Evolutionary History of <i>Cer</i> Elements and Their Impact on the <i>C. elegans</i> Genome

Ganko, Eric W.; Fielman, Kevin T.; McDonald, John F.

doi:10.1101/gr.196201

Cited by 51 publications

(70 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…C. elegans was reported to have 20 full-length elements (Ganko et al 2001); we found 19 in our original search, 15 of which were retained after removal of degenerate elements. In S. pombe, we identified 16 elements (14 were retained); 11 elements were reported in the annotated genome sequence (Wood et al 2002).…”

Section: Resultsmentioning

confidence: 99%

Translational recoding signals between gag and pol in diverse LTR retrotransposons

Gao

Havecker

Baranov

et al. 2003

RNA

View full text Add to dashboard Cite

Because of their compact genomes, retroelements (including retrotransposons and retroviruses) employ a variety of translational recoding mechanisms to express Gag and Pol. To assess the diversity of recoding strategies, we surveyed gag/pol gene organization among retroelements from diverse host species, including elements exhaustively recovered from the genome sequences of Caenorhabditis elegans, Drosophila melanogaster, Schizosaccharomyces pombe, Candida albicans, and Arabidopsis thaliana. In contrast to the retroviruses, which typically encode pol in the −1 frame relative to gag, nearly half of the retroelements surveyed encode a single gag-pol open reading frame. This was particularly true for the Ty1/copia group retroelements. Most animal Ty3/gypsy retroelements, on the other hand, encode gag and pol in separate reading frames, and likely express Pol through +1 or −1 frameshifting. Conserved sequences conforming to slippery sites that specify viral ribosomal frameshifting were identified among retroelements with pol in the −1 frame. None of the plant retroelements encoded pol in the −1 frame relative to gag; however, two closely related plant Ty3/gypsy elements encode pol in the +1 frame. Interestingly, a group of plant Ty1/copia retroelements encode pol either in a +1 frame relative to gag or in two nonoverlapping reading frames. These retroelements have a conserved stem-loop at the end of gag, and likely express pol either by a novel means of internal ribosomal entry or by a bypass mechanism.

show abstract

Section: Resultsmentioning

confidence: 99%

Translational recoding signals between gag and pol in diverse LTR retrotransposons

Gao

Havecker

Baranov

et al. 2003

RNA

View full text Add to dashboard Cite

show abstract

“…Moreover, although C. elegans contains full-length RNA transposons of the LTR class (Ganko et al 2001), their transposition has not been reported (Bessereau 2006). There may be a link between the absence of RNA:DNA hybrid formation on RNA transposons and their lack of transposition.…”

Section: Repetitive Elements and The Danger Of Their Expressionmentioning

confidence: 99%

“…More recent studies additionally showed that XRN-2 is involved in the degradation of many endogenous transcripts when transcriptional processivity is impaired (Davidson et al 2012). Given that the RNA transposons in C. elegans are considered to be evolutionary very young (Ganko et al 2001), their transcripts may not be efficiently processed for export and thus be preferred targets for XRN-2 mediated degradation. Given that retrotransposons are particularly enriched for H3K9me3, a mark that frequently co-occurs with H3K27me3 in worms, it is conceivable that the transcripts from RNA transposons are specifically targeted for degradation by one or the other mark.…”

Section: Repetitive Elements and The Danger Of Their Expressionmentioning

confidence: 99%

The Importance of Satellite Sequence Repression for Genome Stability

Zeller

Gasser

2017

Cold Spring Harb Symp Quant Biol

View full text Add to dashboard Cite

Up to two-thirds of eukaryotic genomes consist of repetitive sequences, which include both transposable elements and tandemly arranged simple or satellite repeats. Whereas extensive progress has been made toward understanding the danger of and control over transposon expression, only recently has it been recognized that DNA damage can arise from satellite sequence transcription. Although the structural role of satellite repeats in kinetochore function and end protection has long been appreciated, it has now become clear that it is not only these functions that are compromised by elevated levels of transcription. RNA from simple repeat sequences can compromise replication fork stability and genome integrity, thus compromising germline viability. Here we summarize recent discoveries on how cells control the transcription of repeat sequence and the dangers that arise from their expression. We propose that the link between the DNA damage response and the transcriptional silencing machinery may help a cell or organism recognize foreign DNA insertions into an evolving genome.

show abstract

“…Although gene/element association have previously been shown for the Cer LTR-retrotransposon family (Ganko et al, 2001;Ganko et al, 2003), the CE1 element/gene associations are extremely high (Fig. 5).…”

Section: Structure and Function Of Ce1(bs258)mentioning

confidence: 98%

“…Tandem and inverted repeats account for 2.7% and 3.6% of the entire genome size and are found, on average, once per 3.6 kb and 4.9 kb, respectively (C. elegans Sequencing Consortium, 1998). The Cer LTR-retrotransposon family is the most abundant class of retrotransposons (Ganko et al, 2001). Many repetitive families are distributed nonuniformly within the genome and are more likely to be found within an intron than an intergenic region ("intergenic region" means the space between gene A and gene B) (C. elegans Sequencing Consortium, 1998).…”

Section: Introductionmentioning

confidence: 99%

A novel non-coding DNA family in Caenorhabditis elegans

Takashima

Bando

Kagawa

2007

Gene

View full text Add to dashboard Cite

A novel non-coding DNA family in Caenorhabditis elegansKeywords: repetitive element; palindrome; gene/element association; enhancer; genome organization. -2 - Yasuo AbstractMany 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 are 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.-3 -

show abstract

Evolutionary History of Cer Elements and Their Impact on the C. elegans Genome

Cited by 51 publications

References 39 publications

Translational recoding signals between gag and pol in diverse LTR retrotransposons

Translational recoding signals between gag and pol in diverse LTR retrotransposons

The Importance of Satellite Sequence Repression for Genome Stability

A novel non-coding DNA family in Caenorhabditis elegans

Contact Info

Product

Resources

About