1
|
Li J, Zhao D, Zhang T, Xiong H, Hu M, Liu H, Zhao F, Sun X, Fan P, Qian Y, Wang D, Lai L, Sui T, Li Z. Precise large-fragment deletions in mammalian cells and mice generated by dCas9-controlled CRISPR/Cas3. SCIENCE ADVANCES 2024; 10:eadk8052. [PMID: 38489357 PMCID: PMC10942115 DOI: 10.1126/sciadv.adk8052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Currently, the Cas9 and Cas12a systems are widely used for genome editing, but their ability to precisely generate large chromosome fragment deletions is limited. Type I-E CRISPR mediates broad and unidirectional DNA degradation, but controlling the size of Cas3-mediated DNA deletions has proven elusive thus far. Here, we demonstrate that the endonuclease deactivation of Cas9 (dCas9) can precisely control Cas3-mediated large-fragment deletions in mammalian cells. In addition, we report the elimination of the Y chromosome and precise retention of the Sry gene in mice using CRISPR/Cas3 and dCas9-controlled CRISPR/Cas3, respectively. In conclusion, dCas9-controlled CRISPR/Cas3-mediated precise large-fragment deletion provides an approach for establishing animal models by chromosome elimination. This method also holds promise as a potential therapeutic strategy for treating fragment mutations or human aneuploidy diseases that involve additional chromosomes.
Collapse
Affiliation(s)
- Jinze Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Ding Zhao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Tao Zhang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Haoyang Xiong
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Mingyang Hu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Hongmei Liu
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Feiyu Zhao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Xiaodi Sun
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Peng Fan
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Yuqiang Qian
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Di Wang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
| | - Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Jilin University, Changchun 130062, China
| |
Collapse
|
2
|
Wenqian C, Fan W, Hu X. Genome-wide DNA methylation analysis of Hashimoto's thyroiditis during pregnancy. FEBS Open Bio 2020; 10:2780-2790. [PMID: 33113271 PMCID: PMC7714066 DOI: 10.1002/2211-5463.13018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/22/2020] [Accepted: 10/26/2020] [Indexed: 12/05/2022] Open
Abstract
Hashimoto's thyroiditis (HT) during pregnancy is usually accompanied by an elevation of thyroid‐stimulating hormone and a reduction of serum‐free thyroxine during gestation, which may lead to abortion, preterm delivery, and reduced intellectual function of the offspring. Epigenetic alterations may provide important insights into genetic–environmental interactions in HT. Here, we examined global DNA methylation patterns in patients with HT during pregnancy. DNA was extracted from 13 women with HT during pregnancy (HTDP) and eight healthy pregnant women as a control group. Genome‐wide methylation was detected with the use of an Illumina Human Methylation 850K Beadchip. A total of 652 differentially methylated positions (DMPs) and 27 differentially methylated regions (DMRs) were identified between the HTDP and control groups. GO analysis revealed that DMPs were significantly enriched in 540 GO terms, which included regulation of the differentiation of keratinocytes, T helper cell differentiation, and alpha‐beta T‐cell differentiation. Moreover, significant enrichment of KEGG pathways of the DMPs included mucin‐type O‐glycan biosynthesis, focal adhesion, and the insulin signaling pathway. The GO items associated with DMRs included muscle cell proliferation, response to biotic stimulus, anatomical structure formation involved in morphogenesis, and genes primarily involved in the FoxO signaling pathway. Finally, the DTNA gene was identified as the seed gene of functional epigenetic modules. In summary, the DNA methylation pattern of the HTDP group was distinct from that of the control group, and thus, changes in DNA methylation may influence the development of HT by regulation of the autoimmunity process.
Collapse
Affiliation(s)
- Cai Wenqian
- Eugenic Genetics Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Wenlei Fan
- Internal Medicine DEPT, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xijiang Hu
- Eugenic Genetics Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| |
Collapse
|
3
|
Cobben JM, Krzyzewska IM, Venema A, Mul AN, Polstra A, Postma AV, Smigiel R, Pesz K, Niklinski J, Chomczyk MA, Henneman P, Mannens MMAM. DNA methylation abundantly associates with fetal alcohol spectrum disorder and its subphenotypes. Epigenomics 2019; 11:767-785. [DOI: 10.2217/epi-2018-0221] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: Fetal alcohol spectrum disorder (FASD) involves prenatal growth delay, impaired facial and CNS development and causes severe clinical, social-economic burdens. Here, we aim to detect DNA-methylation aberrations associated with FASD and potential FASD diagnostic and prognostic biomarkers. Patients & methods: The FASD diagnosis was established according to golden-standard protocols in a discovery and independent replication cohort. Genome-wide differential methylation association and replication analyses were performed. Results: We identified several loci that were robustly associated with FASD or one of its sub phenotypes. Our findings were evaluated using previously reported genome-wide surveys. Conclusion: We have detected robust FASD associated differentially methylated positions and differentially methylated regions for FASD in general and for FASD subphenotypes, in other words on growth delay, impaired facial and CNS development.
Collapse
Affiliation(s)
- Jan Maarten Cobben
- Department of Pediatrics, Amsterdam University Medical Centers, Location AMC, Emma Children's Hospital, Amsterdam, The Netherlands
| | - Izabela M Krzyzewska
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Andrea Venema
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Adri N Mul
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Abeltje Polstra
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Alex V Postma
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
- Department of Anatomy, Embryology & Physiology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Robert Smigiel
- Department of Pediatrics & Rare Disorders, Medical University of Wroclaw, Poland
| | - Karolina Pesz
- Department of Genetics, Medical University of Wroclaw, Poland
| | - Jacek Niklinski
- Department of Molecular Biology, Medical University of Bialystok, Poland
| | - Monika A Chomczyk
- Department of Molecular Biology, Medical University of Bialystok, Poland
| | - Peter Henneman
- Department of Anatomy, Embryology & Physiology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Marcel MAM Mannens
- Department of Anatomy, Embryology & Physiology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| |
Collapse
|