Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Low-Dose Ionizing Radiation-Crosslinking Immunoprecipitation (LDIR-CLIP) Identified Irradiation-Sensitive RNAs for RNA-Binding Protein HuR-Mediated Decay

Ji Won Lee
,
Hyejin Mun
,
Jeong-Hyun Kim
,
Seungbeom Ko
,
Young-kook Kim
,
Min Ji Shim
,
Kyungmin Kim
,
Chul Woong Ho
,
Hyun Bong Park
,
Meesun Kim
,
Chaeyoung Lee
,
Si Ho Choi
,
Jung-Woong Kim
ORCID logo ,
Je-Hyun Yoon
* ,
Kyung-Won Min
* ORCID logo ,
Tae Gen Son
*
Version 1 : Received: 31 October 2023 / Approved: 31 October 2023 / Online: 31 October 2023 (17:18:23 CET)

A peer-reviewed article of this Preprint also exists.

Lee, J.W.; Mun, H.; Kim, J.-H.; Ko, S.; Kim, Y.-K.; Shim, M.J.; Kim, K.; Ho, C.W.; Park, H.B.; Kim, M.; Lee, C.; Choi, S.H.; Kim, J.-W.; Jeong, J.-H.; Yoon, J.-H.; Min, K.-W.; Son, T.G. Low-Dose Ionizing Radiation-Crosslinking Immunoprecipitation (LDIR-CLIP) Identified Irradiation-Sensitive RNAs for RNA-Binding Protein HuR-Mediated Decay. Biology 2023, 12, 1533. Lee, J.W.; Mun, H.; Kim, J.-H.; Ko, S.; Kim, Y.-K.; Shim, M.J.; Kim, K.; Ho, C.W.; Park, H.B.; Kim, M.; Lee, C.; Choi, S.H.; Kim, J.-W.; Jeong, J.-H.; Yoon, J.-H.; Min, K.-W.; Son, T.G. Low-Dose Ionizing Radiation-Crosslinking Immunoprecipitation (LDIR-CLIP) Identified Irradiation-Sensitive RNAs for RNA-Binding Protein HuR-Mediated Decay. Biology 2023, 12, 1533.

Abstract

Although ionizing radiation (IR) is widely used for therapeutic and research purposes, studies on low-dose ionizing radiation (LDIR) are limited compared with those on other IR approaches, such as high-dose gamma irradiation and ultraviolet irradiation. High-dose IR affects DNA damage response and nucleotide-protein crosslinking, among other processes; however, the molecular consequences of LDIR have been poorly investigated. Here, we developed a method to profile RNA species crosslinked to an RNA-binding protein, human antigen R (HuR), using LDIR and high-throughput RNA sequencing. The RNA fragments isolated via LDIR-crosslinking and immunoprecipitation sequencing were crosslinked to HuR and protected from RNase-mediated digestion. Upon crosslinking HuR to target mRNAs, such as PAX6, ZFP91, NR2F6, and CAND2, the transcripts degraded rapidly in human cell lines. Additionally, PAX6 and NR2F6 downregulation mediated the beneficial effects of LDIR on cell viability. Thus, our approach provides a method for investigating post-transcriptional gene regulation using LDIR.

Keywords

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Subject

Biology and Life Sciences, Biochemistry and Molecular Biology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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