1
|
Peng QY, An Y, Jiang ZZ, Xu Y. The Role of Immune Cells in DKD: Mechanisms and Targeted Therapies. J Inflamm Res 2024; 17:2103-2118. [PMID: 38601771 PMCID: PMC11005934 DOI: 10.2147/jir.s457526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Diabetic kidney disease (DKD), is a common microvascular complication and a major cause of death in patients with diabetes. Disorders of immune cells and immune cytokines can accelerate DKD development of in a number of ways. As the kidney is composed of complex and highly differentiated cells, the interactions among different cell types and immune cells play important regulatory roles in disease development. Here, we summarize the latest research into the molecular mechanisms underlying the interactions among various immune and renal cells in DKD. In addition, we discuss the most recent studies related to single cell technology and bioinformatics analysis in the field of DKD. The aims of our review were to explore immune cells as potential therapeutic targets in DKD and provide some guidance for future clinical treatments.
Collapse
Affiliation(s)
- Qiu-Yue Peng
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Ying An
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Zong-Zhe Jiang
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| | - Yong Xu
- Department of Endocrinology and Metabolism, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Metabolic Vascular Disease Key Laboratory of Sichuan Province, Sichuan, People’s Republic of China
- Sichuan Clinical Research Center for Nephropathy, Luzhou, Sichuan, People’s Republic of China
| |
Collapse
|
2
|
Li M, Li J, Zhang Y, Zhai Y, Chen Y, Lin L, Peng J, Zheng H, Chen J, Yan F, Lu Y. Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa. MOLECULAR PLANT PATHOLOGY 2024; 25:e13446. [PMID: 38502176 PMCID: PMC10950023 DOI: 10.1111/mpp.13446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact. Here, rice infected by rice stripe virus (RSV) was used to investigate virus-induced changes in chromatin accessibility. Our analysis identified a total of 6462 open- and 3587 closed-differentially accessible chromatin regions (DACRs) in rice under RSV infection by ATAC-seq. Additionally, by integrating ATAC-seq and RNA-seq, 349 up-regulated genes in open-DACRs and 126 down-regulated genes in closed-DACRs were identified, of which 34 transcription factors (TFs) were further identified by search of upstream motifs. Transcription levels of eight of these TFs were validated by reverse transcription-PCR. Importantly, four of these TFs (OsWRKY77, OsWRKY28, OsZFP12 and OsERF91) interacted with RSV proteins and are therefore predicted to play important roles in RSV infection. This is the first application of ATAC-seq and RNA-seq techniques to analyse changes in rice chromatin accessibility caused by RSV infection. Integrating ATAC-seq and RNA-seq provides a new approach to select candidate TFs in response to virus infection.
Collapse
Affiliation(s)
- Miaomiao Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jing Li
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yan Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yushan Zhai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Lin Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Jianping Chen
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant VirologyNingbo UniversityNingboChina
| |
Collapse
|
3
|
Cai B, Ma M, Yuan R, Zhou Z, Zhang J, Kong S, Lin D, Lian L, Li J, Zhang X, Nie Q. MYH1G-AS is a chromatin-associated lncRNA that regulates skeletal muscle development in chicken. Cell Mol Biol Lett 2024; 29:9. [PMID: 38177995 PMCID: PMC10765903 DOI: 10.1186/s11658-023-00525-x] [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: 05/16/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Skeletal muscle development is pivotal for animal growth and health. Recently, long noncoding RNAs (lncRNAs) were found to interact with chromatin through diverse roles. However, little is known about how lncRNAs act as chromatin-associated RNAs to regulate skeletal muscle development. Here, we aim to investigate the regulation of chromatin-associated RNA (MYH1G-AS) during skeletal muscle development. METHODS We provided comprehensive insight into the RNA profile and chromatin accessibility of different myofibers, combining RNA sequencing (RNA-seq) with an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). The dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay were used to analyze the transcriptional regulation mechanism of MYH1G-AS. ALKBH5-mediated MYH1G-AS N6-methyladenosine (m6A) demethylation was assessed by a single-base elongation and ligation-based qPCR amplification method (SELECT) assay. Functions of MYH1G-AS were investigated through a primary myoblast and lentivirus/cholesterol-modified antisense oligonucleotide (ASO)-mediated animal model. To validate the interaction of MYH1G-AS with fibroblast growth factor 18 (FGF18) protein, RNA pull down and an RNA immunoprecipitation (RIP) assay were performed. Specifically, the interaction between FGF18 and SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5) protein was analyzed by coimmunoprecipitation (Co-IP) and a yeast two-hybrid assay. RESULTS A total of 45 differentially expressed (DE) lncRNAs, with DE ATAC-seq peaks in their promoter region, were classified as open chromatin-associated lncRNAs. A skeletal muscle-specific lncRNA (MSTRG.15576.9; MYH1G-AS), which is one of the open chromatin-associated lncRNA, was identified. MYH1G-AS transcription is coordinately regulated by transcription factors (TF) SMAD3 and SP2. Moreover, SP2 represses ALKBH5 transcription to weaken ALKBH5-mediated m6A demethylation of MYH1G-AS, thus destroying MYH1G-AS RNA stability. MYH1G-AS accelerates myoblast proliferation but restrains myoblast differentiation. Moreover, MYH1G-AS drives a switch from slow-twitch to fast-twitch fibers and causes muscle atrophy. Mechanistically, MYH1G-AS inhibits FGF18 protein stabilization to reduce the interaction of FGF18 to SMARCA5, thus repressing chromatin accessibility of the SMAD4 promoter to activate the SMAD4-dependent pathway. CONCLUSIONS Our results reveal a new pattern of the regulation of lncRNA expression at diverse levels and help expound the regulation of m6A methylation on chromatin status.
Collapse
Affiliation(s)
- Bolin Cai
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Manting Ma
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Rongshuai Yuan
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Zhen Zhou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Jing Zhang
- Randall Centre of Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, New Hunt's House, King's College London, Guy's Campus, London, UK
| | - Shaofen Kong
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Duo Lin
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Ling Lian
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiquan Zhang
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China
| | - Qinghua Nie
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.
| |
Collapse
|
4
|
Analysis of Chromatin Openness in Testicle Tissue of Yak and Cattle-Yak. Int J Mol Sci 2022; 23:ijms232415810. [PMID: 36555451 PMCID: PMC9785434 DOI: 10.3390/ijms232415810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Cattle-yak, a crossbreed of yak and cattle, which can exhibit obvious heterosis and can adapt to the harsh environmental conditions of the Qinghai Tibet Plateau (QTP). However, F1 cattle-yak were found to be sterile because they were unable to produce sperm, which adversely restricted the fixation of heterosis. Many prior attempts have been made to decipher the mechanism underlying the spermatogenesis stagnation of cattle-yak. However, the open chromatin region (OCR) map of yak and cattle-yak testes has not been generated yet. Here, we have analyzed the OCRs landscape of testicular tissues of cattle-yak and yaks by performing ATAC-seq technology. The OCRs of cattle-yak and yak testes displayed similar genome distribution and showed priority in intergenic regions, introns and promoters. The pathway enrichment analysis indicated that the differential OCRs-related genes were involved in spermatogenesis, involving the cell cycle, as well as Hippo, mTOR, MAPK, Notch, and Wnt signaling pathways. The integration of ATAC-seq and mRNA-seq indicated that the majority of the gene expression levels were positively correlated with chromatin openness. At the same time, we have identified a number of transcription factors (TFs) related to spermatogenesis and the differential expression of these TFs may contribute to the spermatogenesis stagnation of the cattle-yak. Overall, the findings of this study provide valuable information for advancing the research related to yak crossbreeding improvement and sperm production stagnation of cattle-yak.
Collapse
|
5
|
Zhang Z, Zhang Y, Bao Q, Gu Y, Liang C, Chu M, Guo X, Bao P, Yan P. The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation. Int J Mol Sci 2022; 23:ijms23179960. [PMID: 36077381 PMCID: PMC9456067 DOI: 10.3390/ijms23179960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Although significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocytes by using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and thus revealed the unique characteristics of open chromatin during yak adipocyte differentiation. The chromatin accessibility of preadipocytes and adipocytes exhibited a similar genomic distribution, displaying a preferential location within the intergenic region, intron, and promoter. The pathway enrichment analysis identified that genes with differential chromatin accessibility were involved in adipogenic metabolism regulation pathways, such as the peroxisome proliferator activated receptor-γ (PPAR) signaling pathway, wingless-type MMTV integration site (Wnt) signaling pathway, and extracellular matrix-receptor (ECM–receptor) interaction. Integration of ATAC-seq and mRNA-seq revealed that genes with a high expression were associated with high levels of chromatin accessibility, especially within 1 kb upstream and downstream of the transcription start site. In addition, we identified a series of transcription factors (TFs) related to adipogenesis and created the TF regulatory network, providing the possible interactions between TFs during yak adipogenesis. This study is crucial for advancing the understanding of transcriptional regulatory mechanisms of adipogenesis and provides valuable information for understanding the adaptation of plateau species to high-altitude environments by maintaining whole body homeostasis through fat metabolism.
Collapse
Affiliation(s)
- Zhilong Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yongfeng Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Qi Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Yarong Gu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Pengjia Bao
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Ping Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: ; Tel.: +86-931-216-4180
| |
Collapse
|
6
|
Leung HW, Foo G, VanDongen A. Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer’s Disease. Biomedicines 2022; 10:biomedicines10081946. [PMID: 36009494 PMCID: PMC9405677 DOI: 10.3390/biomedicines10081946] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023] Open
Abstract
The immediate early gene Arc is a master regulator of synaptic function and a critical determinant of memory consolidation. Here, we show that Arc interacts with dynamic chromatin and closely associates with histone markers for active enhancers and transcription in cultured rat hippocampal neurons. Both these histone modifications, H3K27Ac and H3K9Ac, have recently been shown to be upregulated in late-onset Alzheimer’s disease (AD). When Arc induction by pharmacological network activation was prevented using a short hairpin RNA, the expression profile was altered for over 1900 genes, which included genes associated with synaptic function, neuronal plasticity, intrinsic excitability, and signalling pathways. Interestingly, about 100 Arc-dependent genes are associated with the pathophysiology of AD. When endogenous Arc expression was induced in HEK293T cells, the transcription of many neuronal genes was increased, suggesting that Arc can control expression in the absence of activated signalling pathways. Taken together, these data establish Arc as a master regulator of neuronal activity-dependent gene expression and suggest that it plays a significant role in the pathophysiology of AD.
Collapse
Affiliation(s)
| | - Gabriel Foo
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antonius VanDongen
- Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
- Correspondence:
| |
Collapse
|
7
|
Bauleo A, Montesanto A, Pace V, Brando R, De Stefano L, Puntorieri D, Cento L, Loddo S, Calacci C, Novelli A, Falcone E. Rare copy number variants in ASTN2 gene in patients with neurodevelopmental disorders. Psychiatr Genet 2021; 31:239-245. [PMID: 34412080 DOI: 10.1097/ypg.0000000000000296] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION In humans the normal development of cortical regions depends on the complex interactions between a number of proteins that promote the migrations of neuronal precursors from germinal zones and assembly into neuronal laminae. ASTN2 is one of the proteins implicated in such a complex process. Recently it has been observed that ASTN2 also regulates the surface expression of multiple synaptic proteins resulting in a modulation of synaptic activity. Several rare copy number variants (CNVs) in ASTN2 gene were identified in patients with neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), attention deficit-hyperactivity disorders and intellectual disability. METHODS By using comparative genomic hybridization array technology, we analyzed the genomic profiles of five patients of three unrelated families with NDDs. Clinical diagnosis of ASD was established according to the Statistical Manual of Mental Disorders, Fifth Edition (APA 2013) criteria. RESULTS We identified new rare CNVs encompassing ASTN2 gene in three unrelated families with different clinical phenotypes of NDDs. In particular, we identified a deletion of about 70 Kb encompassing intron 19, a 186 Kb duplication encompassing the sequence between the 5'-end and the first intron of the gene and a 205 Kb deletion encompassing exons 6-11. CONCLUSION The CNVs reported here involve regions not usually disrupted in patients with NDDs with two of them affecting only the expression of the long isoforms. Further studies will be needed to analyze the impact of these CNVs on gene expression regulation and to better understand their impact on the protein function.
Collapse
Affiliation(s)
- Alessia Bauleo
- BIOGENET, Medical and Forensic Genetics Laboratory, Cosenza
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende
| | - Vincenza Pace
- BIOGENET, Medical and Forensic Genetics Laboratory, Cosenza
| | | | | | - Domenica Puntorieri
- Dipartimento Materno Infantile Neuropsichiatria Infanzia e Adolescenza Rossano - Cariati, Azienda Sanitaria Provinciale di Cosenza, Cosenza
| | - Luca Cento
- Translational Cytogenomics Research Unit, Associazione Equilibri Pedagogici, Studio Pedagogico Interdisciplinare, Reggio Calabria
| | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Calacci
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elena Falcone
- BIOGENET, Medical and Forensic Genetics Laboratory, Cosenza
| |
Collapse
|
8
|
Kuppe C, Perales-Patón J, Saez-Rodriguez J, Kramann R. Experimental and computational technologies to dissect the kidney at the single-cell level. Nephrol Dial Transplant 2020; 37:628-637. [PMID: 33332571 DOI: 10.1093/ndt/gfaa233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Indexed: 02/06/2023] Open
Abstract
The field of single-cell technologies, in particular single-cell genomics with transcriptomics and epigenomics, and most recently single-cell proteomics, is rapidly growing and holds promise to advance our understanding of organ homoeostasis and disease, and facilitate the identification of novel therapeutic targets and biomarkers. This review offers an introduction to these technologies. In addition, as the size and complexity of the data require sophisticated computational methods for analysis and interpretation, we will also provide an overview of these methods and summarize the single-cell literature specifically pertaining to the kidney.
Collapse
Affiliation(s)
- Christoph Kuppe
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Javier Perales-Patón
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany
- Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Rafael Kramann
- Division of Nephrology, RWTH Aachen University, Aachen, Germany
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands
| |
Collapse
|
9
|
Halstead MM, Kern C, Saelao P, Wang Y, Chanthavixay G, Medrano JF, Van Eenennaam AL, Korf I, Tuggle CK, Ernst CW, Zhou H, Ross PJ. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC Genomics 2020; 21:698. [PMID: 33028202 PMCID: PMC7541309 DOI: 10.1186/s12864-020-07078-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/17/2020] [Indexed: 12/25/2022] Open
Abstract
Background Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues. Results Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions. Conclusions The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.
Collapse
Affiliation(s)
- Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Colin Kern
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Perot Saelao
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ying Wang
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ganrea Chanthavixay
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Juan F Medrano
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | | | - Ian Korf
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | | | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, 48824, MI, USA
| | - Huaijun Zhou
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA.
| |
Collapse
|
10
|
Corless S, Höcker S, Erhardt S. Centromeric RNA and Its Function at and Beyond Centromeric Chromatin. J Mol Biol 2020; 432:4257-4269. [DOI: 10.1016/j.jmb.2020.03.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/21/2022]
|
11
|
Kuhn TM, Capelson M. Nuclear Pore Proteins in Regulation of Chromatin State. Cells 2019; 8:cells8111414. [PMID: 31717499 PMCID: PMC6912232 DOI: 10.3390/cells8111414] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/31/2022] Open
Abstract
Nuclear pore complexes (NPCs) are canonically known to regulate nucleocytoplasmic transport. However, research efforts over the last decade have demonstrated that NPCs and their constituent nucleoporins (Nups) also interact with the genome and perform important roles in regulation of gene expression. It has become increasingly clear that many Nups execute these roles specifically through regulation of chromatin state, whether through interactions with histone modifiers and downstream changes in post-translational histone modifications, or through relationships with chromatin-remodeling proteins that can result in physical changes in nucleosome occupancy and chromatin compaction. This review focuses on these findings, highlighting the functional connection between NPCs/Nups and regulation of chromatin structure, and how this connection can manifest in regulation of transcription.
Collapse
|
12
|
Sun Y, Miao N, Sun T. Detect accessible chromatin using ATAC-sequencing, from principle to applications. Hereditas 2019; 156:29. [PMID: 31427911 PMCID: PMC6696680 DOI: 10.1186/s41065-019-0105-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023] Open
Abstract
Background Chromatin accessibility is crucial for gene expression regulation in specific cells and in multiple biological processes. Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is an effective way to reveal chromatin accessibility at a genome-wide level. Through ATAC-seq, produced reads from a small number of cells reflect accessible regions that correspond to nucleosome positioning and transcription factor binding sites, due to probing hyperactive Tn5 transposase to DNA sequence. Conclusion In this review, we summarize both principle and features of ATAC-seq, highlight its applications in basic and clinical research. ATAC-seq has generated comprehensive chromatin accessible maps, and is becoming a powerful tool to understand dynamic gene expression regulation in stem cells, early embryos and tumors.
Collapse
Affiliation(s)
- Yuanyuan Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 Fujian China
| | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 Fujian China
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 Fujian China
| |
Collapse
|
13
|
P311, a novel intrinsically disordered protein, regulates adipocyte development. Biochem Biophys Res Commun 2019; 515:234-240. [PMID: 31146912 PMCID: PMC6561663 DOI: 10.1016/j.bbrc.2019.05.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
Adipocyte development and adipose tissue expansion have many implications for human diseases, including obesity. Obesity is a debilitating disorder and a risk factor for metabolic disorders including insulin resistance and diabetes mellitus, due in part to an overabundance of adipocytes and adipocyte dysfunction. In recent years, obesity has become a global pandemic with approximately one-third of US adults classified as obese. Adipose tissue has recently been identified as a major metabolic organ, classified into white adipose tissue (WAT) and brown adipose tissue (BAT). Other than lifestyle modifications and invasive surgeries, only a very limited number of drugs are available to treat obesity and overweight. P311 has been shown to play a key role in blood pressure regulation, vascular contractility and tissue remodeling. Here we present a role for P311 in adipogenesis using a 3T3-L1 cell culture model. P311 expression is initiated with the induction of adipogenesis and increased during adipogenesis. This increase correlates with an increase in the expression of the key adipogenic transcriptional factors PPARγ2 and C/EBPα. In addition, siRNA-mediated P311 knockdown inhibits adipogenic differentiation in 3T3-L1 cells. Finally, P311 binds to the PPARγ2 promoter, implicating P311 mediates adipogenesis partly through PPARγ activation.
Collapse
|