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Li J, Lin Y, Li D, He M, Kui H, Bai J, Chen Z, Gou Y, Zhang J, Wang T, Tang Q, Kong F, Jin L, Li M. Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305706. [PMID: 38582509 PMCID: PMC11200017 DOI: 10.1002/advs.202305706] [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: 08/15/2023] [Revised: 03/07/2024] [Indexed: 04/08/2024]
Abstract
Haplotype-resolved 3D chromatin architecture related to allelic differences in avian skeletal muscle development has not been addressed so far, although chicken husbandry for meat consumption has been prevalent feature of cultures on every continent for more than thousands of years. Here, high-resolution Hi-C diploid maps (1.2-kb maximum resolution) are generated for skeletal muscle tissues in chicken across three developmental stages (embryonic day 15 to day 30 post-hatching). The sequence features governing spatial arrangement of chromosomes and characterize homolog pairing in the nucleus, are identified. Multi-scale characterization of chromatin reorganization between stages from myogenesis in the fetus to myofiber hypertrophy after hatching show concordant changes in transcriptional regulation by relevant signaling pathways. Further interrogation of parent-of-origin-specific chromatin conformation supported that genomic imprinting is absent in birds. This study also reveals promoter-enhancer interaction (PEI) differences between broiler and layer haplotypes in skeletal muscle development-related genes are related to genetic variation between breeds, however, only a minority of breed-specific variations likely contribute to phenotypic divergence in skeletal muscle potentially via allelic PEI rewiring. Beyond defining the haplotype-specific 3D chromatin architecture in chicken, this study provides a rich resource for investigating allelic regulatory divergence among chicken breeds.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Yu Lin
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Diyan Li
- School of PharmacyChengdu UniversityChengdu610106China
| | - Mengnan He
- Wildlife Conservation Research DepartmentChengdu Research Base of Giant Panda BreedingChengdu610057China
| | - Hua Kui
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Jingyi Bai
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Ziyu Chen
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Yuwei Gou
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Jiaman Zhang
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Tao Wang
- School of PharmacyChengdu UniversityChengdu610106China
| | - Qianzi Tang
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Fanli Kong
- College of Life ScienceSichuan Agricultural UniversityYa'an625014China
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding IndustryCollege of Animal Science and TechnologySichuan Agricultural UniversityChengdu611130China
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2
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Fu W, Liao Q, Shi Y, Liu W, Ren H, Xu C, Zeng C. Transient induction of actin cytoskeletal remodeling associated with dedifferentiation, proliferation, and redifferentiation stimulates cardiac regeneration. Acta Pharm Sin B 2024; 14:2537-2553. [PMID: 38828141 PMCID: PMC11143747 DOI: 10.1016/j.apsb.2024.01.021] [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: 11/02/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 06/05/2024] Open
Abstract
The formation of new and functional cardiomyocytes requires a 3-step process: dedifferentiation, proliferation, and redifferentiation, but the critical genes required for efficient dedifferentiation, proliferation, and redifferentiation remain unknown. In our study, a circular trajectory using single-nucleus RNA sequencing of the pericentriolar material 1 positive (PCM1+) cardiomyocyte nuclei from hearts 1 and 3 days after surgery-induced myocardial infarction (MI) on postnatal Day 1 was reconstructed and demonstrated that actin remodeling contributed to the dedifferentiation, proliferation, and redifferentiation of cardiomyocytes after injury. We identified four top actin-remodeling regulators, namely Tmsb4x, Tmsb10, Dmd, and Ctnna3, which we collectively referred to as 2D2P. Transiently expressed changes of 2D2P, using a polycistronic non-integrating lentivirus driven by Tnnt2 (cardiac-specific troponin T) promoters (Tnnt2-2D2P-NIL), efficiently induced transiently proliferative activation and actin remodeling in postnatal Day 7 cardiomyocytes and adult hearts. Furthermore, the intramyocardial delivery of Tnnt2-2D2P-NIL resulted in a sustained improvement in cardiac function without ventricular dilatation, thickened septum, or fatal arrhythmia for at least 4 months. In conclusion, this study highlights the importance of actin remodeling in cardiac regeneration and provides a foundation for new gene-cocktail-therapy approaches to improve cardiac repair and treat heart failure using a novel transient and cardiomyocyte-specific viral construct.
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Affiliation(s)
- Wenbin Fu
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Qiao Liao
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Yu Shi
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Wujian Liu
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Hongmei Ren
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Chunmei Xu
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, the Third Military Medical University (Army Medical University), Chongqing 400042, China
- Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China, Chongqing 400042, China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, China
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, the Third Military Medical University, Chongqing 400042, China
- Cardiovascular Research Center, Chongqing College, University of Chinese Academy of Sciences, Chongqing 400042, China
- State Key Laboratory of Trauma and Chemical Poisoning, Chongqing 400042, China
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3
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Hang M, Tse MCL, Pang BPS, Bi X, Jin F, Lee CW, Wong AOL, Chan CB. Differential regulation of hepatic SH3 domain binding kinase 1 (SBK1) expression in mouse and goldfish. Gen Comp Endocrinol 2023; 344:114372. [PMID: 37652166 DOI: 10.1016/j.ygcen.2023.114372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
SH3 domain binding kinase 1 (SBK1) is a serine/threonine kinase that belongs to the new kinase family (NFK) with limited information on its function. Previous studies reported that SBK1 plays a role in memory formation, lipid metabolism, and cancer cell progression. Nevertheless, the regulatory mechanism of Sbk1 expression in various tissues remains unknown. We report here that Sbk1 expression in mouse hepatocytes was downregulated by glucocorticoid, whereas saturated and unsaturated fatty acids were stimulators of Sbk1 expression. The regulatory role of glucocorticoid and fatty acid was further confirmed by the Sbk1 promoter assay, which aligned with the presence of several glucocorticoid-response elements (GRE) and peroxisome proliferator responsive elements (PPRE) in the mouse Sbk1 promoter. The inhibitory effect of glucocorticoids on hepatic Sbk1 expression and protein content could also be demonstrated in vivo after prednisolone injection. Moreover, the expression of SBK1 in goldfish (gfSBK1) was also sensitive to glucocorticoid suppression as their mouse orthologues. In contrast, insulin had a differential action on SBK1 expression that it promoted the expression of all SBK1 isoforms in the goldfish hepatocytes but inhibited Sbk1 expression in the mouse hepatocytes. Together, our findings indicate that SBK1 expression is hormone- and nutrient-sensitive with a species-specific response.
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Affiliation(s)
- Miaojia Hang
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Margaret Chui Ling Tse
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Brian Pak Shing Pang
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Xinyi Bi
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Fanming Jin
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Chi Wai Lee
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Anderson O L Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Chi Bun Chan
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region.
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4
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Sweat ME, Cao Y, Zhang X, Burnicka-Turek O, Perez-Cervantes C, Arulsamy K, Lu F, Keating EM, Akerberg BN, Ma Q, Wakimoto H, Gorham JM, Hill LD, Kyoung Song M, Trembley MA, Wang P, Gianeselli M, Prondzynski M, Bortolin RH, Bezzerides VJ, Chen K, Seidman JG, Seidman CE, Moskowitz IP, Pu WT. Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network. NATURE CARDIOVASCULAR RESEARCH 2023; 2:881-898. [PMID: 38344303 PMCID: PMC10854392 DOI: 10.1038/s44161-023-00334-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/21/2023] [Indexed: 02/15/2024]
Abstract
Understanding how the atrial and ventricular heart chambers maintain distinct identities is a prerequisite for treating chamber-specific diseases. Here, we selectively knocked out (KO) the transcription factor Tbx5 in the atrial working myocardium to evaluate its requirement for atrial identity. Atrial Tbx5 inactivation downregulated atrial cardiomyocyte (aCM) selective gene expression. Using concurrent single nucleus transcriptome and open chromatin profiling, genomic accessibility differences were identified between control and Tbx5 KO aCMs, revealing that 69% of the control-enriched ATAC regions were bound by TBX5. Genes associated with these regions were downregulated in KO aCMs, suggesting they function as TBX5-dependent enhancers. Comparing enhancer chromatin looping using H3K27ac HiChIP identified 510 chromatin loops sensitive to TBX5 dosage, and 74.8% of control-enriched loops contained anchors in control-enriched ATAC regions. Together, these data demonstrate TBX5 maintains the atrial gene expression program by binding to and preserving the tissue-specific chromatin architecture of atrial enhancers.
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Affiliation(s)
- Mason E Sweat
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Yangpo Cao
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Ozanna Burnicka-Turek
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Carlos Perez-Cervantes
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Kulandai Arulsamy
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Fujian Lu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Erin M Keating
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren D Hill
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Mi Kyoung Song
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Michael A Trembley
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Peizhe Wang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Matteo Gianeselli
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | | | - Raul H Bortolin
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Vassilios J Bezzerides
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Kaifu Chen
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
| | - Jonathan G Seidman
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Christine E Seidman
- Department of Pediatrics, Pathology, and Human Genetics, The University of Chicago, Chicago, IL
| | - Ivan P Moskowitz
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA 02115
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5
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Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D’Eustachio P, Wu G. Illuminating Dark Proteins using Reactome Pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543335. [PMID: 37333417 PMCID: PMC10274615 DOI: 10.1101/2023.06.05.543335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Limited knowledge about a substantial portion of protein coding genes, known as "dark" proteins, hinders our understanding of their functions and potential therapeutic applications. To address this, we leveraged Reactome, the most comprehensive, open source, open-access pathway knowledgebase, to contextualize dark proteins within biological pathways. By integrating multiple resources and employing a random forest classifier trained on 106 protein/gene pairwise features, we predicted functional interactions between dark proteins and Reactome-annotated proteins. We then developed three scores to measure the interactions between dark proteins and Reactome pathways, utilizing enrichment analysis and fuzzy logic simulations. Correlation analysis of these scores with an independent single-cell RNA sequencing dataset provided supporting evidence for this approach. Furthermore, systematic natural language processing (NLP) analysis of over 22 million PubMed abstracts and manual checking of the literature associated with 20 randomly selected dark proteins reinforced the predicted interactions between proteins and pathways. To enhance the visualization and exploration of dark proteins within Reactome pathways, we developed the Reactome IDG portal, deployed at https://idg.reactome.org, a web application featuring tissue-specific protein and gene expression overlay, as well as drug interactions. Our integrated computational approach, together with the user-friendly web platform, offers a valuable resource for uncovering potential biological functions and therapeutic implications of dark proteins.
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Affiliation(s)
| | - Nasim Sanati
- Oregon Health & Science University, Portland, OR 97239, USA
| | | | - Robin Haw
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Deidre Beavers
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Solomon Shorser
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Guilherme Viteri
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Patrick Conley
- Oregon Health & Science University, Portland, OR 97239, USA
| | - Karen Rothfels
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A1, Canada
| | | | - Guanming Wu
- Oregon Health & Science University, Portland, OR 97239, USA
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6
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Sweat ME, Cao Y, Zhang X, Burnicka-Turek O, Perez-Cervantes C, Akerberg BN, Ma Q, Wakimoto H, Gorham JM, Song MK, Trembley MA, Wang P, Lu F, Gianeselli M, Prondzynski M, Bortolin RH, Seidman JG, Seidman CE, Moskowitz IP, Pu WT. Tbx5 maintains atrial identity by regulating an atrial enhancer network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.21.537535. [PMID: 37131696 PMCID: PMC10153240 DOI: 10.1101/2023.04.21.537535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding how the atrial and ventricular chambers of the heart maintain their distinct identity is a prerequisite for treating chamber-specific diseases. Here, we selectively inactivated the transcription factor Tbx5 in the atrial working myocardium of the neonatal mouse heart to show that it is required to maintain atrial identity. Atrial Tbx5 inactivation downregulated highly chamber specific genes such as Myl7 and Nppa , and conversely, increased the expression of ventricular identity genes including Myl2 . Using combined single nucleus transcriptome and open chromatin profiling, we assessed genomic accessibility changes underlying the altered atrial identity expression program, identifying 1846 genomic loci with greater accessibility in control atrial cardiomyocytes compared to KO aCMs. 69% of the control-enriched ATAC regions were bound by TBX5, demonstrating a role for TBX5 in maintaining atrial genomic accessibility. These regions were associated with genes that had higher expression in control aCMs compared to KO aCMs, suggesting they act as TBX5-dependent enhancers. We tested this hypothesis by analyzing enhancer chromatin looping using HiChIP and found 510 chromatin loops that were sensitive to TBX5 dosage. Of the loops enriched in control aCMs, 73.7% contained anchors in control-enriched ATAC regions. Together, these data demonstrate a genomic role for TBX5 in maintaining the atrial gene expression program by binding to atrial enhancers and preserving tissue-specific chromatin architecture of atrial enhancers.
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