High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration
We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromoso...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
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2017
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| Online Access: | https://hdl.handle.net/10356/83042 http://hdl.handle.net/10220/42380 |
| _version_ | 1811694394316685312 |
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| author | Hong, Ru Lin, Bingqing Lu, Xinyi Lai, Lan-Tian Chen, Xin Sanyal, Amartya Ng, Huck-Hui Zhang, Kun Zhang, Li-Feng |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Hong, Ru Lin, Bingqing Lu, Xinyi Lai, Lan-Tian Chen, Xin Sanyal, Amartya Ng, Huck-Hui Zhang, Kun Zhang, Li-Feng |
| author_sort | Hong, Ru |
| collection | NTU |
| description | We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromosome inactivation (XCI) in early embryos, is conditionally deleted from Xi in somatic cells (Xi∆Xist). We also monitored the behaviors of X-linked non-coding transcripts before and after XCI. In each mutant cell line, gene reactivation occurs to ~6% genes along Xi∆Xist in a recognizable pattern. Genes with upstream regions enriched for SINEs are prone to be reactivated. SINE is a class of retrotransposon transcribed by RNA polymerase III (Pol III). Intriguingly, a significant fraction of Pol III transcription from non-coding regions is not subjected to Xist-mediated transcriptional silencing. Pol III inhibition affects gene reactivation status along Xi∆Xist, alters chromatin configuration and interferes with the establishment XCI during in vitro differentiation of ES cells. These results suggest that Pol III transcription is involved in chromatin structure re-organization during the onset of XCI and functions as a general mechanism regulating chromatin configuration in mammalian cells. |
| first_indexed | 2024-10-01T07:06:53Z |
| format | Journal Article |
| id | ntu-10356/83042 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T07:06:53Z |
| publishDate | 2017 |
| record_format | dspace |
| spelling | ntu-10356/830422023-02-28T16:56:33Z High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration Hong, Ru Lin, Bingqing Lu, Xinyi Lai, Lan-Tian Chen, Xin Sanyal, Amartya Ng, Huck-Hui Zhang, Kun Zhang, Li-Feng School of Biological Sciences School of Physical and Mathematical Sciences Epigenomics Gene silencing We carried out padlock capture, a high-resolution RNA allelotyping method, to study X chromosome inactivation (XCI). We examined the gene reactivation pattern along the inactive X (Xi), after Xist (X-inactive specific transcript), a prototype long non-coding RNA essential for establishing X chromosome inactivation (XCI) in early embryos, is conditionally deleted from Xi in somatic cells (Xi∆Xist). We also monitored the behaviors of X-linked non-coding transcripts before and after XCI. In each mutant cell line, gene reactivation occurs to ~6% genes along Xi∆Xist in a recognizable pattern. Genes with upstream regions enriched for SINEs are prone to be reactivated. SINE is a class of retrotransposon transcribed by RNA polymerase III (Pol III). Intriguingly, a significant fraction of Pol III transcription from non-coding regions is not subjected to Xist-mediated transcriptional silencing. Pol III inhibition affects gene reactivation status along Xi∆Xist, alters chromatin configuration and interferes with the establishment XCI during in vitro differentiation of ES cells. These results suggest that Pol III transcription is involved in chromatin structure re-organization during the onset of XCI and functions as a general mechanism regulating chromatin configuration in mammalian cells. NRF (Natl Research Foundation, S’pore) NMRC (Natl Medical Research Council, S’pore) MOH (Min. of Health, S’pore) Published version 2017-05-11T07:39:19Z 2019-12-06T15:10:45Z 2017-05-11T07:39:19Z 2019-12-06T15:10:45Z 2017 Journal Article Hong, R., Lin, B., Lu, X., Lai, L.-T., Chen, X., Sanyal, A., et al. (2017). High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration. Scientific Reports, 7, 45460-. 2045-2322 https://hdl.handle.net/10356/83042 http://hdl.handle.net/10220/42380 10.1038/srep45460 en Scientific Reports © 2017 The Author(s). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ 13 p. application/pdf |
| spellingShingle | Epigenomics Gene silencing Hong, Ru Lin, Bingqing Lu, Xinyi Lai, Lan-Tian Chen, Xin Sanyal, Amartya Ng, Huck-Hui Zhang, Kun Zhang, Li-Feng High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration |
| title | High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration |
| title_full | High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration |
| title_fullStr | High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration |
| title_full_unstemmed | High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration |
| title_short | High-resolution RNA allelotyping along the inactive X chromosome: evidence of RNA polymerase III in regulating chromatin configuration |
| title_sort | high resolution rna allelotyping along the inactive x chromosome evidence of rna polymerase iii in regulating chromatin configuration |
| topic | Epigenomics Gene silencing |
| url | https://hdl.handle.net/10356/83042 http://hdl.handle.net/10220/42380 |
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