Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription
Abstract Background Small RNAs (sRNAs) extensively mediate gene‐specific chromatin regulation in lower organisms. As a dominant type of functional sRNAs in mature mammals, microRNAs mainly regulate gene expression at post‐transcription level in the cytoplasm. Currently, whether there exists a type o...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2021-02-01
|
| Series: | Cancer Communications |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/cac2.12131 |
| _version_ | 1819297113072205824 |
|---|---|
| author | Yang Shi Qingzhu Shi Qicong Shen Qian Zhang Xuetao Cao |
| author_facet | Yang Shi Qingzhu Shi Qicong Shen Qian Zhang Xuetao Cao |
| author_sort | Yang Shi |
| collection | DOAJ |
| description | Abstract Background Small RNAs (sRNAs) extensively mediate gene‐specific chromatin regulation in lower organisms. As a dominant type of functional sRNAs in mature mammals, microRNAs mainly regulate gene expression at post‐transcription level in the cytoplasm. Currently, whether there exists a type of nuclear‐localized sRNAs mediating gene‐specific epigenetic regulation in mature mammalian cells remains largely unclear. Here, we profiled sRNAs enriched in the nucleus and investigated their function in mediating gene‐specific epigenetic regulation in anti‐tumor immunity. Methods We established cytoplasmic and nuclear transcriptomes of sRNAs of dendritic cells (DCs) using high‐throughput sequencing. Transcription abundances of sRNAs and mRNAs were analyzed by reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) assay. The associations between sRNAs and Argonaute (AGO) proteins were detected by RNA immunoprecipitation analysis. Synthesized sRNAs and locked nucleic acid (LNA) ‐modified sRNA inhibitors were used to screen the function of sRNAs in innate immune cells. The effect of sRNA on the enrichment of either chromatin remodeler or histone modification at the gene promoter was analyzed by chromatin immunoprecipitation (ChIP)‐qPCR assay. Chromatin accessibility qPCR assay was used to detect the accessibility of gene promoters. A B16 melanoma‐bearing mouse model was established to determine the function of sRNAs in tumor‐associated macrophages (TAMs) and their effect on tumor growth. Results We identified a new class of nucleus‐localized sRNAs, named snRNA/snoRNA‐derived nuclear RNAs (sdnRNAs). Some sdnRNAs were Dicer‐independent and had no association with Argonaute proteins. sdnRNA‐3, the most abundant Dicer‐independent sdnRNAs identified in our analysis, was selected as a representative to examine the biological function of sdnRNAs. sdnRNA‐3 selectively inhibited the transcription of Nos2 in macrophages during innate immune response by repressing the chromatin accessibility at Nos2 gene promoter. sdnRNA‐3 promoted the enrichments of repressive chromatin‐remodeling regulator Mi‐2β and the repressive histone modification H3K27me3 at Nos2 gene promoter. In the B16 melanoma mouse model, we found higher expression of sdnRNA‐3 in M2 TAMs than M1 TAMs and DCs. Transfer of sdnRNA‐3‐silenced macrophages inhibited tumor growth with increased expression of inducible nitric oxide synthase (iNOS) in TAMs. Conclusions Our results demonstrated that the sdnRNA‐3 repressed the transcription of Nos2 by repressing chromatin accessibility at the promoter, providing new insights into the regulation of macrophage function in tumor immunity. |
| first_indexed | 2024-12-24T05:08:50Z |
| format | Article |
| id | doaj.art-cc52601e96034dc18aba79f3ab762c69 |
| institution | Directory Open Access Journal |
| issn | 2523-3548 |
| language | English |
| last_indexed | 2024-12-24T05:08:50Z |
| publishDate | 2021-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cancer Communications |
| spelling | doaj.art-cc52601e96034dc18aba79f3ab762c692022-12-21T17:13:45ZengWileyCancer Communications2523-35482021-02-0141214015310.1002/cac2.12131Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcriptionYang Shi0Qingzhu Shi1Qicong Shen2Qian Zhang3Xuetao Cao4Institute of Immunology Zhejiang University School of Medicine Hangzhou Zhejiang 310058 P. R. ChinaInstitute of Immunology Zhejiang University School of Medicine Hangzhou Zhejiang 310058 P. R. ChinaNational Key Laboratory of Medical Immunology & Institute of Immunology Second Military Medical University Shanghai 200433 P. R. ChinaNational Key Laboratory of Medical Immunology & Institute of Immunology Second Military Medical University Shanghai 200433 P. R. ChinaInstitute of Immunology Zhejiang University School of Medicine Hangzhou Zhejiang 310058 P. R. ChinaAbstract Background Small RNAs (sRNAs) extensively mediate gene‐specific chromatin regulation in lower organisms. As a dominant type of functional sRNAs in mature mammals, microRNAs mainly regulate gene expression at post‐transcription level in the cytoplasm. Currently, whether there exists a type of nuclear‐localized sRNAs mediating gene‐specific epigenetic regulation in mature mammalian cells remains largely unclear. Here, we profiled sRNAs enriched in the nucleus and investigated their function in mediating gene‐specific epigenetic regulation in anti‐tumor immunity. Methods We established cytoplasmic and nuclear transcriptomes of sRNAs of dendritic cells (DCs) using high‐throughput sequencing. Transcription abundances of sRNAs and mRNAs were analyzed by reverse transcription‐quantitative polymerase chain reaction (RT‐qPCR) assay. The associations between sRNAs and Argonaute (AGO) proteins were detected by RNA immunoprecipitation analysis. Synthesized sRNAs and locked nucleic acid (LNA) ‐modified sRNA inhibitors were used to screen the function of sRNAs in innate immune cells. The effect of sRNA on the enrichment of either chromatin remodeler or histone modification at the gene promoter was analyzed by chromatin immunoprecipitation (ChIP)‐qPCR assay. Chromatin accessibility qPCR assay was used to detect the accessibility of gene promoters. A B16 melanoma‐bearing mouse model was established to determine the function of sRNAs in tumor‐associated macrophages (TAMs) and their effect on tumor growth. Results We identified a new class of nucleus‐localized sRNAs, named snRNA/snoRNA‐derived nuclear RNAs (sdnRNAs). Some sdnRNAs were Dicer‐independent and had no association with Argonaute proteins. sdnRNA‐3, the most abundant Dicer‐independent sdnRNAs identified in our analysis, was selected as a representative to examine the biological function of sdnRNAs. sdnRNA‐3 selectively inhibited the transcription of Nos2 in macrophages during innate immune response by repressing the chromatin accessibility at Nos2 gene promoter. sdnRNA‐3 promoted the enrichments of repressive chromatin‐remodeling regulator Mi‐2β and the repressive histone modification H3K27me3 at Nos2 gene promoter. In the B16 melanoma mouse model, we found higher expression of sdnRNA‐3 in M2 TAMs than M1 TAMs and DCs. Transfer of sdnRNA‐3‐silenced macrophages inhibited tumor growth with increased expression of inducible nitric oxide synthase (iNOS) in TAMs. Conclusions Our results demonstrated that the sdnRNA‐3 repressed the transcription of Nos2 by repressing chromatin accessibility at the promoter, providing new insights into the regulation of macrophage function in tumor immunity.https://doi.org/10.1002/cac2.12131dendritic cellsiNOSMi‐2βNos2sdnRNAsmall RNAs |
| spellingShingle | Yang Shi Qingzhu Shi Qicong Shen Qian Zhang Xuetao Cao Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription Cancer Communications dendritic cells iNOS Mi‐2β Nos2 sdnRNA small RNAs |
| title | Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription |
| title_full | Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription |
| title_fullStr | Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription |
| title_full_unstemmed | Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription |
| title_short | Dicer‐independent snRNA/snoRNA‐derived nuclear RNA 3 regulates tumor‐associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription |
| title_sort | dicer independent snrna snorna derived nuclear rna 3 regulates tumor associated macrophage function by epigenetically repressing inducible nitric oxide synthase transcription |
| topic | dendritic cells iNOS Mi‐2β Nos2 sdnRNA small RNAs |
| url | https://doi.org/10.1002/cac2.12131 |
| work_keys_str_mv | AT yangshi dicerindependentsnrnasnornaderivednuclearrna3regulatestumorassociatedmacrophagefunctionbyepigeneticallyrepressinginduciblenitricoxidesynthasetranscription AT qingzhushi dicerindependentsnrnasnornaderivednuclearrna3regulatestumorassociatedmacrophagefunctionbyepigeneticallyrepressinginduciblenitricoxidesynthasetranscription AT qicongshen dicerindependentsnrnasnornaderivednuclearrna3regulatestumorassociatedmacrophagefunctionbyepigeneticallyrepressinginduciblenitricoxidesynthasetranscription AT qianzhang dicerindependentsnrnasnornaderivednuclearrna3regulatestumorassociatedmacrophagefunctionbyepigeneticallyrepressinginduciblenitricoxidesynthasetranscription AT xuetaocao dicerindependentsnrnasnornaderivednuclearrna3regulatestumorassociatedmacrophagefunctionbyepigeneticallyrepressinginduciblenitricoxidesynthasetranscription |