Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues

Carlile, Mark; Swan, Daniel; Jackson, Kelly A.; Preston-Fayers, Keziah; Ballester, Benoît; Flicek, Paul; Werner, Andreas

doi:10.1093/nar/gkp088

Cited by 39 publications

(45 citation statements)

References 45 publications

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“…It has been shown that the sense/antisense dsRNA pairs in vertebrates are processed in the nucleus but not the cytoplasm [67,68]. Therefore, some plant nat-siRNAs may also be produced in the nucleus before introns are spliced out from the NATs.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

et al. 2012

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BackgroundMany eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, and yeasts. However, many questions remain regarding the features and biogenesis of nat-siRNAs.ResultsThrough deep sequencing, we identified more than 17,000 unique siRNAs corresponding to cis-NATs from biotic and abiotic stress-challenged Arabidopsis thaliana and 56,000 from abiotic stress-treated rice. These siRNAs were enriched in the overlapping regions of NATs and exhibited either site-specific or distributed patterns, often with strand bias. Out of 1,439 and 767 cis-NAT pairs identified in Arabidopsis and rice, respectively, 84 and 119 could generate at least 10 siRNAs per million reads from the overlapping regions. Among them, 16 cis-NAT pairs from Arabidopsis and 34 from rice gave rise to nat-siRNAs exclusively in the overlap regions. Genetic analysis showed that the overlapping double-stranded RNAs could be processed by Dicer-like 1 (DCL1) and/or DCL3. The DCL3-dependent nat-siRNAs were also dependent on RNA-dependent RNA polymerase 2 (RDR2) and plant-specific RNA polymerase IV (PolIV), whereas only a fraction of DCL1-dependent nat-siRNAs was RDR- and PolIV-dependent. Furthermore, the levels of some nat-siRNAs were regulated by specific biotic or abiotic stress conditions in Arabidopsis and rice.ConclusionsOur results suggest that nat-siRNAs display distinct distribution patterns and are generated by DCL1 and/or DCL3. Our analysis further supported the existence of nat-siRNAs in plants and advanced our understanding of their characteristics.

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Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

et al. 2012

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“…19,24,28,29 The fact that these NATs share complementarity with their cognate mRNAs 30–33 make the related piRNAs and endo siRNAs perfect guides to target effector complexes to protein-coding transcripts. We propose that sense–antisense hybrid formation and germ cell–specific RNA interference represent key events in the genomic quality-control mechanism that is essential to mitigating the consequences of enhanced transposition.…”

Section: Improving Selection Filters: Optimizing Part 2 Of the Evolutmentioning

confidence: 99%

Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms

Werner

Piatek

Mattick

2014

Annals of the New York Academy of Sciences

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Complex organisms, particularly mammals, have long generation times and produce small numbers of progeny that undergo increasingly entangled developmental programs. This reduces the ability of such organisms to explore evolutionary space, and, consequently, strategies that mitigate this problem likely have a strategic advantage. Here, we suggest that animals exploit the controlled shuffling of transposons to enhance genomic variability in conjunction with a molecular screening mechanism to exclude deleterious events. Accordingly, the removal of repressive DNA-methylation marks during male germ cell development is an evolved function that exploits the mutagenic potential of transposable elements. A wave of transcription during the meiotic phase of spermatogenesis produces the most complex transcriptome of all mammalian cells, including genic and noncoding sense–antisense RNA pairs that enable a genome-wide quality-control mechanism. Cells that fail the genomic quality test are excluded from further development, eventually resulting in a positively selected mature sperm population. We suggest that these processes, enhanced variability and stringent molecular quality control, compensate for the apparent reduced potential of complex animals to adapt and evolve.

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“…Alternatively, antisense transcripts may instead block the translation of the sense mRNAs without changing the levels of the latter (21,22). It has been known that antisense transcripts are highly expressed in the testis, particularly in haploid cells (23,24). Therefore, antisense transcripts are likely active regulators of gene expression during spermatogenesis.…”

mentioning

confidence: 99%

Integrative Proteomic and Transcriptomic Analyses Reveal Multiple Post-transcriptional Regulatory Mechanisms of Mouse Spermatogenesis

Gan

Cai

Lin

et al. 2013

Molecular & Cellular Proteomics

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Mammalian spermatogenesis consists of many cell types and biological processes and serves as an excellent model for studying gene regulation at transcriptional and post-transcriptional levels. Many key proteins, miRNAs, and perhaps piRNAs have been shown to be involved in post-transcriptional regulation of spermatogenesis. However, a systematic method for assessing the relationship between protein and mRNA expression has not been available for studying mechanisms of post-transcriptional regulation. In the present study, we used the iTRAQbased quantitative proteomic approach to identify 2008 proteins in mouse type A spermatogonia, pachytene spermatocytes, round spermatids, and elongative spermatids with high confidence. Of these proteins, 1194 made up four dynamically changing clusters, which reflect the mitotic amplification, meiosis, and post-meiotic development of germ cells. We identified five major regulatory mechanisms termed "transcript only," "transcript degradation," "translation repression," "translation de-repression," and "protein degradation" based on changes in protein level relative to changes in mRNA level at the mitosis/meiosis transition and the meiosis/post-meiotic development transition. We found that post-transcriptional regulatory mechanisms are related to the generation of piRNAs and antisense transcripts. Our results provide a valuable inventory of proteins produced during mouse spermatogenesis and contribute to elucidating the mechanisms of the post-transcriptional regulation of gene expression in mammalian spermatogenesis. Molecular &

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Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues

Cited by 39 publications

References 45 publications

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms

Integrative Proteomic and Transcriptomic Analyses Reveal Multiple Post-transcriptional Regulatory Mechanisms of Mouse Spermatogenesis

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