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Wu D, Wang S, Hai C, Wang L, Pei D, Bai C, Su G, Liu X, Zhao Y, Liu Z, Yang L, Li G. The Effect of MSTN Mutation on Bile Acid Metabolism and Lipid Metabolism in Cattle. Metabolites 2023; 13:836. [PMID: 37512543 PMCID: PMC10384915 DOI: 10.3390/metabo13070836] [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: 03/30/2023] [Revised: 06/29/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Myostatin (MSTN) is a negative regulator of skeletal muscle genesis during development. MSTN mutation leads to increased lean meat production and reduced fat deposition in livestock. However, the mechanism by which MSTN promotes myogenesis by regulating metabolism is not clear. In this study, we compared the metabolomics of the livers of wild-type (WT) and MSTN mutation cattle (MT), and found changes in the content and proportion of fatty acids and bile acids in MT cattle. The differential metabolites were enriched in sterol synthesis and primary bile acid synthesis. We further analyzed the expression of genes involved in the regulation of lipid and bile acid metabolism, and found that the loss of MSTN may alter lipid synthesis and bile acid metabolism. This study provides new basic data for MSTN mutations in beef cattle breeding.
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Affiliation(s)
- Di Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Song Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Chao Hai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Linfeng Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Dongchao Pei
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Xuefei Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Yuefang Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Lei Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot 010021, China
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Sun T, Pei S, Liu Y, Hanif Q, Xu H, Chen N, Lei C, Yue X. Whole genome sequencing of simmental cattle for SNP and CNV discovery. BMC Genomics 2023; 24:179. [PMID: 37020271 PMCID: PMC10077681 DOI: 10.1186/s12864-023-09248-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
BACKGROUD The single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) are two major genomic variants, which play crucial roles in evolutionary and phenotypic diversity. RESULTS In this study, we performed a comprehensive analysis to explore the genetic variations (SNPs and CNVs) of high sperm motility (HSM) and poor sperm motility (PSM) Simmental bulls using the high-coverage (25×) short-read next generation sequencing and single-molecule long reads sequencing data. A total of ~ 15 million SNPs and 2,944 CNV regions (CNVRs) were detected in Simmental bulls, and a set of positive selected genes (PSGs) and CNVRs were found to be overlapped with quantitative trait loci (QTLs) involving immunity, muscle development, reproduction, etc. In addition, we detected two new variants in LEPR, which may be related to the artificial breeding to improve important economic traits. Moreover, a set of genes and pathways functionally related to male fertility were identified. Remarkably, a CNV on SPAG16 (chr2:101,427,468 - 101,429,883) was completely deleted in all poor sperm motility (PSM) bulls and half of the bulls in high sperm motility (HSM), which may play a crucial role in the bull-fertility. CONCLUSIONS In conclusion, this study provides a valuable genetic variation resource for the cattle breeding and selection programs.
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Affiliation(s)
- Ting Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710062, China
| | - Shengwei Pei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Yangkai Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, College of Pastoral Agriculture Science and Technology, Ministry of Education, Lanzhou University, Lanzhou, 730020, P. R. China.
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3
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Lin H, Ma X, Sun Y, Peng H, Wang Y, Thomas SS, Hu Z. Decoding the transcriptome of denervated muscle at single-nucleus resolution. J Cachexia Sarcopenia Muscle 2022; 13:2102-2117. [PMID: 35726356 PMCID: PMC9398230 DOI: 10.1002/jcsm.13023] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 02/18/2022] [Accepted: 05/09/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Skeletal muscle exhibits remarkable plasticity under both physiological and pathological conditions. One major manifestation of this plasticity is muscle atrophy that is an adaptive response to catabolic stimuli. Because the heterogeneous transcriptome responses to catabolism in different types of muscle cells are not fully characterized, we applied single-nucleus RNA sequencing (snRNA-seq) to unveil muscle atrophy related transcriptional changes at single nucleus resolution. METHODS Using a sciatic denervation mouse model of muscle atrophy, snRNA-seq was performed to generate single-nucleus transcriptional profiles of the gastrocnemius muscle from normal and denervated mice. Various bioinformatics analyses, including unsupervised clustering, functional enrichment analysis, trajectory analysis, regulon inference, metabolic signature characterization and cell-cell communication prediction, were applied to illustrate the transcriptome changes of the individual cell types. RESULTS A total of 29 539 muscle nuclei (normal vs. denervation: 15 739 vs. 13 800) were classified into 13 nuclear types according to the known cell markers. Among these, the type IIb myonuclei were further divided into two subgroups, which we designated as type IIb1 and type IIb2 myonuclei. In response to denervation, the proportion of type IIb2 myonuclei increased sharply (78.12% vs. 38.45%, P < 0.05). Concomitantly, trajectory analysis revealed that denervated type IIb2 myonuclei clearly deviated away from the normal type IIb2 myonuclei, indicating that this subgroup underwent robust transcriptional reprogramming upon denervation. Signature genes in denervated type IIb2 myonuclei included Runx1, Gadd45a, Igfn1, Robo2, Dlg2, and Sh3d19 (P < 0.001). The gene regulatory network analysis captured a group of atrophy-related regulons (Foxo3, Runx1, Elk4, and Bhlhe40) whose activities were enhanced (P < 0.01), especially in the type IIb2 myonuclei. The metabolic landscape in the myonuclei showed that most of the metabolic pathways were down-regulated by denervation (P < 0.001), while some of the metabolic signalling, such as glutathione metabolism, was specifically activated in the denervated type IIb2 myonulei. We also investigated the transcriptomic alterations in the type I myofibres, muscle stem cells, fibro-adipogenic progenitors, macrophages, endothelial cells and pericytes and characterized their signature responses to denervation. By predicting the cell-cell interactions, we observed that the communications between myofibres and muscle resident cells were diminished by denervation. CONCLUSIONS Our results define the myonuclear transition, metabolic remodelling, and gene regulation networks reprogramming associated with denervation-induced muscle atrophy and illustrate the molecular basis of the heterogeneity and plasticity of muscle cells in response to catabolism. These results provide a useful resource for exploring the molecular mechanism of muscle atrophy.
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Affiliation(s)
- Hongchun Lin
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xinxin Ma
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yuxiang Sun
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hui Peng
- Nephrology Division, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yanlin Wang
- Division of Nephrology, Department of Medicine, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Sandhya Sara Thomas
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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Yang M, Chen J, Li X, Huang J, Wang Q, Wang S, Wei S, Qin Q. The transcription factor NFYC positively regulates expression of MHCIa in the red-spotted grouper (Epinephelus akaara). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104272. [PMID: 34600022 DOI: 10.1016/j.dci.2021.104272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/09/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Mammalian studies have shown that the nuclear transcription factor Y (NFYC) regulates the expression of major histocompatibility complex (MHC) by binding to CCAAT-box on promoters. However, few studies have focused on the regulatory mechanisms of NFYC in MHC pathway in fish. To explore the transcriptional regulatory mechanism of MHCIa in fish, we characterized NFYC and MHCIa of red-spotted grouper (Epinephelus akaara) (named EaNFYC and EaMHCIa, respectively). The EaNFYC genome sequence is 13,796 bp and contains 1,065 bp open reading frame. It is composed of ten exons and nine introns and encode a 354 amino acid sequence. The putative EaNFYC protein sequence shared 67.2-99.4% identity to vertebrate NFYC and possesses a typically conserved domain (histone- or haem-associated protein 5 domain (HAP5)) at the N-terminus. Transcripts of both EaNFYC and EaMHCIa were ubiquitously expressed in all detect tissues, and higher mRNA levels were detected in immune-relevant tissues (middle-kidney). EaNFYC expression increased after treatment with polyinosinic: polycytidylic acid, lipopolysaccharide, nervous necrosis virus, zymosan A, and Singapore grouper iridovirus. Analysis of subcellular localization indicated that EaNFYC was localized at the cell nucleus only. Furthermore, overexpression of EaNFYC significantly stimulated the expression of EaMHCIa, interferon signalling molecules and inflammatory cytokine. The region -878 bp to +82 bp of EaMHCIa promoter was identified to be the core promoter which EaNFYC take effect on. Additionally, point mutations and electrophoretic mobility shift assays verified that NFYC activate MHCIa expression by binding at the M1 and M2 binding sites that do not contain CCAAT-box. These results contribute to elucidating the function of fish NFYC on MHC transcriptional mechanisms, and provide the first evidence of positive regulation of MHCIa expression by NFYC in fish.
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Affiliation(s)
- Min Yang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Jinpeng Chen
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xinshuai Li
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jianling Huang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qing Wang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shaowen Wang
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shina Wei
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Qiwei Qin
- University JointLaboratory of Guangdong Province, Hong Kong and Macao Region on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai 519000, China
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Esposito P, Picciotto D, Battaglia Y, Costigliolo F, Viazzi F, Verzola D. Myostatin: Basic biology to clinical application. Adv Clin Chem 2022; 106:181-234. [PMID: 35152972 DOI: 10.1016/bs.acc.2021.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Myostatin is a member of the transforming growth factor (TGF)-β superfamily. It is expressed by animal and human skeletal muscle cells where it limits muscle growth and promotes protein breakdown. Its effects are influenced by complex mechanisms including transcriptional and epigenetic regulation and modulation by extracellular binding proteins. Due to its actions in promoting muscle atrophy and cachexia, myostatin has been investigated as a promising therapeutic target to counteract muscle mass loss in experimental models and patients affected by different muscle-wasting conditions. Moreover, growing evidence indicates that myostatin, beyond to regulate skeletal muscle growth, may have a role in many physiologic and pathologic processes, such as obesity, insulin resistance, cardiovascular and chronic kidney disease. In this chapter, we review myostatin biology, including intracellular and extracellular regulatory pathways, and the role of myostatin in modulating physiologic processes, such as muscle growth and aging. Moreover, we discuss the most relevant experimental and clinical evidence supporting the extra-muscle effects of myostatin. Finally, we consider the main strategies developed and tested to inhibit myostatin in clinical trials and discuss the limits and future perspectives of the research on myostatin.
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Affiliation(s)
- Pasquale Esposito
- Clinica Nefrologica, Dialisi, Trapianto, Department of Internal Medicine, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genova, Italy.
| | - Daniela Picciotto
- Clinica Nefrologica, Dialisi, Trapianto, Department of Internal Medicine, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Yuri Battaglia
- Nephrology and Dialysis Unit, St. Anna University Hospital, Ferrara, Italy
| | - Francesca Costigliolo
- Clinica Nefrologica, Dialisi, Trapianto, Department of Internal Medicine, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Francesca Viazzi
- Clinica Nefrologica, Dialisi, Trapianto, Department of Internal Medicine, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Daniela Verzola
- Clinica Nefrologica, Dialisi, Trapianto, Department of Internal Medicine, University of Genoa and IRCCS Ospedale Policlinico San Martino, Genova, Italy
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Lim H, Xie L. A New Weighted Imputed Neighborhood-Regularized Tri-Factorization One-Class Collaborative Filtering Algorithm: Application to Target Gene Prediction of Transcription Factors. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:126-137. [PMID: 31995498 PMCID: PMC7382975 DOI: 10.1109/tcbb.2020.2968442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Identifying target genes of transcription factors (TFs) is crucial to understand transcriptional regulation. However, our understanding of genome-wide TF targeting profile is limited due to the cost of large-scale experiments and intrinsic complexity of gene regulation. Thus, computational prediction methods are useful to predict unobserved TF-gene associations. Here, we develop a new Weighted Imputed Neighborhood-regularized Tri-Factorization one-class collaborative filtering algorithm, WINTF. It predicts unobserved target genes for TFs using known but noisy, incomplete, and biased TF-gene associations and protein-protein interaction networks. Our benchmark study shows that WINTF significantly outperforms its counterpart matrix factorization-based algorithms and tri-factorization methods that do not include weight, imputation, and neighbor-regularization, for TF-gene association prediction. When evaluated by independent datasets, accuracy is 37.8 percent on the top 495 predicted associations, an enrichment factor of 4.19 compared with random guess. Furthermore, many predicted novel associations are supported by literature evidence. Although we only use canonical TF-gene interaction data, WINTF can directly be applied to tissue-specific data when available. Thus, WINTF provides a potentially useful framework to integrate multiple omics data for further improvement of TF-gene prediction and applications to other sparse and noisy biological data. The benchmark dataset and source code are freely available at https://github.com/XieResearchGroup/WINTF.
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Paul S, Zhang X, He JQ. Homeobox gene Meis1 modulates cardiovascular regeneration. Semin Cell Dev Biol 2019; 100:52-61. [PMID: 31623926 DOI: 10.1016/j.semcdb.2019.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Regeneration of cardiomyocytes, endothelial cells and vascular smooth muscle cells (three major lineages of cardiac tissues) following myocardial infarction is the critical step to recover the function of the damaged heart. Myeloid ecotropic viral integration site 1 (Meis1) was first discovered in leukemic mice in 1995 and its biological function has been extensively studied in leukemia, hematopoiesis, the embryonic pattering of body axis, eye development and various genetic diseases, such as restless leg syndrome. It was found that Meis1 is highly associated with Hox genes and their cofactors to exert its regulatory effects on multiple intracellular signaling pathways. Recently with the advent of bioinformatics, biochemical methods and advanced genetic engineering tools, new function of Meis1 has been found to be involved in the cell cycle regulation of cardiomyocytes and endothelial cells. For example, inhibition of Meis1 expression increases the proliferative capacity of neonatal mouse cardiomyocytes, whereas overexpression of Meis1 results in the reduction in the length of cardiomyocyte proliferative window. Interestingly, downregulation of one of the circular RNAs, which acts downstream of Meis1 in the cardiomyocytes, promotes angiogenesis and restores the myocardial blood supply, thus reinforcing better regeneration of the damaged heart. It appears that Meis1 may play double roles in modulating proliferation and regeneration of cardiomyocytes and endothelial cells post-myocardial infarction. In this review, we propose to summarize the major findings of Meis1 in modulating fetal development and adult abnormalities, especially focusing on the recent discoveries of Meis1 in controlling the fate of cardiomyocytes and endothelial cells.
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Affiliation(s)
- Swagatika Paul
- Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA
| | - Xiaonan Zhang
- Beijing Yulong Shengshi Biotechnology, Haidian District, Beijing, 100085, China
| | - Jia-Qiang He
- Department of Biomedical Sciences & Pathobiology, College of Veterinary Medicine, Virginia Tech, Blacksburg, VA 24061, USA.
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Lim H, Xie L. Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2018:1-10. [PMID: 31061989 DOI: 10.1145/3233547.3233551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Identifying the target genes of transcription factors (TFs) is one of the key factors to understand transcriptional regulation. However, our understanding of genome-wide TF targeting profile is limited due to the cost of large scale experiments and intrinsic complexity. Thus, computational prediction methods are useful to predict the unobserved associations. Here, we developed a new one-class collaborative filtering algorithm tREMAP that is based on regularized, weighted nonnegative matrix tri-factorization. The algorithm predicts unobserved target genes for TFs using known gene-TF associations and protein-protein interaction network. Our benchmark study shows that tREMAP significantly outperforms its counterpart REMAP, a bi-factorization-based algorithm, for transcription factor target gene prediction in all four performance metrics AUC, MAP, MPR, and HLU. When evaluated by independent data sets, the prediction accuracy is 37.8% on the top 495 predicted associations, an enrichment factor of 4.19 compared with the random guess. Furthermore, many of the predicted novel associations by tREMAP are supported by evidence from literature. Although we only use canonical TF-target gene interaction data in this study, tREMAP can be directly applied to tissue-specific data sets. tREMAP provides a framework to integrate multiple omics data for the further improvement of TF target gene prediction. Thus, tREMAP is a potentially useful tool in studying gene regulatory networks. The benchmark data set and the source code of tREMAP are freely available at https://github.com/hansaimlim/REMAP/tree/master/TriFacREMAP.
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Affiliation(s)
- Hansaim Lim
- PhD program in Biochemistry, Graduate Center of the City University of New York NY 10016 United States
| | - Lei Xie
- Department of Computer Science, Hunter College and Graduate Center, the City University of New York NY 10065 United States
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Grade CVC, Mantovani CS, Alvares LE. Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation. J Anim Sci Biotechnol 2019; 10:32. [PMID: 31044074 PMCID: PMC6477727 DOI: 10.1186/s40104-019-0338-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 02/19/2019] [Indexed: 12/12/2022] Open
Abstract
Myostatin (MSTN) is one of the key factors regulating myogenesis. Because of its role as a negative regulator of muscle mass deposition, much interest has been given to its protein and, in recent years, several studies have analysed MSTN gene regulation. This review discusses the MSTN gene promoter, focusing on its structure in several animal species, both vertebrate and invertebrate. We report the important binding sites considering their degree of phylogenetic conservation and roles they play in the promoter activity. Finally, we discuss recent studies focusing on MSTN gene regulation via promoter manipulation and the potential applications they have both in medicine and agriculture.
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Affiliation(s)
- Carla Vermeulen Carvalho Grade
- 1Universidade Federal da Integração Latino-Americana, UNILA, Instituto Latino-Americano de Ciências da Vida e da Natureza, Avenida Tarquínio Joslin dos Santos, 1000, Foz do Iguaçu, PR CEP 85870-901 Brazil
| | - Carolina Stefano Mantovani
- 2Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, SP CEP 13083-862 Brazil
| | - Lúcia Elvira Alvares
- 2Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas - UNICAMP, Rua Monteiro Lobato, 255, Campinas, SP CEP 13083-862 Brazil
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Pérez-Baos S, Prieto-Potin I, Román-Blas JA, Sánchez-Pernaute O, Largo R, Herrero-Beaumont G. Mediators and Patterns of Muscle Loss in Chronic Systemic Inflammation. Front Physiol 2018; 9:409. [PMID: 29740336 PMCID: PMC5928215 DOI: 10.3389/fphys.2018.00409] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
Besides its primary function in locomotion, skeletal muscle (SKM), which represents up to half of human's weight, also plays a fundamental homeostatic role. Through the secretion of soluble peptides, or myokines, SKM interacts with major organs involved in metabolic processes. In turn, metabolic cues from these organs are received by muscle cells, which adapt their response accordingly. This is done through an intricate intracellular signaling network characterized by the cross-talking between anabolic and catabolic pathways. A fine regulation of the network is required to protect the organism from an excessive energy expenditure. Systemic inflammation evokes a catabolic reaction in SKM known as sarcopenia. In turn this response comprises several mechanisms, which vary depending on the nature of the insult and its magnitude. In this regard, aging, chronic inflammatory systemic diseases, osteoarthritis and idiopathic inflammatory myopathies can lead to muscle loss. Interestingly, sarcopenia may persist despite remission of chronic inflammation, an issue which warrants further research. The Janus kinase/signal transducer and activator of transcription (JAK/STAT) system stands as a major participant in muscle loss during systemic inflammation, while it is also a well-recognized orchestrator of muscle cell turnover. Herein we summarize current knowledge about models of sarcopenia, their triggers and major mediators and their effect on both protein and cell growth yields. Also, the dual action of the JAK/STAT pathway in muscle mass changes is discussed. We highlight the need to unravel the precise contribution of this system to sarcopenia in order to design targeted therapeutic strategies.
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Affiliation(s)
- Sandra Pérez-Baos
- Bone and Joint Research Unit, Service of Rheumatology, IIS-Fundación Jiménez Díaz, Autonomous University of Madrid, Madrid, Spain
| | - Iván Prieto-Potin
- Bone and Joint Research Unit, Service of Rheumatology, IIS-Fundación Jiménez Díaz, Autonomous University of Madrid, Madrid, Spain
| | - Jorge A Román-Blas
- Bone and Joint Research Unit, Service of Rheumatology, IIS-Fundación Jiménez Díaz, Autonomous University of Madrid, Madrid, Spain
| | - Olga Sánchez-Pernaute
- Bone and Joint Research Unit, Service of Rheumatology, IIS-Fundación Jiménez Díaz, Autonomous University of Madrid, Madrid, Spain
| | - Raquel Largo
- Bone and Joint Research Unit, Service of Rheumatology, IIS-Fundación Jiménez Díaz, Autonomous University of Madrid, Madrid, Spain
| | - Gabriel Herrero-Beaumont
- Bone and Joint Research Unit, Service of Rheumatology, IIS-Fundación Jiménez Díaz, Autonomous University of Madrid, Madrid, Spain
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