Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47
Abstract At least 70% of the human protein-coding genes contain multiple polyadenylation sites (PAS) and undergo alternative polyadenylation (APA), generating distinct transcripts from a single gene. While APA has been implicated in various physiological and pathological processes, its regulatory fa...
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Nature Portfolio
2025-08-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-14782-7 |
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| author | Chayanin Wuttinontananchai Junichi Yamamoto Satoshi Sakamoto Yuki Yamaguchi |
| author_facet | Chayanin Wuttinontananchai Junichi Yamamoto Satoshi Sakamoto Yuki Yamaguchi |
| author_sort | Chayanin Wuttinontananchai |
| collection | DOAJ |
| description | Abstract At least 70% of the human protein-coding genes contain multiple polyadenylation sites (PAS) and undergo alternative polyadenylation (APA), generating distinct transcripts from a single gene. While APA has been implicated in various physiological and pathological processes, its regulatory factors and cellular mechanisms remain incompletely understood. A previous study demonstrated that APA influences the localization of the cell surface marker CD47. Here, we present the results of a genome-wide CRISPR screen aimed at identifying APA regulators using CD47 as a reporter. Given that isoform-specific knockdown of CD47, as well as knockdown of core 3′ end processing factors, alters CD47 localization, we developed an immunofluorescence-based method that simultaneously detects cell surface and intracellular CD47 protein, enabling the visualization of APA-dependent changes at the single-cell level. Leveraging this approach, we conducted a CRISPR screen and identified multiple genes affecting CD47 cell-surface expression. In addition to known membrane trafficking factors, we uncovered several nuclear factors, among which POLDIP2 emerged as a potential novel APA regulator with a global impact on APA. This study provides a foundation for further investigations into the molecular mechanisms governing APA. |
| format | Article |
| id | doaj-art-3905f7bd99834c5babe0563832b35870 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-3905f7bd99834c5babe0563832b358702025-08-20T04:03:01ZengNature PortfolioScientific Reports2045-23222025-08-0115111510.1038/s41598-025-14782-7Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47Chayanin Wuttinontananchai0Junichi Yamamoto1Satoshi Sakamoto2Yuki Yamaguchi3School of Life Science and Technology, Institute of Science TokyoSchool of Life Science and Technology, Institute of Science TokyoSchool of Life Science and Technology, Institute of Science TokyoSchool of Life Science and Technology, Institute of Science TokyoAbstract At least 70% of the human protein-coding genes contain multiple polyadenylation sites (PAS) and undergo alternative polyadenylation (APA), generating distinct transcripts from a single gene. While APA has been implicated in various physiological and pathological processes, its regulatory factors and cellular mechanisms remain incompletely understood. A previous study demonstrated that APA influences the localization of the cell surface marker CD47. Here, we present the results of a genome-wide CRISPR screen aimed at identifying APA regulators using CD47 as a reporter. Given that isoform-specific knockdown of CD47, as well as knockdown of core 3′ end processing factors, alters CD47 localization, we developed an immunofluorescence-based method that simultaneously detects cell surface and intracellular CD47 protein, enabling the visualization of APA-dependent changes at the single-cell level. Leveraging this approach, we conducted a CRISPR screen and identified multiple genes affecting CD47 cell-surface expression. In addition to known membrane trafficking factors, we uncovered several nuclear factors, among which POLDIP2 emerged as a potential novel APA regulator with a global impact on APA. This study provides a foundation for further investigations into the molecular mechanisms governing APA.https://doi.org/10.1038/s41598-025-14782-7Genome-wide CRISPR screenAlternative polyadenylationCD47POLDIP2RNA-seq |
| spellingShingle | Chayanin Wuttinontananchai Junichi Yamamoto Satoshi Sakamoto Yuki Yamaguchi Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47 Scientific Reports Genome-wide CRISPR screen Alternative polyadenylation CD47 POLDIP2 RNA-seq |
| title | Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47 |
| title_full | Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47 |
| title_fullStr | Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47 |
| title_full_unstemmed | Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47 |
| title_short | Genome-wide CRISPR screen for human factors involved in alternative polyadenylation based on differential localization of CD47 |
| title_sort | genome wide crispr screen for human factors involved in alternative polyadenylation based on differential localization of cd47 |
| topic | Genome-wide CRISPR screen Alternative polyadenylation CD47 POLDIP2 RNA-seq |
| url | https://doi.org/10.1038/s41598-025-14782-7 |
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