Differential subcellular localization of DNA topoisomerase-1 isoforms and their roles during Caenorhabditis elegans development

Seok, Dong; Hollis, Sarah; Datla, Udaya Sree; Lee, Se-Jin; Ryu, Jinsun; Jung, Hyo Won; Kim, Eunsuk; Kim, Kyuhyung; Lee, Myeongwoo; Li, Chris; Lee, Myon‐Hee

doi:10.1016/j.gep.2012.03.002

Cited by 7 publications

(7 citation statements)

References 43 publications

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“…For example, top-1 alternative cassette exon splicing patterns change during development (Lee et al 1998), and RNAi knockdown of the developmentally regulated splicing factor gene hrpf-1 leads to a change in cassette exon inclusion in top-1 isoforms (Barberan-Soler and Zahler 2008). A recent study used immunostaining with antipeptide antibodies specific to the alternative cassette exon of top-1 to demonstrate detection of the skipping isoform of top-1 in almost all cells and the inclusion isoform of top-1 in neuronal cells, excretory cells, and the germline (Cha et al 2012). We set out to test whether alternative splicing of top-1 pre-mRNA changes with the onset of development of the mature gonad, which corresponds with developmental expansion of the germline.…”

Section: Resultsmentioning

confidence: 99%

Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites inC. elegans

et al. 2015

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Adjacent alternative 3′ splice sites, those separated by ≤18 nucleotides, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define the adjacent sites. Identification of the intron's 3 ′ end depends upon sequence elements that define the branchpoint, polypyrimidine tract, and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched Caenorhabditis elegans samples, we identify hundreds of introns with adjacent alternative 3 ′ splice sites. We identify 203 events that undergo tissue-specific alternative splicing. For these, the regulation is monodirectional, with somatic cells preferring to splice at the distal 3 ′ splice site (furthest from the 5 ′ end of the intron) and germline cells showing a distinct shift toward usage of the adjacent proximal 3 ′ splice site (closer to the 5 ′ end of the intron). Splicing patterns in somatic cells follow C. elegans consensus rules of 3 ′ splice site definition; a short stretch of pyrimidines preceding an AG dinucleotide. Splicing in germline cells occurs at proximal 3 ′ splice sites that lack a preceding polypyrimidine tract, and in three instances the germline-specific site lacks the AG dinucleotide. We provide evidence that use of germline-specific proximal 3 ′ splice sites is conserved across Caenorhabditis species. We propose that there are differences between germline and somatic cells in the way that the basal splicing machinery functions to determine the intron terminus. [Supplemental material is available for this article.]Alternative splicing is a highly regulated process by which a cell can produce multiple messenger RNAs, potentially encoding multiple proteins, from a common precursor transcript. The de novo assembly of a spliceosome on each intron of a pre-mRNA transcript requires cis-elements within the intron that are recognized as signals marking the beginning, end, and branchpoint (Ares and Weiser 1995). A cassette exon is a form of alternative splicing in which an exon is either included or skipped in the mature mRNA. Conserved enhancer or silencer elements within the exon or the surrounding introns interact with an array of constitutive and tissue-specific trans-factors that promote or inhibit assembly of a functional spliceosome (Wang and Burge 2008). The use of alternative 3 ′ or 5 ′ splice sites modifies gene expression by including or skipping coding sequences at the ends of exons. Many examples of adjacent alternative 3 ′ splice sites, defined as being separated by 18 nucleotides (nt) or less, have been observed. In many species, a form of alternative 3 ′ splice site usage has been identified in which the alternative splicing acceptors are only 3 nt apart. Except for the rare example of AC dinucleotides observed for substrates of the minor spliceosome, introns end with AG dinucleotides. Alternative 3 ′ splice sites separated by only 3 nt are referred to as NAGNAGs, as the end of the intron consists of two AG splice acceptors separated by 3 nt. A...

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Section: Resultsmentioning

confidence: 99%

Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites inC. elegans

et al. 2015

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“…Notably, we failed to obtain the double deletion mutant line even after three transformation attempts, indicating that TOP1 activity is essential for cell survival, protoplast regeneration or normal protonema growth. Given the requirement of TOP1 activity for cell survival in other organisms (Lee et al ., 1993; Takahashi et al ., 2002; Cha et al ., 2012), TOP1 activity is similarly most likely to be essential for general cell activities in P. patens .…”

Section: Resultsmentioning

confidence: 99%

Topoisomerase 1α is required for synchronous spermatogenesis in Physcomitrium patens

Chen

Kabeya

et al. 2022

New Phytologist

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Summary DNA topoisomerase 1 (TOP1) plays general roles in DNA replication and transcription by regulating DNA topology in land plants and metazoans. TOP1 is also involved in specific developmental events; however, whether TOP1 plays a conserved developmental role among multicellular organisms is unknown. Here, we investigated the developmental roles of TOP1 in the moss Physcomitrium (Physcomitrella) patens with gene targeting, microscopy, 3D image segmentation and crossing experiments. We discovered that the disruption of TOP1α, but not its paralogue TOP1β, leads to a defect in fertilisation and subsequent sporophyte formation in P. patens. In the top1α mutant, the egg cell was functional for fertilisation, while sperm cells were fewer and infertile with disordered structures. We observed that the nuclei volume of wild‐type sperm cells synchronously decreases during antheridium development, indicating chromatin condensation towards the compact sperm head. By contrast, the top1α mutant exhibited attenuated cell divisions and asynchronous and defective contraction of the nuclei of sperm cells throughout spermatogenesis. These results indicate that TOP1α is involved in cell division and chromatin condensation during spermatogenesis in P. patens. Our results suggest that the regulation of DNA topology by TOP1 plays a key role in spermatogenesis in both land plants and metazoans.

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“…Topoisomerase I is highly enriched in the nucleolus of many organisms and is thought to be important for supporting rRNA transcription (Muller et al, 1985, Huang et al, 2021, Fleischmann et al, 1984, Cha et al, 2012). However, topoisomerase I may also have additional, transcription-independent roles, as topoisomerase I enrichment in nucleoli precedes detectable enrichment of RNAPI in bovine embryos (Laurincik et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

Topoisomerase I promotes formation of a novel DNA intermediate in the ribosomal DNA

Molinar

Sultanov

Klein

et al. 2022

Preprint

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The ribosomal DNA (rDNA) is a conserved but highly unstable multi-gene locus that codes for the RNA components of the ribosome (rRNA). Despite being essential for protein translation and survival, rRNA gene-copy numbers fluctuate frequently. Here, we describe a novel rDNA intermediate that may be involved in these copy-number changes in Saccharomyces cerevisiae. Two-dimensional gel analyses revealed a structure that includes a large single-stranded tail and arises from the promoter of the 35S rRNA gene. Formation of this intermediate is unaffected by reduced 35S transcription but relies on topoisomerase I (Top1). Unexpectedly, intermediate formation is also independent of S phase or the rDNA-instability factor Fob1, even though Fob1 is mediates the major peak of Top1 cleavage complexes in the rDNA. Indeed, we find that the known rDNA instability phenotypes of top1 mutants, including increased formation of extrachromosomal rDNA circles, elevated genetic marker loss, and instability of critically short rDNA arrays, are also largely independent of Fob1. We therefore speculate that failure to form this intermediate leads to rDNA instability in top1 mutants.

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Differential subcellular localization of DNA topoisomerase-1 isoforms and their roles during Caenorhabditis elegans development

Cited by 7 publications

References 43 publications

Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites inC. elegans

Coordinated tissue-specific regulation of adjacent alternative 3′ splice sites inC. elegans

Topoisomerase 1α is required for synchronous spermatogenesis in Physcomitrium patens

Topoisomerase I promotes formation of a novel DNA intermediate in the ribosomal DNA

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