Characteristics of Transposable Element Exonization within Human and Mouse

Sela, Noa; Mersch, Britta; Hotz‐Wagenblatt, Agnes; Ast, Gil

doi:10.1371/journal.pone.0010907

Cited by 65 publications

(56 citation statements)

References 74 publications

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“…A biological function of SNORD27 could thus be the repression of pre-mRNA sequences that have the potential to be recognized as weak alternative exons. Because some of these weak exons are generated through short (Alu) or long (LINE) interspersed elements (63)(64)(65), SNORDs might have a more general role in suppressing newly formed exons.…”

Section: Discussionmentioning

confidence: 99%

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

Falaleeva

Pagès

Matuszek

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

165

152

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C/D box small nucleolar RNAs (SNORDs) are small noncoding RNAs, and their best-understood function is to target the methyltransferase fibrillarin to rRNA (for example, SNORD27 performs 2′-Omethylation of A27 in 18S rRNA). Unexpectedly, we found a subset of SNORDs, including SNORD27, in soluble nuclear extract made under native conditions, where fibrillarin was not detected, indicating that a fraction of the SNORD27 RNA likely forms a protein complex different from canonical snoRNAs found in the insoluble nuclear fraction. As part of this previously unidentified complex, SNORD27 regulates the alternative splicing of the transcription factor E2F7 pre-mRNA through direct RNA-RNA interaction without methylating the RNA, likely by competing with U1 small nuclear ribonucleoprotein (snRNP). Furthermore, knockdown of SNORD27 activates previously "silent" exons in several other genes through base complementarity across the entire SNORD27 sequence, not just the antisense boxes. Thus, some SNORDs likely function in both rRNA and pre-mRNA processing, which increases the repertoire of splicing regulators and links both processes.alternative splicing | gene regulation | snoRNAs | pre-mRNA processing S mall nucleolar RNAs (snoRNAs) are 60-to 300-nt-long noncoding RNAs that accumulate in the nucleolus. Based on conserved sequence elements, snoRNAs are classified as C/D box small nucleolar RNAs (SNORDs) or H/ACA box snoRNAs (SNORAs). SNORDs contain sequence elements termed C (RUGAUGA) and D (CUGA) boxes, usually present in duplicates (C′ and D′ boxes), and up to two antisense boxes that hybridize to the target RNA (1). In humans, SNORDs are usually derived from introns. After the splicing reaction, introns are excised as lariats, which are then opened by the debranching enzyme and subsequently degraded. Intronic SNORDs escape this degradation by forming a protein complex that consists of non-histone chromosome protein 2-like 1 (NHP2L1, 15.5K, SNU13), nucleolar protein 5A (NOP56), nucleolar protein 5 (NOP58), and fibrillarin (2-4). The SNORD protein complex forms through the entry of the snoRNA and fibrillarin to a complex containing NHP2L1, NOP58, and at least five assembly factors (5). The SNORD acts as a scaffold for the final protein complex formation and also controls recognition of other RNAs using the antisense boxes. The antisense boxes recognize sequences in rRNA, resulting in the fifth nucleotide upstream of the D or D′ box being 2′-O-methylated by fibrillarin (1). Structural studies indicate that the active form of SNORDs is dimeric (6).The conserved overall structure of SNORDs allows the identification of their putative target RNA binding sites. However, numerous SNORDs without obvious target RNAs have been identified (7-10) and are termed "orphan snoRNAs." Genome-wide deep sequencing experiments identified shorter but stable SNORD fragments that were found in all species tested, ranging from mammals to the protozoan Giardia lamblia (11) and EpsteinBarr virus (12). Fragments longer than 27 nt generated by SNORDs will ...

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Section: Discussionmentioning

confidence: 99%

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

Falaleeva

Pagès

Matuszek

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

165

152

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“…The evolutionary process by which TE sequences are subverted for novel function by the host genome is known as "exaptation" (de Souza et al 2013). There is extensive literature demonstrating that TEs have contributed repeatedly and profoundly to the evolution of genome structure and function through the insertion of preformed sequence elements, both at the level of genomic DNA, e.g., transcription factor binding sites (Johnson et al 2006), splice sites (Sela et al 2010), enhancer elements (Huda et al 2011b), and promoters (Huda et al 2011a), and at the level of RNA, e.g., microRNA genes (Spengler et al 2014), recognition elements (Piriyapongsa and Jordan 2007), and protein-coding domains (Bowen and Jordan 2007).…”

Section: Te Sequences Are Abundantly Found In Lncrna Exonsmentioning

confidence: 99%

“…In another recent paper, Cedric Feschotte and colleagues found numerous examples in which lncRNA promoters, splice donor, and splice acceptor and polyadenylation sites are composed of TE-derived sequence (Kapusta et al 2013), echoing a previous study demonstrating widespread alternative promoter contributions by TEs (Faulkner et al 2009). The TE content of lncRNA genes far exceeds that of protein-coding genes, almost certainly due to the inability of protein-coding sequence to tolerate insertions (Sela et al 2010). Kelley and Rinn (2012) went further to show that the 127 lncRNAs promoted by HERVH elements are specifically up-regulated in pluripotent cell types (Kelley and Rinn 2012), which is consistent with previous observations of the overexpression of these elements in human embryonic stem cells (Santoni et al 2012).…”

Section: Te Sequences Are Abundantly Found In Lncrna Exonsmentioning

confidence: 99%

“…In the case of an inserted internal exon, for example, just one in three insertions will result in a viable protein (Marsh and Teichmann 2010;Schad et al 2013). Similarly, although TEs have been shown to occasionally contribute novel exonic sequence to protein-coding genes, the insertion of a TE within a coding exon, or else the spliced inclusion of an entire TE-derived exon, only has a one-in-three probability of creating a viable protein, and even then it would likely be a stretch of nonsense protein (Sela et al 2010). In contrast, lncRNA would be expected to accept TE sequence much more readily without adversely affecting their function since the RNA sequence function is not dependent on a strict frame or register.…”

Section: Tes and The Evolution Of Complex Lncrna Regulatory Networkmentioning

confidence: 99%

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The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Johnson

Guigó

2014

RNA

270

231

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Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional domains, but the nature of these and their identification remain elusive. One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation. Here, we link these two concepts by proposing that exonic TEs act as RNA domains that are essential for lncRNA function. We term such elements Repeat Insertion Domains of LncRNAs (RIDLs). A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. We propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. We discuss a series of genomic screens that may be used in the future to systematically discover RIDLs. The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function.

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“…Class II로 분류되는 DNA transposon의 경우 진화 과정에서 그들의 위치를 옮기는 방 법으로 게놈 상에 자리잡았고, 현재에는 화석화된 상태로 존 재하고 있다 [64,65]. 이러한 이동성 유전인자는 유전체 내에 서 프로모터 [40,55], 인핸서 [31,52], poly A 신호 제공 [69,83], 액손화 현상 [72,77], miRNA 생성 [3,78] It induces the degradation of aggrecan (major proteoglycan of cartilage) and brevican (brain-specific extracellular matrix).…”

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Recent Strategy for Superior Horses

Gim¹,

Kim²

2016

Journal of Life Science

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The horse is relatively earlier domesticated animal species. Domesticated horses have been selected for their ability of racing, robustness, and disease-resistance. As a result, the thoroughbred horse genome has been condensed many genotypes related to exercise ability. In recent years, with the advent of NGS technologies, many studies were concentrated on finding superior genetic species in the horse genome in terms of genomics. Consequently, GWAS (Genome-wide Association study) is applied to horse genome, then genetic marker is revealed for superior racing ability. In addition, RNA-Seq is utilized as a method for analyze of whole transcript profiling in specific samples. By using this approach, specific gene expression patterns and transcript sequences can be revealed in various samples such as each individual, before and after exercise state, and each tissue. DNA methylation, a strong factor that regulate gene expression without the change of DNA sequence, have got a lot of attention. In horse genome, exercise-or individual-specific DNA methylation patterns were detected, and could be useful to develop selective marker of superior horses. MicroRNAs inhibit gene expression, and transposable elements accounted for half of the mammalian genome. These two elements are the crucial factors in functional genomics, and could be applied to the selection of superior horses. As the functional genomics and epigenomics advance, then these technologies introduced in this paper were applied to select superior horses. In this paper, the studies for selection of superior horses through genetic technologies, and development possibilities of these studies were discussed.

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Characteristics of Transposable Element Exonization within Human and Mouse

Cited by 65 publications

References 74 publications

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

Dual function of C/D box small nucleolar RNAs in rRNA modification and alternative pre-mRNA splicing

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

Recent Strategy for Superior Horses

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