51
|
Zhang S, Kang Z, Sun X, Cao X, Pan C, Dang R, Lei C, Chen H, Lan X. Novel lncRNA lncFAM200B: Molecular Characteristics and Effects of Genetic Variants on Promoter Activity and Cattle Body Measurement Traits. Front Genet 2019; 10:968. [PMID: 31649734 PMCID: PMC6795090 DOI: 10.3389/fgene.2019.00968] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/10/2019] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle is one of the three major muscle types in an organism and has key roles in the motor system, metabolism, and homeostasis. RNA-Seq analysis showed that novel lncRNA, lncFAM200B, was differentially expressed in embryonic, neonatal, and adult cattle skeletal muscles. The main aim of this study was to investigate the molecular and expression characteristics of lncFAM200B along with its crucial genetic variations. Our results showed that bovine lncFAM200B was a 472 nucleotide (nt) non-coding RNA containing two exons. The transcription factor binding site prediction analysis found that lncFAM200B promoter region was enriched with SP1 transcription factor, which promotes the binding of myogenic regulatory factor MyoD and DNA sequence. The mRNA expression analysis showed that lncFAM200B was differentially expressed in embryonic, neonatal, adult bovine muscle tissues, and the lncFAM200B expression trend positively correlated with that of MyoG and Myf5 in myoblast proliferation and differential stages. To identify the promoter active region of lncFAM200B, we constructed promoter luciferase reporter gene vector pGL3-Basic plasmids containing lncFAM200B promoter sequences and transfected them into 293T, C2C12, and 3T3-L1 cells. Our results suggested that lncFAM200B promoter active region was from −403 to −139 (264 nt) of its transcription start site, covering 6 SP1 potential binding sites. Furthermore, we found a novel C-T variation, named as SNP2 (ERZ990081 in European Variation Archive) in the promoter active region, which was linked to the nearby SNP1 (rs456951291 in Ensembl database). The genotypes of SNP1 and combined genotypes of SNP1 and SNP2 were significantly associated with Jinnan cattle hip height. The luciferase activity analysis found that the SNP1-SNP2 haplotype CC had the highest luciferase activity, which was consistent with the association analysis result that the combined genotype CC-CC carriers had the highest hip height in Jinnan cattle. In conclusion, our data showed that lncFAM200B is a positive regulator of muscle development and that SNP1 and SNP2 could be used as genetic markers for marker-assisted selection (MAS) breeding of beef cattle.
Collapse
Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zihong Kang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaomei Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| |
Collapse
|
52
|
Oishi Y, Manabe I. Macrophages in inflammation, repair and regeneration. Int Immunol 2019; 30:511-528. [PMID: 30165385 DOI: 10.1093/intimm/dxy054] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/22/2018] [Indexed: 12/12/2022] Open
Abstract
Tissue injury triggers a complex series of cellular responses, starting from inflammation activated by tissue and cell damage and proceeding to healing. By clearing cell debris, activating and resolving inflammation and promoting fibrosis, macrophages play key roles in most, if not all, phases of the response to injury. Recent studies of the mechanisms underlying the initial inflammation and later tissue regeneration and repair revealed that macrophages bridge these processes in part by supporting and activating stem/progenitor cells, clearing damaged tissue, remodeling extracellular matrix to prepare scaffolding for regeneration and promoting angiogenesis. However, macrophages also have a central role in the development of pathology induced by failed resolution (e.g. chronic inflammation) and excessive scarring. In this review, we summarize the activities of macrophages in inflammation and healing in response to acute injury in tissues with differing regenerative capacities. While macrophages lead similar processes in response to tissue injury in these tissues, their priorities and the consequences of their activities differ among tissues. Moreover, the magnitude, nature and duration of injury also greatly affect cellular responses and healing processes. In particular, continuous injury and/or failed resolution of inflammation leads to chronic ailments in which macrophage activities may become detrimental.
Collapse
Affiliation(s)
- Yumiko Oishi
- Department of Biochemistry & Molecular Biology, Nippon Medical School, Bunkyo-ku, Tokyo, Japan
| | - Ichiro Manabe
- Department of Disease Biology and Molecular Medicine, Chiba University Graduate School of Medicine, Chuo-ku, Chiba, Japan
| |
Collapse
|
53
|
Hirata Y, Toyono T, Kokabu S, Obikane Y, Kataoka S, Nakatomi M, Masaki C, Hosokawa R, Seta Y. Krüppel-like factor 5 (Klf5) regulates expression of mouse T1R1 amino acid receptor gene (Tas1r1) in C2C12 myoblast cells. Biomed Res 2019; 40:67-78. [PMID: 30982802 DOI: 10.2220/biomedres.40.67] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
T1R1 and T1R3 are receptors expressed in taste buds that detect L-amino acids. These receptors are also expressed throughout diverse organ systems, such as the digestive system and muscle tissue, and are thought to function as amino acid sensors. The mechanism of transcriptional regulation of the mouse T1R1 gene (Tas1r1) has not been determined; therefore, in this study, we examined the function of Tas1r1 promoter in the mouse myoblast cell line, C2C12. Luciferase reporter assays showed that a 148-bp region upstream of the ATG start codon of Tas1r1 had a promoter activity. The GT box in the Tas1r1 promoter was conserved in the dog, human, mouse, and pig. Site-directed mutagenesis of this GT box significantly reduced the promoter activation. The GT box in promoters is a recurring motif for Sp/KLF family members. RNAi-mediated depletion of Sp4 and Klf5 decreased Tas1r1 expression, while overexpression of Klf5, but not Sp4, significantly increased Tas1r1 expression. The ENCODE data of chromatin immunoprecipitation and sequencing (ChIP-seq) showed that Klf5 bound to the GT box during the myogenic differentiation. Furthermore, the Klf5 knockout cell lines led to a considerable decrease in the levels of Tas1r1 expression. Collectively, these results showed that Klf5 binds to the GT box in the Tas1r1 promoter and regulates Tas1r1 expression in C2C12 cells.
Collapse
Affiliation(s)
- Yuki Hirata
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Takashi Toyono
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| | - Shoichiro Kokabu
- Division of Molecular Signaling and Biochemistry, Department of Health Promotion, Kyushu Dental University
| | - Yui Obikane
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Shinji Kataoka
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| | - Mitsushiro Nakatomi
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| | - Chihiro Masaki
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Ryuji Hosokawa
- Division of Oral Reconstruction and Rehabilitation, Department of Oral Functions, Kyushu Dental University
| | - Yuji Seta
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University
| |
Collapse
|
54
|
Sato T, Higashioka K, Sakurai H, Yamamoto T, Goshima N, Ueno M, Sotozono C. Core Transcription Factors Promote Induction of PAX3-Positive Skeletal Muscle Stem Cells. Stem Cell Reports 2019; 13:352-365. [PMID: 31353225 PMCID: PMC6700474 DOI: 10.1016/j.stemcr.2019.06.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 06/14/2019] [Accepted: 06/25/2019] [Indexed: 12/22/2022] Open
Abstract
The use of adult skeletal muscle stem cells (MuSCs) for cell therapy has been attempted for decades, but still encounters considerable difficulties. MuSCs derived from human induced pluripotent stem cells (hiPSCs) are promising candidates for stem cell therapy to treat Duchenne muscular dystrophy (DMD). Here we report that four transcription factors, HEYL, KLF4, MYOD, and PAX3, selected by comprehensive screening of different MuSC populations, enhance the derivation of PAX3-positive myogenic progenitors from fibroblasts and hiPSCs, using medium that promotes the formation of presomitic mesoderm. These induced PAX3-positive cells contribute efficiently to the repair of DMD-damaged myofibers and also reconstitute the MuSC population. These studies demonstrate how a combination of core transcription factors can fine-tune the derivation of MuSCs capable of contributing to the repair of adult skeletal muscle. Persistent single MyoD can induce myogenic cells, not muscle stem cells The combination of Heyl, Klf4, Pax3, and transient MyoD can induce muscle stem cells Induced PAX3+ cells revealed incorporation into regenerating myofibers of DMD mice
Collapse
Affiliation(s)
- Takahiko Sato
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Department of Anatomy, Fujita Health University, Toyoake, Aichi, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda, Tokyo, Japan.
| | - Koki Higashioka
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Hidetoshi Sakurai
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; AMED-CREST, AMED, 1-7-1 Otemachi, Chiyoda, Tokyo, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Morio Ueno
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| |
Collapse
|
55
|
Kapitansky O, Gozes I. ADNP differentially interact with genes/proteins in correlation with aging: a novel marker for muscle aging. GeroScience 2019; 41:321-340. [PMID: 31264075 DOI: 10.1007/s11357-019-00079-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/10/2019] [Indexed: 12/25/2022] Open
Abstract
Activity-dependent neuroprotective protein (ADNP) is essential for embryonic development with ADNP mutations leading to syndromic autism, coupled with intellectual disabilities and motor developmental delays. Here, mining human muscle gene-expression databases, we have investigated the association of ADNP transcripts with muscle aging. We discovered increased ADNP and its paralogue ADNP2 expression in the vastus lateralis muscle of aged compared to young subjects, as well as altered expression of the ADNP and the ADNP2 genes in bicep brachii muscle of elderly people, in a sex-dependent manner. Prolonged exercise resulted in decreased ADNP expression, and increased ADNP2 expression in an age-dependent manner in the vastus lateralis muscle. ADNP expression level was further correlated with 49 genes showing age-dependent changes in muscle transcript expression. A high degree of correlation with ADNP was discovered for 24 genes with the leading gene/protein being NMNAT1 (nicotinamide nucleotide adenylyl transferase 1). Looking at correlations differentiating the young and the old muscles and comparing protein interactions revealed an association of ADNP with the cell division cycle 5-like protein (CDC5L), and an aging-muscle-related interactive pathway in the vastus lateralis. In the bicep brachii, very high correlation was detected with genes associated with immune functions as well as mitochondrial structure and function among others. Taken together, the results suggest a direct association of ADNP with muscle strength and implicate ADNP fortification in the protection against age-associated muscle wasting.
Collapse
Affiliation(s)
- Oxana Kapitansky
- The Lily and Avraham Gildor Chair for the Investigation of Growth Factors; The Elton Laboratory for Neuroendocrinology; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Illana Gozes
- The Lily and Avraham Gildor Chair for the Investigation of Growth Factors; The Elton Laboratory for Neuroendocrinology; Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Sagol School of Neuroscience and Adams Super Center for Brain Studies, Tel Aviv University, 69978, Tel Aviv, Israel.
| |
Collapse
|
56
|
Zhang XX, Lian T, Ran JS, Li ZQ, Han SS, Liu YP. KLF5 functions in proliferation, differentiation, and apoptosis of chicken satellite cells. 3 Biotech 2019; 9:222. [PMID: 31114746 DOI: 10.1007/s13205-019-1752-2] [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: 02/28/2019] [Accepted: 05/09/2019] [Indexed: 01/25/2023] Open
Abstract
KLF5 is an important regulator of cell proliferation, differentiation, and apoptosis in mammals. Little is known about the function of KLF5 in the regulation of chicken. Hence, qPCR was used to detect the expression of KLF5 in different tissues of chicken. And chicken skeletal muscle satellite cells (SMSCs) were transfected KLF5-specific small interfering RNA (siRNA) to assay SMSCs' proliferation, differentiation, and apoptosis. The results showed that KLF5 expressed higher in skeletal muscle than in the other tissues of chicken. Knockdown of KLF5 significantly inhibited the differentiation and increased apoptosis of chicken SMSCs, but it had no significant effect on proliferation of SMSCs. These results indicate that KLF5 plays an essential role during myogenesis, which will affect muscle repair and muscle regeneration, and may ameliorate muscle aging or sarcopenia.
Collapse
|
57
|
Yu D, Cattoglio C, Xue Y, Zhou Q. A complex between DYRK1A and DCAF7 phosphorylates the C-terminal domain of RNA polymerase II to promote myogenesis. Nucleic Acids Res 2019; 47:4462-4475. [PMID: 30864669 PMCID: PMC6511856 DOI: 10.1093/nar/gkz162] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/24/2019] [Accepted: 03/02/2019] [Indexed: 12/11/2022] Open
Abstract
The general transcription factor P-TEFb, a master regulator of RNA polymerase (Pol) II elongation, phosphorylates the C-terminal domain (CTD) of Pol II and negative elongation factors to release Pol II from promoter-proximal pausing. We show here that P-TEFb surprisingly inhibits the myoblast differentiation into myotubes, and that P-TEFb and its two positive complexes are eliminated in this process. In contrast, DYRK1A, another CTD kinase known to control transcription of a subset of genes important for development and tissue homeostasis, is found to activate transcription of key myogenic genes. We show that active DYRK1A exists in a complex with the WD40-repeat protein DCAF7 that stabilizes and tethers DYRK1A to Pol II, so that DYRK1A-DCAF7 can co-migrate with and phosphorylate Pol II along the myogenic gene loci. Thus, DCAF7 modulates the kinase signaling output of DYRK1A on Pol II to stimulate myogenic transcription after active P-TEFb function is shut off.
Collapse
Affiliation(s)
- Dan Yu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yuhua Xue
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Qiang Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| |
Collapse
|
58
|
He L, Tian X, Yan C, Liu D, Wang S, Han Y. Nicotine promotes the differentiation of C2C12 myoblasts and improves skeletal muscle regeneration in obese mice. Biochem Biophys Res Commun 2019; 511:739-745. [DOI: 10.1016/j.bbrc.2019.02.137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 01/04/2023]
|
59
|
Huang J, Luo X, Zeng L, Huang Z, Huang M, You W, Ke C. Expression profiling of lncRNAs and mRNAs reveals regulation of muscle growth in the Pacific abalone, Haliotis discus hannai. Sci Rep 2018; 8:16839. [PMID: 30442913 PMCID: PMC6237873 DOI: 10.1038/s41598-018-35202-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are known to play a major role in the epigenetic regulation of muscle development. Unfortunately there is little understanding of the mechanisms with which they regulate muscle growth in abalone. Therefore, we used RNA-seq to study the muscle transcriptomes of six Haliotis discus hannai specimens: three large (L_HD group) and three small (S_HD group). We identified 2463 lncRNAs in abalone muscle belonging to two subtypes: 160 anti-sense lncRNAs and 2303 intergenic lncRNAs (lincRNAs). In the L_HD group, we identified 204 significantly differentially expressed lncRNAs (55 upregulated and 149 downregulated), and 2268 significantly differentially expressed mRNAs (994 upregulated and 1274 downregulated), as compared to the S_HD group. The bioinformatics analysis indicated that lncRNAs were relate to cell growth, regulation of growth, MAPK signaling pathway, TGF-β signaling pathway, PI3K-Akt and insulin signaling pathway, which involved in regulating muscle growth. These findings contribute to understanding the possible regulatory mechanisms of muscle growth in Pacific abalone.
Collapse
Affiliation(s)
- Jianfang Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China
| | - Xuan Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China
| | - Liting Zeng
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China
| | - Zekun Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China
| | - Miaoqin Huang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China
| | - Weiwei You
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China. .,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China. .,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China.
| | - Caihuan Ke
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, China. .,College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China. .,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361102, China.
| |
Collapse
|
60
|
Jin S, MacLean AL, Peng T, Nie Q. scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data. Bioinformatics 2018; 34:2077-2086. [PMID: 29415263 PMCID: PMC6658715 DOI: 10.1093/bioinformatics/bty058] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/11/2018] [Accepted: 02/03/2018] [Indexed: 01/18/2023] Open
Abstract
Motivation Single-cell RNA-sequencing (scRNA-seq) offers unprecedented resolution for studying cellular decision-making processes. Robust inference of cell state transition paths and probabilities is an important yet challenging step in the analysis of these data. Results Here we present scEpath, an algorithm that calculates energy landscapes and probabilistic directed graphs in order to reconstruct developmental trajectories. We quantify the energy landscape using 'single-cell energy' and distance-based measures, and find that the combination of these enables robust inference of the transition probabilities and lineage relationships between cell states. We also identify marker genes and gene expression patterns associated with cell state transitions. Our approach produces pseudotemporal orderings that are-in combination-more robust and accurate than current methods, and offers higher resolution dynamics of the cell state transitions, leading to new insight into key transition events during differentiation and development. Moreover, scEpath is robust to variation in the size of the input gene set, and is broadly unsupervised, requiring few parameters to be set by the user. Applications of scEpath led to the identification of a cell-cell communication network implicated in early human embryo development, and novel transcription factors important for myoblast differentiation. scEpath allows us to identify common and specific temporal dynamics and transcriptional factor programs along branched lineages, as well as the transition probabilities that control cell fates. Availability and implementation A MATLAB package of scEpath is available at https://github.com/sqjin/scEpath. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Suoqin Jin
- Department of Mathematics and Center for Complex Biological Systems
| | - Adam L MacLean
- Department of Mathematics and Center for Complex Biological Systems
| | - Tao Peng
- Department of Mathematics and Center for Complex Biological Systems
| | - Qing Nie
- Department of Mathematics and Center for Complex Biological Systems
- Department of Development and Cell Biology, University of California, Irvine, CA, USA
| |
Collapse
|
61
|
Oishi Y, Manabe I. Krüppel-Like Factors in Metabolic Homeostasis and Cardiometabolic Disease. Front Cardiovasc Med 2018; 5:69. [PMID: 29942807 PMCID: PMC6004387 DOI: 10.3389/fcvm.2018.00069] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 05/21/2018] [Indexed: 12/16/2022] Open
Abstract
Members of the Krüppel-like factor (KLF) family of transcription factors, which are characterized by the presence of three conserved Cys2/His2 zinc-fingers in their C-terminal domains, control a wide variety of biological processes. In particular, recent studies have revealed that KLFs play diverse and essential roles in the control of metabolism at the cellular, tissue and systemic levels. In both liver and skeletal muscle, KLFs control glucose, lipid and amino acid metabolism so as to coordinate systemic metabolism in the steady state and in the face of metabolic stresses, such as fasting. The functions of KLFs within metabolic tissues are also important contributors to the responses to injury and inflammation within those tissues. KLFs also control the function of immune cells, such as macrophages, which are involved in the inflammatory processes underlying both cardiovascular and metabolic diseases. This review focuses mainly on the physiological and pathological functions of KLFs in the liver and skeletal muscle. The involvement of KLFs in inflammation in these tissues is also summarized. We then discuss the implications of KLFs' control of metabolism and inflammation in cardiometabolic diseases.
Collapse
Affiliation(s)
- Yumiko Oishi
- Department of Biochemistry & Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Ichiro Manabe
- Department of Disease Biology and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| |
Collapse
|
62
|
Lai JKH, Collins MM, Uribe V, Jiménez-Amilburu V, Günther S, Maischein HM, Stainier DYR. The Hippo pathway effector Wwtr1 regulates cardiac wall maturation in zebrafish. Development 2018; 145:145/10/dev159210. [PMID: 29773645 DOI: 10.1242/dev.159210] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/23/2018] [Indexed: 12/14/2022]
Abstract
Cardiac trabeculation is a highly regulated process that starts with the delamination of compact layer cardiomyocytes. The Hippo signaling pathway has been implicated in cardiac development but many questions remain. We have investigated the role of Wwtr1, a nuclear effector of the Hippo pathway, in zebrafish and find that its loss leads to reduced cardiac trabeculation. However, in mosaic animals, wwtr1-/- cardiomyocytes contribute more frequently than wwtr1+/- cardiomyocytes to the trabecular layer of wild-type hearts. To investigate this paradox, we examined the myocardial wall at early stages and found that compact layer cardiomyocytes in wwtr1-/- hearts exhibit disorganized cortical actin structure and abnormal cell-cell junctions. Accordingly, wild-type cardiomyocytes in mosaic mutant hearts contribute less frequently to the trabecular layer than when present in mosaic wild-type hearts, indicating that wwtr1-/- hearts are not able to support trabeculation. We also found that Nrg/Erbb2 signaling, which is required for trabeculation, could promote Wwtr1 nuclear export in cardiomyocytes. Altogether, these data suggest that Wwtr1 establishes the compact wall architecture necessary for trabeculation, and that Nrg/Erbb2 signaling negatively regulates its nuclear localization and therefore its activity.
Collapse
Affiliation(s)
- Jason K H Lai
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Michelle M Collins
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Veronica Uribe
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Vanesa Jiménez-Amilburu
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Stefan Günther
- Max Planck Institute for Heart and Lung Research, ECCPS Bioinformatics and Deep Sequencing Platform, Bad Nauheim 61231, Germany
| | - Hans-Martin Maischein
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| | - Didier Y R Stainier
- Max Planck Institute for Heart and Lung Research, Department of Developmental Genetics, Bad Nauheim 61231, Germany
| |
Collapse
|
63
|
Okada H, Yamada M, Kamimoto K, Kok CYY, Kaneko K, Ema M, Miyajima A, Itoh T. The transcription factor Klf5 is essential for intrahepatic biliary epithelial tissue remodeling after cholestatic liver injury. J Biol Chem 2018. [PMID: 29523685 DOI: 10.1074/jbc.ra118.002372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Under various conditions of liver injury, the intrahepatic biliary epithelium undergoes dynamic tissue expansion and remodeling, a process known as ductular reaction. Mouse models defective in inducing such a tissue-remodeling process are more susceptible to liver injury, suggesting a crucial role of this process in liver regeneration. However, the molecular mechanisms regulating the biliary epithelial cell (BEC) dynamics in the ductular reaction remain largely unclear. Here, we demonstrate that the transcription factor Krüppel-like factor 5 (Klf5) is highly enriched in mouse liver BECs and plays a key role in regulating the ductular reaction, specifically under cholestatic injury conditions. Although mice lacking Klf5 in the entire liver epithelium, including both hepatocytes and BECs (Klf5-LKO (liver epithelial-specific knockout) mice), did not exhibit any apparent phenotype in the hepatobiliary system under normal conditions, they exhibited significant defects in biliary epithelial tissue remodeling upon 3,5-diethoxycarbonyl-1,4-dihydrocollidine-induced cholangitis, concomitantly with exacerbated cholestasis and reduced survival rate. In contrast, mice lacking Klf5 solely in hepatocytes did not exhibit any such phenotypes, confirming Klf5's specific role in BECs. RNA-sequencing analyses of BECs isolated from the Klf5-LKO mouse livers revealed that the Klf5 deficiency primarily affected expression of cell cycle-related genes. Moreover, immunostaining analysis with the proliferation marker Ki67 disclosed that the Klf5-LKO mice had significantly reduced BEC proliferation levels upon injury. These results indicate that Klf5 plays a critical role in the ductular reaction and biliary epithelial tissue expansion and remodeling by inducing BEC proliferation and thereby contributing to liver regeneration.
Collapse
Affiliation(s)
- Hajime Okada
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Minami Yamada
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Kenji Kamimoto
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Cindy Yuet-Yin Kok
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Kota Kaneko
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Masatsugu Ema
- the Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Atsushi Miyajima
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| | - Tohru Itoh
- From the Laboratory of Cell Growth and Differentiation, Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032 and
| |
Collapse
|
64
|
Baghdadi MB, Tajbakhsh S. Regulation and phylogeny of skeletal muscle regeneration. Dev Biol 2018; 433:200-209. [DOI: 10.1016/j.ydbio.2017.07.026] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022]
|
65
|
Cassandri M, Smirnov A, Novelli F, Pitolli C, Agostini M, Malewicz M, Melino G, Raschellà G. Zinc-finger proteins in health and disease. Cell Death Discov 2017; 3:17071. [PMID: 29152378 PMCID: PMC5683310 DOI: 10.1038/cddiscovery.2017.71] [Citation(s) in RCA: 438] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 02/07/2023] Open
Abstract
Zinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and have a wide range of molecular functions. Given the wide variety of zinc-finger domains, ZNFs are able to interact with DNA, RNA, PAR (poly-ADP-ribose) and other proteins. Thus, ZNFs are involved in the regulation of several cellular processes. In fact, ZNFs are implicated in transcriptional regulation, ubiquitin-mediated protein degradation, signal transduction, actin targeting, DNA repair, cell migration, and numerous other processes. The aim of this review is to provide a comprehensive summary of the current state of knowledge of this class of proteins. Firstly, we describe the actual classification of ZNFs, their structure and functions. Secondly, we focus on the biological role of ZNFs in the development of organisms under normal physiological and pathological conditions.
Collapse
Affiliation(s)
- Matteo Cassandri
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Artem Smirnov
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Flavia Novelli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Consuelo Pitolli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Massimiliano Agostini
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Michal Malewicz
- Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, UK
| | - Gerry Melino
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome 00133, Italy.,Medical Research Council, Toxicology Unit, Leicester University, Leicester LE1 9HN, UK
| | - Giuseppe Raschellà
- ENEA Research Center Casaccia, Laboratory of Biosafety and Risk Assessment, Via Anguillarese, Rome, Italy
| |
Collapse
|