1
|
Becker TJ, Enkhmandakh B, Bayarsaihan D. Single-cell RNA analysis of chromodomain-encoding genes in mesenchymal stromal cells of the mouse dental pulp. J Cell Biochem 2024. [PMID: 38779967 DOI: 10.1002/jcb.30608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The chromodomain helicase DNA-binding (CHD) and chromobox (CBX) families of proteins play crucial roles in cell fate decisions, differentiation, and cell proliferation in a broad variety of tissues and cell types. CHD proteins are ATP-dependent epigenetic enzymes actively engaged in transcriptional regulation, DNA replication, and DNA damage repair, whereas CBX proteins are transcriptional repressors mainly involved in the formation of heterochromatin. The pleiotropic effects of CHD and CBX proteins are largely dependent on their versatility to interact with other key components of the epigenetic and transcriptional machinery. Although the function and regulatory modes of CHD and CBX factors are well established in many cell types, little is known about their roles during osteogenic differentiation. A single-cell RNA-sequencing analysis of the mouse incisor dental pulp revealed distinct spatiotemporal expression patterns of CHD- and CBX-encoding genes within different clusters of mesenchymal stromal cells (MSCs) representing various stages of osteogenic differentiation. Additionally, genes encoding interaction partners of CHD and CBX proteins, such as subunits of the trithorax-COMPASS and polycomb chromatin remodeling complexes, exhibited differential co-expression behaviors within MSC subpopulations. Thus, CHD- and CBX-encoding genes show partially overlapping but distinct expression patterns in MSCs, suggesting their differential roles in osteogenic cell fate decisions.
Collapse
Affiliation(s)
- Timothy James Becker
- Department of Computer Science, Connecticut College, New London, Connecticut, USA
| | - Badam Enkhmandakh
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
- Institute for System Genomics, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
2
|
Pechanec MY, Mienaltowski MJ. Decoding the transcriptomic expression and genomic methylation patterns in the tendon proper and its peritenon region in the aging horse. BMC Res Notes 2023; 16:267. [PMID: 37821884 PMCID: PMC10566085 DOI: 10.1186/s13104-023-06562-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023] Open
Abstract
OBJECTIVES Equine tendinopathies are challenging because of the poor healing capacity of tendons commonly resulting in high re-injury rates. Within the tendon, different regions - tendon proper (TP) and peritenon (PERI) - contribute to the tendon matrix in differing capacities during injury and aging. Aged tendons have decreased repair potential; the underlying transcriptional and epigenetic changes that occur in the TP and PERI regions are not well understood. The objective of this study was to assess TP and PERI regional differences in adolescent, midlife, and geriatric horses using RNA sequencing and DNA methylation techniques. RESULTS Differences existed between TP and PERI regions of equine superficial digital flexor tendons by age as evidenced by RNASeq and DNA methylation. Cluster analysis indicated that regional distinctions existed regardless of age. Genes such as DCN, COMP, FN1, and LOX maintained elevated TP expression while genes such as GSN and AHNAK were abundant in PERI. Increased gene activity was present in adolescent and geriatric populations but decreased during midlife. Regional differences in DNA methylation were also noted. Notably, when evaluating all ages of TP against PERI, five genes (HAND2, CHD9, RASL11B, ADGRD1, and COL14A1) had regions of differential methylation as well as differential gene expression.
Collapse
Affiliation(s)
- Monica Y Pechanec
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA
| | - Michael J Mienaltowski
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA.
| |
Collapse
|
3
|
Kaken H, Wang S, Zhao W, Asihaer B, Wang L. P53 Regulates Osteogenic Differentiation Through miR-153-5p/miR-183-5p-X-Linked IAP (XIAP) Signal in Bone Marrow Mesenchymal Stem Cell (BMSC). J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study assessed P53′s role in BMSC osteogenic differentiation. Osteoporosis model was established and P53 expression in the osteogenic differentiation was detected by RT-PCR. BMSC was cultivated and transfected with siRNA followed by measuring presentation of osteogenic differentiation
was detected after cells were. The apoptotic condition of osteogenic differentiation was detected through IF method and protein analysis. The relation between P53 and miR-153-5p/miR-183-5p-XIAP signal axis was detected through bioinformatics and luciferase reporter gene assay. P53 expression
was significantly increased after osteogenic differentiation was induced. There was a binding site between P53 and miR-153-5p/miR-183-5p-XIAP signal axis. The apoptotic ability of osteoblast was enhanced after inhibition of the expression of P53. In conclusion, P53 develops crucial action
on the regulation of BMSC osteogenic differentiation through miR-153-5p/miR-183-5p-XIAP axis.
Collapse
Affiliation(s)
- Habaxi Kaken
- Department of Joint Surgery, People’s Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, China
| | - Shanshan Wang
- Department of Radiology, People’s Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, China
| | - Wei Zhao
- Department of Joint Surgery, People’s Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, China
| | - Baoerjiang. Asihaer
- Department of Joint Surgery, People’s Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, China
| | - Li Wang
- Department of Joint Surgery, People’s Hospital of Xinjiang Uygur Autonomous Region Urumqi, Xinjiang, 830001, China
| |
Collapse
|
4
|
Yi M, Wang G, Niu J, Peng M, Liu Y. Pterostilbene attenuates the proliferation and differentiation of TNF‑α‑treated human periodontal ligament stem cells. Exp Ther Med 2022; 23:304. [PMID: 35340874 PMCID: PMC8931590 DOI: 10.3892/etm.2022.11233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Min Yi
- Department of Integrative Therapy, Shanghai Huangpu District 2nd Dental Disease Prevention and Treatment Institute, Shanghai 200001, P.R. China
| | - Guanglei Wang
- Department of Stomatology, Jiading District Central Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| | - Jianhua Niu
- Department of Integrative Therapy, Shanghai Huangpu District 2nd Dental Disease Prevention and Treatment Institute, Shanghai 200001, P.R. China
| | - Minghui Peng
- Department of Integrative Therapy, Shanghai Huangpu District 2nd Dental Disease Prevention and Treatment Institute, Shanghai 200001, P.R. China
| | - Yi Liu
- Department of Stomatology, Jiading District Central Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai 201800, P.R. China
| |
Collapse
|
5
|
Cardoso AR, Lopes-Marques M, Oliveira M, Amorim A, Prata MJ, Azevedo L. Genetic Variability of the Functional Domains of Chromodomains Helicase DNA-Binding (CHD) Proteins. Genes (Basel) 2021; 12:genes12111827. [PMID: 34828433 PMCID: PMC8623811 DOI: 10.3390/genes12111827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
In the past few years, there has been an increasing neuroscientific interest in understanding the function of mammalian chromodomains helicase DNA-binding (CHD) proteins due to their association with severe developmental syndromes. Mammalian CHDs include nine members (CHD1 to CHD9), grouped into subfamilies according to the presence of specific functional domains, generally highly conserved in evolutionary terms. Mutations affecting these domains hold great potential to disrupt protein function, leading to meaningful pathogenic scenarios, such as embryonic defects incompatible with life. Here, we analysed the evolution of CHD proteins by performing a comparative study of the functional domains of CHD proteins between orthologous and paralogous protein sequences. Our findings show that the highest degree of inter-species conservation was observed at Group II (CHD3, CHD4, and CHD5) and that most of the pathological variations documented in humans involve amino acid residues that are conserved not only between species but also between paralogs. The parallel analysis of both orthologous and paralogous proteins, in cases where gene duplications have occurred, provided extra information showing patterns of flexibility as well as interchangeability between amino acid positions. This added complexity needs to be considered when the impact of novel mutations is assessed in terms of evolutionary conservation.
Collapse
Affiliation(s)
- Ana R. Cardoso
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Mónica Lopes-Marques
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Manuela Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - António Amorim
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Maria J. Prata
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Luísa Azevedo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (A.R.C.); (M.L.-M.); (M.O.); (A.A.); (M.J.P.)
- IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal
- FCUP—Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
- Correspondence:
| |
Collapse
|
6
|
Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
Collapse
Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| |
Collapse
|
7
|
Komaki S, Matsunami M, Lin JW, Lee KH, Lin YP, Lee Y, Lin SM, Igawa T. Transcriptomic Changes in Hot Spring Frog Tadpoles (Buergeria otai) in Response to Heat Stress. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.706887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Buergeria frog tadpoles exhibit high thermal tolerance and are occasionally found in water pools that temporarily exceed 40°C. With the aim of understanding how they can cope with the severe heat stress, we performed RNA-seq of three heat-treated (38°C) and three control (25°C) tadpoles and compared their transcriptomic profiles. We identified 382 differentially expressed transcripts. A protein-protein interaction (PPI) network analysis of these transcripts further identified hub proteins involved in protein degradation, stress granule assembly, and global suppression of DNA transcription and mRNA translation. Along with the avoidance behavior against high water temperature, these endurance mechanisms potentially support tadpoles to survive in high temperatures for short periods of time. Similar mechanisms may exist in many other amphibian species whose habitats are prone to high temperatures.
Collapse
|
8
|
Wu B, Feng C, Zhu C, Xu W, Yuan Y, Hu M, Yuan K, Li Y, Ren Y, Zhou Y, Jiang H, Qiu Q, Wang W, He S, Wang K. The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts. Mol Biol Evol 2021; 38:2413-2427. [PMID: 33533895 PMCID: PMC8136490 DOI: 10.1093/molbev/msab035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Endothermy is a typical convergent phenomenon which has evolved independently at least eight times in vertebrates, and is of significant advantage to organisms in extending their niches. However, how vertebrates other than mammals or birds, especially teleosts, achieve endothermy has not previously been fully understood. In this study, we sequenced the genomes of two billfishes (swordfish and sailfish), members of a representative lineage of endothermic teleosts. Convergent amino acid replacements were observed in proteins related to heat production and the visual system in two endothermic teleost lineages, billfishes and tunas. The billfish-specific genetic innovations were found to be associated with heat exchange, thermoregulation, and the specialized morphology, including elongated bill, enlarged dorsal fin in sailfish and loss of the pelvic fin in swordfish.
Collapse
Affiliation(s)
- Baosheng Wu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chenguang Feng
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.,The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chenglong Zhu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wenjie Xu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yuan Yuan
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Mingliang Hu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Ke Yuan
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yongxin Li
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yandong Ren
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Yang Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haifeng Jiang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Qiu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Wen Wang
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kun Wang
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, China
| |
Collapse
|
9
|
Yoo H, La H, Lee EJ, Choi HJ, Oh J, Thang NX, Hong K. ATP-Dependent Chromatin Remodeler CHD9 Controls the Proliferation of Embryonic Stem Cells in a Cell Culture Condition-Dependent Manner. BIOLOGY 2020; 9:biology9120428. [PMID: 33261017 PMCID: PMC7760864 DOI: 10.3390/biology9120428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/23/2022]
Abstract
Emerging evidence suggests that chromodomain-helicase-DNA-binding (CHD) proteins are involved in stem cell maintenance and differentiation via the coordination of chromatin structure and gene expression. However, the molecular function of some CHD proteins in stem cell regulation is still poorly understood. Herein, we show that Chd9 knockdown (KD) in mouse embryonic stem cells (ESCs) cultured in normal serum media, not in 2i-leukemia inhibitory factor (LIF) media, causes rapid cell proliferation. This is caused by transcriptional regulation related to the cell cycle and the response to growth factors. Our analysis showed that, unlike the serum cultured-Chd9 KD ESCs, the 2i-LIF-cultured-Chd9 KO ESCs displayed elevated levels of critical G1 phase regulators such as p21 and p27. Consistently, the DNA binding sites of CHD9 overlap with some transcription factor DNA motifs that are associated with genes regulating the cell cycle and growth pathways. These transcription factors include the cycle gene homology region (CHR), Arid5a, and LIN54. Collectively, our results provide new insights into CHD9-mediated gene transcription for controlling the cell cycle of ESCs.
Collapse
|