. The structural analysis predicted a large hairpin structure with four major loops along the structure in both DNA and RNA states, respectively. The CE1(bs258) transcript was detected by RT-PCR, suggests that this intronic element is transcribed and is stable in the animal. The CE1 elements contain various kinds of transcriptional regulator-binding sites, transcriptional regulators and chromatin recognition proteins those were isolated as the CE1(bs258)-binding proteins by yeast one-hybrid screening. The C46H11.6::gfp reporter gene harboring the CE1(bs258) was expressed in skeletal muscles, whereas that without the element was not expressed in these tissues, suggests that the CE1(bs258) are not a essential promoter but an enhancer element for the C46H11.6 expression. We conclude that the CE1 family is involved in the adjacent gene expressions, and SINEs have biological significances for gene and genome evolutions.

Takashima Y et al. (2012) Genes Genet Syst "Expression profiles and unc-27 mutation rescue of the striated muscle type troponin I isoform-3 in Caenorhabditis elegans."

Kagawa H, Bando T, Kitaoka S, Takashima Y

[Genes Genet Syst, 2012]

Transcription control of multiple genes in tissue- and stage-specific patterns is still of major interest. We show here that troponin I (TNI) is expressed under the control of upstream non-coding sequences and had functions as an isoform of intermediate type between pharynx and body-wall of the gene. In Caenorhabditis elegans, three striated muscle TNIs are expressed in body-wall muscles and a cardiac isoform is expressed in the pharynx. We have analyzed the gene expression mechanisms of tni-3 gene and motility function of its protein product. Promoter deletion analysis of the tni-3 gene identified muscle enhancers including the head enhancer. The CBF1/Su(H)/LAG-1-binding motif was included in the head enhancer. Yeast one-hybrid screening isolated the lag-1 clone in five candidates. Functional differences between the three striated muscle TNIs were investigated by the expression of promoter-fusion genes into tni-2/unc-27(e155) null mutant animals. The results suggest that the cis-elements in the promoters of the three genes are important for their tissue-specific expression and that from the function of TNI-3, the tni-3 gene would be an intermediate in the evolution of these genes by gene duplication. Mechanisms of tni-3 expression and its molecular function may contribute to our understanding of gene evolution and developmental programs.

Yasuo Takashima et al. (2006) East Asia C. elegans Meeting "A noncoding DNA element associated with the body-wall muscle troponin C gene, pat-10 forms a novel repetitive family and functions as an enhancer in C. elegans genome"

Hiroaki Kagawa, Yasuo Takashima, Tetsuya Bando

[East Asia C. elegans Meeting, 2006]

Noncoding RNAs including microRNAs and snoRNAs have been known as transcriptional regulator and RNA processing machinery, respectively. Apart from these noncoding RNAs, there are so many noncoding DNAs which are interspersed into genomes, for example SINEs (short interspersed elements), LINEs (long-), LTR (long terminal repeat)-retrotransposons, and SSRs (simple sequence repeats). To understand the biological function of noncoding DNA elements in the C. elegans genome, we found a novel noncoding DNA family, designated CE1 family, one of which, CE1(bs258) locates at 1 kb upstream of the body-wall muscle troponin C gene, pat-10, and corresponds to the first intron of a novel gene, C46H11.6 encoding a PDZ/DHR/GLGF domain protein. pat-10 and C46H11.6 genes are bidirectionally oriented to a head-to-head manner. gfp reporter gene assays with or without CE1(bs258) indicated an enhancer activity of this element for the C46H11.6 gene expression. Moreover the lacZ enhancer assay confirmed that CE1(bs258) has an enhancer activity. We also performed genome wide computational and biochemical studies. The CE1 elements were interspersed at 95 sites in the genome. Most of the CE1 elements were associated with or within protein-coding genes. The palindrome sequence of the CE1 elements indicated that some could form a cruciform structure in which many transcription factor-binding sites were embedded. In yeast one-hybrid screening using CE1(bs258) as bait, we isolated many transcription factors and different chromatin recognition proteins supported our computational predictions. Based on these results from experimental and computational analyses, we propose that noncoding DNA elements including some CE1 elements have a potential enhancer activity on adjacent gene expression and genomic reservoir for gene expression control. This result adds a new approach to find novel noncoding DNA elements.

Ferree A et al. (2012) Neurodegener Dis "Regulation of physiologic actions of LRRK2: focus on autophagy."

Weigele M, Collins JJ, Li H, Smith K, Ferree A, Guillily M, Squillace R, Wolozin B, Takashima A

[Neurodegener Dis, 2012]

BACKGROUND: Mutations in LRRK2 are associated with familial and sporadic Parkinson's disease (PD). Subjects with PD caused by LRRK2 mutations show pleiotropic pathology that can involve inclusions containing -synuclein, tau or neither protein. The mechanisms by which mutations in LRRK2 lead to this pleiotropic pathology remain unknown. OBJECTIVES: To investigate mechanisms by which LRRK2 might cause PD. METHODS: We used systems biology to investigate the transcriptomes from human brains, human blood cells and Caenorhabditis elegans expressing wild-type LRRK2. The role of autophagy was tested in lines of C. elegans expressing LRRK2, V337M tau or both proteins. Neuronal function was measured by quantifying thrashing. RESULTS: Genes regulating autophagy were coordinately regulated with LRRK2. C. elegans expressing V337M tau showed reduced thrashing, as has been noted previously. Coexpressing mutant LRRK2 (R1441C or G2019S) with V337M tau increased the motor deficits. Treating the lines of C. elegans with an mTOR inhibitor that enhances autophagic flux, ridaforolimus, increased the thrashing behavior to the same level as nontransgenic nematodes. CONCLUSION: These data support a role for LRRK2 in autophagy, raise the possibility that deficits in autophagy contribute to the pathophysiology of LRRK2, and point to a potential therapeutic approach addressing the pathophysiology of LRRK2 in PD.

Quartey MO et al. (2021) Sci Rep "The A(1-38) peptide is a negative regulator of the A(1-42) peptide implicated in Alzheimer disease progression."

Pennington PR, Heistad RM, Nyarko JNK, Barnes JR, Bolanos MAC, Parsons MP, Knudsen KJ, De Carvalho CE, Leary SC, Mousseau DD, Buttigieg J, Maley JM, Quartey MO

[Sci Rep, 2021]

The pool of -Amyloid (A) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for A peptides. We examined how a naturally occurring variant, e.g. A(1-38), interacts with the AD-related variant, A(1-42), and the predominant physiological variant, A(1-40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that A(1-38) interacts differently with A(1-40) and A(1-42) and, in general, A(1-38) interferes with the conversion of A(1-42) to a -sheet-rich aggregate. Functionally, A(1-38) reverses the negative impact of A(1-42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an A(1-42) phenotype in Caenorhabditis elegans. A(1-38) also reverses any loss of MTT conversion induced by A(1-40) and A(1-42) in HT-22 hippocampal neurons and APOE 4-positive human fibroblasts, although the combination of A(1-38) and A(1-42) inhibits MTT conversion in APOE 4-negative fibroblasts. A greater ratio of soluble A(1-42)/A(1-38) [and A(1-42)/A(1-40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that A(1-38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant A(1-42).

Danielle Thierry-Mieg et al. (2003) Worm Breeder's Gazette "www.wormgenes.org , a new gene centered database"

Vahan Simonyan, Michel Potdevin, Mark Sienkiewicz, Yuji KOHARA, Jean Thierry-Mieg, Danielle Thierry-Mieg, Tadasu SHIN-I

[Worm Breeder's Gazette, 2003]

Wormgenes is a new resource for C.elegans offering a detailed summary about each gene and a powerful query system.