SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells
Abstract We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA across various cell types. Using SiCLAT, we accurately...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-01-01
|
| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-024-03463-9 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559353605226496 |
|---|---|
| author | Xin Wan Jie Kong Xiaodi Hu Lulu Liu Yuanping Yang Hu Li Gaoao Liu Xingchen Niu Fengling Chen Dan Zhang Dahai Zhu Yong Zhang |
| author_facet | Xin Wan Jie Kong Xiaodi Hu Lulu Liu Yuanping Yang Hu Li Gaoao Liu Xingchen Niu Fengling Chen Dan Zhang Dahai Zhu Yong Zhang |
| author_sort | Xin Wan |
| collection | DOAJ |
| description | Abstract We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA across various cell types. Using SiCLAT, we accurately labeled chromatin loop anchor interactions and associated gene transcription during myogenic differentiation. This imaging system offers a novel means of directly observing cis-element interactions and the corresponding gene transcription in living primary cells, thus providing real-time imaging for comprehensive mechanistic investigations of dynamic enhancer-promoter or enhancer-enhancer interactions in regulating transcription activation within living cells. |
| format | Article |
| id | doaj-art-46c0d91e8ee24f22a93875f1a156529d |
| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-46c0d91e8ee24f22a93875f1a156529d2025-01-05T12:32:00ZengBMCGenome Biology1474-760X2025-01-0126112510.1186/s13059-024-03463-9SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cellsXin Wan0Jie Kong1Xiaodi Hu2Lulu Liu3Yuanping Yang4Hu Li5Gaoao Liu6Xingchen Niu7Fengling Chen8Dan Zhang9Dahai Zhu10Yong Zhang11State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical CollegeState Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical CollegeState Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical CollegeCenter for Biomedical Technology of National Infrastructures for Translational Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases in Peking Union Medical College HospitalBioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical CollegeExperimental Center, Shandong University of Traditional Chinese MedicineCenter for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, New Cornerstone Science Laboratory, School of Life Sciences, Tsinghua UniversityExperimental Center, Shandong University of Traditional Chinese MedicineState Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical CollegeState Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical CollegeAbstract We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurrent labeling of DNA and RNA across various cell types. Using SiCLAT, we accurately labeled chromatin loop anchor interactions and associated gene transcription during myogenic differentiation. This imaging system offers a novel means of directly observing cis-element interactions and the corresponding gene transcription in living primary cells, thus providing real-time imaging for comprehensive mechanistic investigations of dynamic enhancer-promoter or enhancer-enhancer interactions in regulating transcription activation within living cells.https://doi.org/10.1186/s13059-024-03463-9CRISPR imagingNon-repetitive DNA and RNA imagingGenetic mouse modelLiving primary cell3D genomeEnhancer and promoter interaction |
| spellingShingle | Xin Wan Jie Kong Xiaodi Hu Lulu Liu Yuanping Yang Hu Li Gaoao Liu Xingchen Niu Fengling Chen Dan Zhang Dahai Zhu Yong Zhang SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells Genome Biology CRISPR imaging Non-repetitive DNA and RNA imaging Genetic mouse model Living primary cell 3D genome Enhancer and promoter interaction |
| title | SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells |
| title_full | SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells |
| title_fullStr | SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells |
| title_full_unstemmed | SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells |
| title_short | SiCLAT: simultaneous imaging of chromatin loops and active transcription in living cells |
| title_sort | siclat simultaneous imaging of chromatin loops and active transcription in living cells |
| topic | CRISPR imaging Non-repetitive DNA and RNA imaging Genetic mouse model Living primary cell 3D genome Enhancer and promoter interaction |
| url | https://doi.org/10.1186/s13059-024-03463-9 |
| work_keys_str_mv | AT xinwan siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT jiekong siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT xiaodihu siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT lululiu siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT yuanpingyang siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT huli siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT gaoaoliu siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT xingchenniu siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT fenglingchen siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT danzhang siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT dahaizhu siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells AT yongzhang siclatsimultaneousimagingofchromatinloopsandactivetranscriptioninlivingcells |