The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells.
PIWI proteins and PIWI-interacting RNAs (piRNAs) play a central role in repressing transposable elements in animal germ cells. It is thought that piRNAs are mainly produced from discrete genomic loci named piRNA clusters, which often contain many "dead" transposon remnants from past invasi...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-02-01
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| Series: | PLoS Genetics |
| Online Access: | https://doi.org/10.1371/journal.pgen.1010632 |
| _version_ | 1811158386689966080 |
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| author | Keisuke Shoji Yusuke Umemura Susumu Katsuma Yukihide Tomari |
| author_facet | Keisuke Shoji Yusuke Umemura Susumu Katsuma Yukihide Tomari |
| author_sort | Keisuke Shoji |
| collection | DOAJ |
| description | PIWI proteins and PIWI-interacting RNAs (piRNAs) play a central role in repressing transposable elements in animal germ cells. It is thought that piRNAs are mainly produced from discrete genomic loci named piRNA clusters, which often contain many "dead" transposon remnants from past invasions and have heterochromatic features. In the genome of silkworm ovary-derived cultured cells called BmN4, a well-established model for piRNA research, torimochi was previously annotated as a unique and specialized genomic region that can capture transgenes and produce new piRNAs bearing a trans-silencing activity. However, the sequence identity of torimochi has remained elusive. Here, we carefully characterized torimochi by utilizing the updated silkworm genome sequence and the long-read sequencer MinION. We found that torimochi is in fact a full-length gypsy-like LTR retrotransposon, which is exceptionally active and has massively expanded its copy number in BmN4 cells. Many copies of torimochi in BmN4 cells have features of open chromatin and the ability to produce piRNAs. Therefore, torimochi may represent a young, growing piRNA cluster, which is still "alive" and active in transposition yet capable of trapping other transposable elements to produce de novo piRNAs. |
| first_indexed | 2024-04-10T05:23:48Z |
| format | Article |
| id | doaj.art-8760bffbf2e04827bf591d91600d0f88 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-10T05:23:48Z |
| publishDate | 2023-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-8760bffbf2e04827bf591d91600d0f882023-03-08T05:31:01ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042023-02-01192e101063210.1371/journal.pgen.1010632The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells.Keisuke ShojiYusuke UmemuraSusumu KatsumaYukihide TomariPIWI proteins and PIWI-interacting RNAs (piRNAs) play a central role in repressing transposable elements in animal germ cells. It is thought that piRNAs are mainly produced from discrete genomic loci named piRNA clusters, which often contain many "dead" transposon remnants from past invasions and have heterochromatic features. In the genome of silkworm ovary-derived cultured cells called BmN4, a well-established model for piRNA research, torimochi was previously annotated as a unique and specialized genomic region that can capture transgenes and produce new piRNAs bearing a trans-silencing activity. However, the sequence identity of torimochi has remained elusive. Here, we carefully characterized torimochi by utilizing the updated silkworm genome sequence and the long-read sequencer MinION. We found that torimochi is in fact a full-length gypsy-like LTR retrotransposon, which is exceptionally active and has massively expanded its copy number in BmN4 cells. Many copies of torimochi in BmN4 cells have features of open chromatin and the ability to produce piRNAs. Therefore, torimochi may represent a young, growing piRNA cluster, which is still "alive" and active in transposition yet capable of trapping other transposable elements to produce de novo piRNAs.https://doi.org/10.1371/journal.pgen.1010632 |
| spellingShingle | Keisuke Shoji Yusuke Umemura Susumu Katsuma Yukihide Tomari The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells. PLoS Genetics |
| title | The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells. |
| title_full | The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells. |
| title_fullStr | The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells. |
| title_full_unstemmed | The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells. |
| title_short | The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells. |
| title_sort | pirna cluster torimochi is an expanding transposon in cultured silkworm cells |
| url | https://doi.org/10.1371/journal.pgen.1010632 |
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