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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 PMCID: PMC11354804 DOI: 10.3390/ijms25168863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | - Guidalberto Manfioletti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
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2
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Palis J. Erythropoiesis in the mammalian embryo. Exp Hematol 2024; 136:104283. [PMID: 39048071 DOI: 10.1016/j.exphem.2024.104283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Red blood cells (RBCs) comprise a critical component of the cardiovascular network, which constitutes the first functional organ system of the developing mammalian embryo. Examination of circulating blood cells in mammalian embryos revealed two distinct types of erythroid cells: large, nucleated "primitive" erythroblasts followed by smaller, enucleated "definitive" erythrocytes. This review describes the current understanding of primitive and definitive erythropoiesis gleaned from studies of mouse and human embryos and induced pluripotent stem cells (iPSCs). Primitive erythropoiesis in the mouse embryo comprises a transient wave of committed primitive erythroid progenitors (primitive erythroid colony-forming cells, EryP-CFC) in the early yolk sac that generates a robust cohort of precursors that mature in the bloodstream and enucleate. In contrast, definitive erythropoiesis has two distinct developmental origins. The first comprises a transient wave of definitive erythroid progenitors (burst-forming units erythroid, BFU-E) that emerge in the yolk sac and seed the fetal liver where they terminally mature to provide the first definitive RBCs. The second comprises hematopoietic stem cell (HSC)-derived BFU-E that terminally mature at sites colonized by HSCs particularly the fetal liver and subsequently the bone marrow. Primitive and definitive erythropoiesis are derived from endothelial identity precursors with distinct developmental origins. Although they share prototypical transcriptional regulation, primitive and definitive erythropoiesis are also characterized by distinct lineage-specific factors. The exquisitely timed, sequential production of primitive and definitive erythroid cells is necessary for the survival and growth of the mammalian embryo.
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Affiliation(s)
- James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY.
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da Silva RSP, Bortolini MAT, Teixeira JB, Batista NC, Fitz FF, Allen-Brady K, Castro RA. Association between the rs1036819 polymorphism of the ZFAT gene and pelvic organ prolapse: a case-control study. Int Urogynecol J 2023; 34:2611-2617. [PMID: 37535103 DOI: 10.1007/s00192-023-05615-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/03/2023] [Indexed: 08/04/2023]
Abstract
INTRODUCTION AND HYPOTHESIS The identification of risk factors for pelvic organ prolapse (POP) would contribute to planning prevention strategies. This study tests the hypothesis that the rs1036819 polymorphism in the ZFAT gene is associated with POP and investigates other risk factors for prolapse development. METHODS A case-control study was carried out including 826 postmenopausal women divided into POP cases (stages III and IV) and controls (stages 0 and I), assessed by anamnesis, examination, and peripheral blood samples. DNA was extracted from blood and genotyped by real-time RT-PCR. We used logistic regression models for the association analyses of variables, with p < 0.05 for significance. RESULTS Five hundred and sixty-eight women were evaluated (315 POP and 253 controls). The minor allele C was found in 19.3% of our sample and the genotype frequencies of AA, AC, and CC were similar in both groups. Age (OR 1.09, 95% CI 1.06-1.13), number of pregnancies (OR 1.23, 95% CI 1.08-1.41), history of one vaginal delivery (OR 3.39, 95% CI 1.38-8.33) or two or more (OR 2.51, 95% CI 1.04-6.07), weight of the largest newborn (OR 1.0001, 95% CI 1-1.001), and family history of POP (OR 2.27, 95% CI 1.24-4.13) were independent risk factors for POP, whereas one cesarean section (OR 0.48, 95% CI 0.27-0.88) or two or more (OR 0.14, 95% CI 0.05-0.38) were protective. CONCLUSIONS No association was detected between the rs1036819 polymorphism of the ZFAT gene and advanced POP. Age, number of pregnancies, at least one vaginal delivery, weight of the newborn, and POP family history were independent risk factors for POP.
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Affiliation(s)
- Rebecca Sotelo Pinheiro da Silva
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil.
- Hospital Federal de Ipanema - Setor de Ginecologia, Rua Antônio Parreiras, 67 - 4º andar, CEP: 22411-020, Rio de Janeiro, RJ, Brazil.
| | - Maria A T Bortolini
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil
| | - Juliana B Teixeira
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil
| | - Nilce C Batista
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil
| | - Fatima F Fitz
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil
| | | | - Rodrigo A Castro
- Division of Urogynecology and Reconstructive Pelvic Surgery, Department of Gynecology, Federal University of São Paulo, São Paulo, Brazil
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Ishikura S, Yoshida K, Hashimoto S, Nakabayashi K, Tsunoda T, Shirasawa S. CENP-B promotes the centromeric localization of ZFAT to control transcription of noncoding RNA. J Biol Chem 2021; 297:101213. [PMID: 34547289 PMCID: PMC8496178 DOI: 10.1016/j.jbc.2021.101213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/28/2022] Open
Abstract
The centromere is a chromosomal locus that is essential for the accurate segregation of chromosomes during cell division. Transcription of noncoding RNA (ncRNA) at the centromere plays a crucial role in centromere function. The zinc-finger transcriptional regulator ZFAT binds to a specific 8-bp DNA sequence at the centromere, named the ZFAT box, to control ncRNA transcription. However, the precise molecular mechanisms by which ZFAT localizes to the centromere remain elusive. Here we show that the centromeric protein CENP-B is required for the centromeric localization of ZFAT to regulate ncRNA transcription. The ectopic expression of CENP-B induces the accumulation of both endogenous and ectopically expressed ZFAT protein at the centromere in human cells, suggesting that the centromeric localization of ZFAT requires the presence of CENP-B. Coimmunoprecipitation analysis reveals that ZFAT interacts with the acidic domain of CENP-B, and depletion of endogenous CENP-B reduces the centromeric levels of ZFAT protein, further supporting that CENP-B is required for the centromeric localization of ZFAT. In addition, knockdown of CENP-B significantly decreased the expression levels of ncRNA at the centromere where ZFAT regulates the transcription, suggesting that CENP-B is involved in the ZFAT-regulated centromeric ncRNA transcription. Thus, we concluded that CENP-B contributes to the establishment of the centromeric localization of ZFAT to regulate ncRNA transcription.
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Affiliation(s)
- Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan; Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Kazumasa Yoshida
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan; Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Sayuri Hashimoto
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan; Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan; Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan.
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Ishikura S, Nagai M, Tsunoda T, Nishi K, Tanaka Y, Koyanagi M, Shirasawa S. The transcriptional regulator Zfat is essential for maintenance and differentiation of the adipocytes. J Cell Biochem 2021; 122:626-638. [PMID: 33522619 PMCID: PMC8248092 DOI: 10.1002/jcb.29890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 01/02/2023]
Abstract
Adipocytes play crucial roles in the control of whole‐body energy homeostasis. Differentiation and functions of the adipocytes are regulated by various transcription factors. Zfat (zinc‐finger protein with AT‐hook) is a transcriptional regulator that controls messenger RNA expression of specific genes through binding to their transcription start sites. Here we report important roles of Zfat in the adipocytes. We establish inducible Zfat‐knockout (Zfat iKO) mice where treatment with tamoxifen causes a marked reduction in Zfat expression in various tissues. Tamoxifen treatment of Zfat iKO mice reduces the white adipose tissues (WATs) mass, accompanied by the decreased triglyceride levels. Zfat is expressed in both the adipose‐derived stem cells (ADSCs) and mature adipocytes in the WATs. In ex vivo assays of the mature adipocytes differentiated from the Zfat iKO ADSCs, loss of Zfat in the mature adipocytes reduces the triglyceride levels, suggesting cell autonomous roles of Zfat in the maintenance of the mature adipocytes. Furthermore, we identify the Atg13, Brf1, Psmc3, and Timm22 genes as Zfat‐target genes in the mature adipocytes. In contrast, loss of Zfat in the ADSCs impairs adipocyte differentiation with the decreased expression of C/EBPα and adiponectin. Thus, we propose that Zfat plays crucial roles in maintenance and differentiation of the adipocytes.
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Affiliation(s)
- Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Masayoshi Nagai
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
| | - Kensuke Nishi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Yoko Tanaka
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Midori Koyanagi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
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Ishikura S, Nakabayashi K, Nagai M, Tsunoda T, Shirasawa S. ZFAT binds to centromeres to control noncoding RNA transcription through the KAT2B-H4K8ac-BRD4 axis. Nucleic Acids Res 2020; 48:10848-10866. [PMID: 32997115 PMCID: PMC7641738 DOI: 10.1093/nar/gkaa815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Centromeres are genomic regions essential for faithful chromosome segregation. Transcription of noncoding RNA (ncRNA) at centromeres is important for their formation and functions. Here, we report the molecular mechanism by which the transcriptional regulator ZFAT controls the centromeric ncRNA transcription in human and mouse cells. Chromatin immunoprecipitation with high-throughput sequencing analysis shows that ZFAT binds to centromere regions at every chromosome. We find a specific 8-bp DNA sequence for the ZFAT-binding motif that is highly conserved and widely distributed at whole centromere regions of every chromosome. Overexpression of ZFAT increases the centromeric ncRNA levels at specific chromosomes, whereas its silencing reduces them, indicating crucial roles of ZFAT in centromeric transcription. Overexpression of ZFAT increases the centromeric levels of both the histone acetyltransferase KAT2B and the acetylation at the lysine 8 in histone H4 (H4K8ac). siRNA-mediated knockdown of KAT2B inhibits the overexpressed ZFAT-induced increase in centromeric H4K8ac levels, suggesting that ZFAT recruits KAT2B to centromeres to induce H4K8ac. Furthermore, overexpressed ZFAT recruits the bromodomain-containing protein BRD4 to centromeres through KAT2B-mediated H4K8ac, leading to RNA polymerase II-dependent ncRNA transcription. Thus, ZFAT binds to centromeres to control ncRNA transcription through the KAT2B-H4K8ac-BRD4 axis.
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Affiliation(s)
- Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.,Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Masayoshi Nagai
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.,Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan.,Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan
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Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep 2019; 9:16672. [PMID: 31723199 PMCID: PMC6853925 DOI: 10.1038/s41598-019-53102-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nam-Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jae-Min Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Kyung-Tai Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Hwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | | | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
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Purfield DC, Evans RD, Berry DP. Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population. BMC Genomics 2019; 20:720. [PMID: 31533623 PMCID: PMC6751660 DOI: 10.1186/s12864-019-6071-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/29/2019] [Indexed: 12/25/2022] Open
Abstract
Background The high narrow sense heritability of carcass traits suggests that the underlying additive genetic potential of an individual should be strongly correlated with both animal carcass quality and quantity, and therefore, by extension, carcass value. Therefore, the objective of the present study was to detect genomic regions associated with three carcass traits, namely carcass weight, conformation and fat cover, using imputed whole genome sequence in 28,470 dairy and beef sires from six breeds with a total of 2,199,926 phenotyped progeny. Results Major genes previously associated with carcass performance were identified, as well as several putative novel candidate genes that likely operate both within and across breeds. The role of MSTN in carcass performance was re-affirmed with the segregating Q204X mutation explaining 1.21, 1.11 and 5.95% of the genetic variance in carcass weight, fat and conformation, respectively in the Charolais population. In addition, a genomic region on BTA6 encompassing the NCAPG/LCORL locus, which is a known candidate locus associated with body size, was associated with carcass weight in Angus, Charolais and Limousin. Novel candidate genes identified included ZFAT in Angus, and SLC40A1 and the olfactory gene cluster on BTA15 in Charolais. Although the majority of associations were breed specific, associations that operated across breeds included SORCS1 on BTA26, MCTP2 on BTA21 and ARL15 on BTA20; these are of particular interest due to their potential informativeness in across-breed genomic evaluations. Genomic regions affecting all three carcass traits were identified in each of the breeds, although these were mainly concentrated on BTA2 and BTA6, surrounding MSTN and NCAPG/LCORL, respectively. This suggests that although major genes may be associated with all three carcass traits, the majority of genes containing significant variants (unadjusted p-value < 10− 4) may be trait specific associations of small effect. Conclusions Although plausible novel candidate genes were identified, the proportion of variance explained by these candidates was minimal thus reaffirming that while carcass performance may be affected by major genes in the form of MSTN and NCAPG/LCORL, the majority of variance is attributed to the additive (and possibly multiplicative) effect of many polymorphisms of small effect. Electronic supplementary material The online version of this article (10.1186/s12864-019-6071-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D C Purfield
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - R D Evans
- Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - D P Berry
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
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Abulaizi A, Abula A, Ababaikeli G, Wan X, Du R, Zhakeer A. Identification of pelvic organ prolapse risk susceptibility gene SNP locus in Xinjiang women. Int Urogynecol J 2019; 31:123-130. [PMID: 31270553 DOI: 10.1007/s00192-019-04039-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/19/2019] [Indexed: 02/03/2023]
Abstract
INTRODUCTION AND HYPOTHESIS Susceptibility genes play an important role and have regional specificity in the occurrence of pelvic organ prolapse (POP). This study aims to identify POP susceptibility genes and their loci in ethnic minorities with different genetic backgrounds from Xinjiang in China, providing a theoretical basis for early POP diagnosis, treatment and prevention. METHODS Genomic DNA from peripheral blood of 196 patients was prepared; there were 88 POP patients and 108 non-pelvic floor dysfunction patients. We selected 16 different susceptibility gene single-nucleotide polymorphism (SNP) loci, which had been identified as associated with POP risk by researchers in other countries, and carried out genotyping through the Snapshot reaction. The allele and genotype frequencies, odds ratio (OR) and 95% confidence interval (CI) were analyzed using SPSS 17.0 software. RESULTS The genotypic and allelic distributions demonstrated significant differences between the patients and the control subjects in the group of minority women, details are as follows: ESR1 rs17847075 AG: OR = 2.738, 95% CI = 1.067-7.025, P = 0.041; ESR1 rs2234693 TC: OR = 2.99, 95% CI = 1.163-7.684, P = 0.024; ZFAT rs1036819 CC: OR = 10.286, 95% CI = 1.158-91.386, P = 0.036; allele C: OR = 2.212, 95% CI = 1.146-4.269; P = 0.02; FBLN5 rs12589592 AA: OR = 0.111, 95% CI = 0.013-0.952, P = 0.029; allele A: OR = 0.482, 95% CI = 0.254-0.913, P = 0.028. CONCLUSIONS ESR1 rs17847075 genotype AG in the dominant model (P = 0.008) or heterozygous model (P = 0.045), ESR1 rs2234693 genotype TC in the dominant model (P = 0.008) or heterozygous model (P = 0.028), and ZFAT rs1036819 genotype CC and allele C in the recessive model (P = 0.042) were significantly associated with POP risk in Xinjiang woman.
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Affiliation(s)
- Aibibuhan Abulaizi
- Department of Gynecology and Reproductive Maternity Assistance Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumchi, China
| | | | - Gulina Ababaikeli
- Department of Gynecology and Reproductive Maternity Assistance Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumchi, China.
| | - Xiaohui Wan
- Department of Gynecology and Reproductive Maternity Assistance Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumchi, China
| | - Rong Du
- Department of Gynecology and Reproductive Maternity Assistance Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumchi, China
| | - Adilai Zhakeer
- Department of Gynecology and Reproductive Maternity Assistance Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumchi, China
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Jenko J, McClure MC, Matthews D, McClure J, Johnsson M, Gorjanc G, Hickey JM. Analysis of a large dataset reveals haplotypes carrying putatively recessive lethal and semi-lethal alleles with pleiotropic effects on economically important traits in beef cattle. Genet Sel Evol 2019; 51:9. [PMID: 30836944 PMCID: PMC6402105 DOI: 10.1186/s12711-019-0452-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. METHODS In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production. RESULTS We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype. CONCLUSIONS We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.
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Affiliation(s)
- Janez Jenko
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | | | | | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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11
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Tsunoda T, Doi K, Ishikura S, Luo H, Nishi K, Matsuzaki H, Koyanagi M, Tanaka Y, Okamura T, Shirasawa S. Zfat expression in ZsGreen reporter gene knock‑in mice: Implications for a novel function of Zfat in definitive erythropoiesis. Int J Mol Med 2018; 42:2595-2603. [PMID: 30106088 PMCID: PMC6192767 DOI: 10.3892/ijmm.2018.3806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/02/2018] [Indexed: 01/17/2023] Open
Abstract
Zinc finger and AT-hook domain containing (Zfat) is a transcriptional regulator harboring an AT-hook domain and 18 repeats of a C2H2 zinc-finger motif, which binds directly to the proximal region of transcription start sites in Zfat-target genes. It was previously reported that deletion of the Zfat gene in mice yields embryonic lethality by embryonic day 8.5 and impairs primitive hematopoiesis in yolk sac blood islands. In addition, Zfat has been reported to be involved in thymic T-cell development and peripheral T-cell homeostasis. In the present study, in order to obtain a precise understanding of the expression and function of Zfat, a knock-in mouse strain (ZfatZsG/+ mice), which expressed ZsGreen in the Zfat locus, was established. ZsGreen signals in tissues and cells of ZfatZsG/+ mice were examined by flow cytometric and histological analyses. Consistent with our previous studies, ZsGreen signals in ZfatZsG/+ mice were detected in the embryo and yolk sac blood islands, as well as in thymocytes, B and T cells. In the ZfatZsG/+ thymus, ZsGreen+ cells were identified not only in T-cell populations but also in thymic epithelial cells, suggesting the role of Zfat in antigen-presenting cells during thymic T-cell development. ZsGreen signals were observed in definitive erythroid progenitor cells in the fetal liver and adult bone marrow of ZfatZsG/+ mice. The proportion of ZsGreen+ cells in these tissues was highest at the early stage of erythroid differentiation, suggesting that Zfat serves particular roles in definitive erythropoiesis. Histological studies demonstrated that ZsGreen signals were detected in the pyramidal cells in the hippocampal CA1 region and the Purkinje cells in the cerebellum, suggesting novel functions of Zfat in nervous tissues. Taken together, these results indicated that the ZfatZsG/+ reporter mouse may be considered a useful tool for elucidating the expression and function of Zfat.
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Affiliation(s)
- Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Keiko Doi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Hao Luo
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Kensuke Nishi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Hiroshi Matsuzaki
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Midori Koyanagi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Yoko Tanaka
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo 162‑8655, Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka 814‑0180, Japan
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12
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Tozaki T, Kikuchi M, Kakoi H, Hirota KI, Nagata SI. A genome-wide association study for body weight in Japanese Thoroughbred racehorses clarifies candidate regions on chromosomes 3, 9, 15, and 18. J Equine Sci 2017; 28:127-134. [PMID: 29270069 PMCID: PMC5735309 DOI: 10.1294/jes.28.127] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/21/2017] [Indexed: 01/24/2023] Open
Abstract
Body weight is an important trait to confirm growth and development in humans and animals. In Thoroughbred racehorses, it is measured in the postnatal, training, and racing periods to evaluate growth and training
degrees. The body weight of mature Thoroughbred racehorses generally ranges from 400 to 600 kg, and this broad range is likely influenced by environmental and genetic factors. Therefore, a genome-wide association study
(GWAS) using the Equine SNP70 BeadChip was performed to identify the genomic regions associated with body weight in Japanese Thoroughbred racehorses using 851 individuals. The average body weight of these horses was
473.9 kg (standard deviation: 28.0) at the age of 3, and GWAS identified statistically significant SNPs on chromosomes 3 (BIEC2_808466, P=2.32E-14), 9 (BIEC2_1105503, P=1.03E-7), 15 (BIEC2_322669, P=9.50E-6), and 18
(BIEC2_417274, P=1.44E-14), which were associated with body weight as a quantitative trait. The genomic regions on chromosomes 3, 9, 15, and 18 included ligand-dependent nuclear receptor compressor-like protein (LCORL),
zinc finger and AT hook domain containing (ZFAT), tribbles pseudokinase 2 (TRIB2), and myostatin (MSTN), respectively, as candidate genes. LCORL and ZFAT are associated with withers height in horses, whereas MSTN affects
muscle mass. Thus, the genomic regions identified in this study seem to affect the body weight of Thoroughbred racehorses. Although this information is useful for breeding and growth management of the horses, the
production of genetically modified animals and gene doping (abuse/misuse of gene therapy) should be prohibited to maintain horse racing integrity.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Kei-Ichi Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
| | - Shun-Ichi Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan
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13
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Molecular mechanisms of transcriptional regulation by the nuclear zinc-finger protein Zfat in T cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1398-1410. [PMID: 27591365 DOI: 10.1016/j.bbagrm.2016.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/18/2016] [Accepted: 08/29/2016] [Indexed: 11/22/2022]
Abstract
Zfat is a nuclear protein with AT-hook and zinc-finger domains. We previously reported that Zfat plays crucial roles in T-cell survival and development in mice. However, the molecular mechanisms whereby Zfat regulates gene expression in T cells remain unexplored. In this study, we analyzed the genome-wide occupancy of Zfat by chromatin immunoprecipitation with sequencing (ChIP-seq), which showed that Zfat bound predominantly to a region around a transcription start site (TSS), and that an 8-bp nucleotide sequence GAA(T/A)(C/G)TGC was identified as a consensus sequence for Zfat-binding sites. Furthermore, about half of the Zfat-binding sites were characterized by histone H3 acetylations at lysine 9 and lysine 27 (H3K9ac/K27ac). Notably, Zfat gene deletion decreased the H3K9ac/K27ac levels at the Zfat-binding sites, suggesting that Zfat may be related to the regulation of H3K9ac/K27ac. Integrated analysis of ChIP-seq and transcriptional profiling in thymocytes identified Zfat-target genes with transcription to be regulated directly by Zfat. We then focused on the chromatin regulator Brpf1, a Zfat-target gene, revealing that Zfat bound directly to a 9-bp nucleotide sequence, CGAANGTGC, which is conserved among mammalian Brpf1 promoters. Furthermore, retrovirus-mediated re-expression of Zfat in Zfat-deficient peripheral T cells restored Brpf1 expression to normal levels, and shRNA-mediated Brpf1 knockdown in peripheral T cells increased the proportion of apoptotic cells, suggesting that Zfat-regulated Brpf1 expression was important for T-cell survival. Our findings demonstrated that Zfat regulates the transcription of target genes by binding directly to the TSS proximal region, and that Zfat-target genes play important roles in T-cell homeostasis.
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14
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Ishikura S, Iwaihara Y, Tanaka Y, Luo H, Nishi K, Doi K, Koyanagi M, Okamura T, Tsunoda T, Shirasawa S. The Nuclear Zinc Finger Protein Zfat Maintains FoxO1 Protein Levels in Peripheral T Cells by Regulating the Activities of Autophagy and the Akt Signaling Pathway. J Biol Chem 2016; 291:15282-91. [PMID: 27226588 DOI: 10.1074/jbc.m116.723734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 01/14/2023] Open
Abstract
Forkhead box O1 (FoxO1) is a key molecule for the development and functions of peripheral T cells. However, the precise mechanisms regulating FoxO1 expression in peripheral T cells remain elusive. We previously reported that Zfat(f/f)-CD4Cre mice showed a marked decline in FoxO1 protein levels in peripheral T cells, partially through proteasomal degradation. Here we have identified the precise mechanisms, apart from proteasome-mediated degradation, of the decreased FoxO1 levels in Zfat-deficient T cells. First, we confirmed that tamoxifen-inducible deletion of Zfat in Zfat(f/f)-CreERT2 mice coincidently decreases FoxO1 protein levels in peripheral T cells, indicating that Zfat is essential for maintaining FoxO1 levels in these cells. Although the proteasome-specific inhibitors lactacystin and epoxomicin only moderately increase FoxO1 protein levels, the inhibitors of lysosomal proteolysis bafilomycin A1 and chloroquine restore the decreased FoxO1 levels in Zfat-deficient T cells to levels comparable with those in control cells. Furthermore, Zfat-deficient T cells show increased numbers of autophagosomes and decreased levels of p62 protein, together indicating that Zfat deficiency promotes lysosomal FoxO1 degradation through autophagy. In addition, Zfat deficiency increases the phosphorylation levels of Thr-308 and Ser-473 of Akt and the relative amounts of cytoplasmic to nuclear FoxO1 protein levels, indicating that Zfat deficiency causes Akt activation, leading to nuclear exclusion of FoxO1. Our findings have demonstrated a novel role of Zfat in maintaining FoxO1 protein levels in peripheral T cells by regulating the activities of autophagy and the Akt signaling pathway.
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Affiliation(s)
- Shuhei Ishikura
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
| | - Yuri Iwaihara
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
| | - Yoko Tanaka
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
| | - Hao Luo
- From the Department of Cell Biology, Faculty of Medicine and
| | - Kensuke Nishi
- From the Department of Cell Biology, Faculty of Medicine and
| | - Keiko Doi
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
| | - Midori Koyanagi
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
| | - Tadashi Okamura
- the Department of Laboratory Animal Medicine and Section of Animal Models, Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Toshiyuki Tsunoda
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
| | - Senji Shirasawa
- From the Department of Cell Biology, Faculty of Medicine and Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka 814-0180, Japan and
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15
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Chen T, Wang F, Wu M, Wang ZZ. Development of hematopoietic stem and progenitor cells from human pluripotent stem cells. J Cell Biochem 2016; 116:1179-89. [PMID: 25740540 DOI: 10.1002/jcb.25097] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 01/23/2015] [Indexed: 01/04/2023]
Abstract
Human pluripotent stem cells (hPSCs), including human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), provide a new cell source for regenerative medicine, disease modeling, drug discovery, and preclinical toxicity screening. Understanding of the onset and the sequential process of hematopoietic cells from differentiated hPSCs will enable the achievement of personalized medicine and provide an in vitro platform for studying of human hematopoietic development and disease. During embryogenesis, hemogenic endothelial cells, a specified subset of endothelial cells in embryonic endothelium, are the primary source of multipotent hematopoietic stem cells. In this review, we discuss current status in the generation of multipotent hematopoietic stem and progenitor cells from hPSCs via hemogenic endothelial cells. We also review the achievements in direct reprogramming from non-hematopoietic cells to hematopoietic stem and progenitor cells. Further characterization of hematopoietic differentiation in hPSCs will improve our understanding of blood development and expedite the development of hPSC-derived blood products for therapeutic purpose.
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Affiliation(s)
- Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Fen Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Mengyao Wu
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zack Z Wang
- Division of Hematology, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205
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16
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Ishikura S, Ogawa M, Doi K, Matsuzaki H, Iwaihara Y, Tanaka Y, Tsunoda T, Hideshima H, Okamura T, Shirasawa S. Zfat-deficient CD4⁺ CD8⁺ double-positive thymocytes are susceptible to apoptosis with deregulated activation of p38 and JNK. J Cell Biochem 2016; 116:149-57. [PMID: 25169027 DOI: 10.1002/jcb.24954] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/22/2014] [Indexed: 11/08/2022]
Abstract
Zfat, which is a nuclear protein harboring an AT-hook domain and 18-repeats of C2H2 zinc-finger motif, is highly expressed in immune-related tissues, including the thymus and spleen. T cell specific deletion of the Zfat gene by crossing Zfat(f/f) mice with LckCre mice yields a significant reduction in the number of CD4(+) CD8(+) double-positive (DP) thymocytes. However, physiological role for Zfat in T cell development in the thymus remains unknown. Here, we found that Zfat-deficient DP thymocytes in Zfat(f/f)-LckCre mice were susceptible to apoptosis both at an unstimulated state and in response to T cell receptor (TCR)-stimulation. The phosphorylation levels of p38 and JNK were elevated in Zfat-deficient thymocytes at an unstimulated state with an enhanced phosphorylation of ATF2 and with an over-expression of Gadd45α⋅ On the other hand, the activation of JNK in the Zfat-deficient thymocytes, but not p38, was strengthened and prolonged in response to TCR-stimulation. All these results demonstrate that Zfat critically participates in the development of DP thymocytes through regulating the activities of p38 and JNK.
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Affiliation(s)
- Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan; Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Fukuoka, Japan
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17
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Tochio N, Umehara T, Nakabayashi K, Yoneyama M, Tsuda K, Shirouzu M, Koshiba S, Watanabe S, Kigawa T, Sasazuki T, Shirasawa S, Yokoyama S. Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT. ACTA ACUST UNITED AC 2015; 16:55-65. [PMID: 25801860 PMCID: PMC4427657 DOI: 10.1007/s10969-015-9196-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 03/12/2015] [Indexed: 11/28/2022]
Abstract
ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4–ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4–ZF5 interfinger linker in the regulation of ZFAT function.
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Affiliation(s)
- Naoya Tochio
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,Department of Mathematical and Life Sciences, Research Center for the Mathematics on Chromatin Live Dynamics, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530 Japan
| | - Takashi Umehara
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,PRESTO, Japan Science and Technology Agency (JST), 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535 Japan
| | - Misao Yoneyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Kengo Tsuda
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Seizo Koshiba
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoru Watanabe
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Takanori Kigawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori, Yokohama, 226-8502 Japan.,RIKEN Quantitative Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Takehiko Sasazuki
- Institute for Advanced Studies, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8582 Japan
| | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, 814-0180 Japan.,Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Shigeyuki Yokoyama
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan.,RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
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18
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Ishida S, Umeyama H, Iwadate M, Taguchi YH. Bioinformatic screening of autoimmune disease genes and protein structure prediction with FAMS for drug discovery. Protein Pept Lett 2015; 21:828-39. [PMID: 23855671 PMCID: PMC4141326 DOI: 10.2174/09298665113209990052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 01/19/2023]
Abstract
Autoimmune diseases are often intractable because their causes are unknown. Identifying which genes contribute to these diseases may allow us to understand the pathogenesis, but it is difficult to determine which genes contribute to disease. Recently, epigenetic information has been considered to activate/deactivate disease-related genes. Thus, it may also be useful to study epigenetic information that differs between healthy controls and patients with autoimmune disease. Among several types of epigenetic information, promoter methylation is believed to be one of the most important factors. Here, we propose that principal component analysis is useful to identify specific gene promoters that are differently methylated between the normal healthy controls and patients with autoimmune disease. Full Automatic Modeling System (FAMS) was used to predict the three-dimensional structures of selected proteins and successfully inferred relatively confident structures. Several possibilities of the application to the drug discovery based on obtained structures are discussed.
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Affiliation(s)
| | | | | | - Y-H Taguchi
- Department of Physics, Chuo University, Tokyo 112-8551, Japan, and Department of Biological Sciences, Chuo University, Tokyo 112-8551, Japan.
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19
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Ogawa M, Okamura T, Ishikura S, Doi K, Matsuzaki H, Tanaka Y, Ota T, Hayakawa K, Suzuki H, Tsunoda T, Sasazuki T, Shirasawa S. Zfat-deficiency results in a loss of CD3ζ phosphorylation with dysregulation of ERK and Egr activities leading to impaired positive selection. PLoS One 2013; 8:e76254. [PMID: 24098453 PMCID: PMC3789737 DOI: 10.1371/journal.pone.0076254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/22/2013] [Indexed: 11/19/2022] Open
Abstract
The human ZFAT gene was originally identified as a susceptibility gene for autoimmune thyroid disease. Mouse Zfat is a critical transcriptional regulator for primitive hematopoiesis and required for peripheral T cell homeostasis. However, its physiological roles in T cell development remain poorly understood. Here, we generated Zfatf/f-LckCre mice and demonstrated that T cell-specific Zfat-deletion in Zfatf/f-LckCre mice resulted in a reduction in the number of CD4+CD8+double-positive (DP) cells, CD4+single positive cells and CD8+single positive cells. Indeed, in Zfatf/f-LckCre DP cells, positive selection was severely impaired. Defects of positive selection in Zfat-deficient thymocytes were not restored in the presence of the exogenous TCR by using TCR-transgenic mice. Furthermore, Zfat-deficient DP cells showed a loss of CD3ζ phosphorylation in response to T cell antigen receptor (TCR)-stimulation concomitant with dysregulation of extracellular signal-related kinase (ERK) and early growth response protein (Egr) activities. These results demonstrate that Zfat is required for proper regulation of the TCR-proximal signalings, and is a crucial molecule for positive selection through ERK and Egr activities, thus suggesting that a full understanding of the precise molecular mechanisms of Zfat will provide deeper insight into T cell development and immune regulation.
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Affiliation(s)
- Masahiro Ogawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | - Tadashi Okamura
- Division of Animal Models, Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shuhei Ishikura
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | - Keiko Doi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | - Hiroshi Matsuzaki
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | - Yoko Tanaka
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | - Takeharu Ota
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | - Kunihiro Hayakawa
- Department of Immunology and Pathology, National Institute for Global Health and Medicine, Chiba, Japan
| | - Harumi Suzuki
- Department of Immunology and Pathology, National Institute for Global Health and Medicine, Chiba, Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
| | | | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- Central Research Institute for Advanced Molecular Medicine, Fukuoka University, Jonan-ku, Fukuoka, Japan
- * E-mail:
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20
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Baron MH, Vacaru A, Nieves J. Erythroid development in the mammalian embryo. Blood Cells Mol Dis 2013; 51:213-9. [PMID: 23932234 DOI: 10.1016/j.bcmd.2013.07.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/25/2013] [Indexed: 12/22/2022]
Abstract
Erythropoiesis is the process by which progenitors for red blood cells are produced and terminally differentiate. In all vertebrates, two morphologically distinct erythroid lineages (primitive, embryonic, and definitive, fetal/adult) form successively within the yolk sac, fetal liver, and marrow and are essential for normal development. Red blood cells have evolved highly specialized functions in oxygen transport, defense against oxidation, and vascular remodeling. Here we review key features of the ontogeny of red blood cell development in mammals, highlight similarities and differences revealed by genetic and gene expression profiling studies, and discuss methods for identifying erythroid cells at different stages of development and differentiation.
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Affiliation(s)
- Margaret H Baron
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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21
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Liu Y, Maxwell S, Feng T, Zhu X, Elston RC, Koyutürk M, Chance MR. Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data. BMC SYSTEMS BIOLOGY 2012; 6 Suppl 3:S15. [PMID: 23281810 PMCID: PMC3524014 DOI: 10.1186/1752-0509-6-s3-s15] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Background Interactions among genomic loci (also known as epistasis) have been suggested as one of the potential sources of missing heritability in single locus analysis of genome-wide association studies (GWAS). The computational burden of searching for interactions is compounded by the extremely low threshold for identifying significant p-values due to multiple hypothesis testing corrections. Utilizing prior biological knowledge to restrict the set of candidate SNP pairs to be tested can alleviate this problem, but systematic studies that investigate the relative merits of integrating different biological frameworks and GWAS data have not been conducted. Results We developed four biologically based frameworks to identify pairwise interactions among candidate SNP pairs as follows: (1) for each human protein-coding gene, a set of SNPs associated with that gene was constructed providing a gene-based interaction model, (2) for each known biological pathway, a set of SNPs associated with the genes in the pathway was constructed providing a pathway-based interaction model, (3) a set of SNPs associated with genes in a disease-related subnetwork provides a network-based interaction model, and (4) a framework is based on the function of SNPs. The last approach uses expression SNPs (eSNPs or eQTLs), which are SNPs or loci that have defined effects on the abundance of transcripts of other genes. We constructed pairs of eSNPs and SNPs located in the target genes whose expression is regulated by eSNPs. For all four frameworks the SNP sets were exhaustively tested for pairwise interactions within the sets using a traditional logistic regression model after excluding genes that were previously identified to associate with the trait. Using previously published GWAS data for type 2 diabetes (T2D) and the biologically based pair-wise interaction modeling, we identify twelve genes not seen in the previous single locus analysis. Conclusion We present four approaches to detect interactions associated with complex diseases. The results show our approaches outperform the traditional single locus approaches in detecting genes that previously did not reach significance; the results also provide novel drug targets and biomarkers relevant to the underlying mechanisms of disease.
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Affiliation(s)
- Yu Liu
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
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22
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Pharmacogenomic update on multiple sclerosis: a focus on actual and new therapeutic strategies. THE PHARMACOGENOMICS JOURNAL 2012; 12:453-61. [PMID: 23044601 DOI: 10.1038/tpj.2012.41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory and demyelinating disease of central nervous system comprising several subtypes. Pharmacological treatment involves only few drugs. Among these, interferon beta (IFN-β) and glatiramer acetate were the most used. Although evidence supports the efficacy of these agents in treating MS symptoms, actual studies allowed to introduce new innovative drugs in clinical practice. Applying pharmacogenetic approach to MS, IFN-β and several other immune pathways were abundantly investigated. Numerous reports identified some promising therapy markers but only few markers have emerged as clinically useful. This may be partially due to differences in clinical and methodological criteria in the studies. Indeed, responder and non-responder definitions lack standardized clinical definition. The goal of this review is to treat advances in research on the pharmacogenetic markers of MS drugs and to highlight possible correlations between type of responses and genetic profile, with regard to clinical and methodological discrepancies in the studies.
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23
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Identification of six loci associated with pelvic organ prolapse using genome-wide association analysis. Obstet Gynecol 2012; 118:1345-1353. [PMID: 22105264 DOI: 10.1097/aog.0b013e318236f4b5] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVE There is evidence that both environmental and genetic factors contribute to pelvic organ prolapse. We conducted a genome-wide association study to investigate whether common genetic variants modify the risk of pelvic organ prolapse. METHODS We recruited women who had been evaluated and treated for pelvic organ prolapse at the University of Utah from 1996 to 2008 and their affected female relatives. Those in the case group were genotyped on the Illumina 550K platform. We genetically matched 2,976 white control participants available from Illumina as the control group. Association tests were adjusted for related participants using two different software programs: EMMAX and Genie. Confirmation of findings was performed in a cohort of Dutch women (n=76) with recurrent pelvic organ prolapse and family history of pelvic organ prolapse. RESULTS The Utah study sample included 115 case group participants treated for pelvic organ prolapse, in most case group participants with surgery (n=78) or repeat surgery (n=35). Results from association analyses using EMMAX software identified five single-nucleotide polymorphisms (SNPs) significantly associated with pelvic organ prolapse (P<1×10). Independent association analysis with Genie software identified three of the same SNPs and one additional SNP. The six SNPs were located at 4q21 (rs1455311), 8q24 (rs1036819), 9q22 (rs430794), 15q11 (rs8027714), 20p13 (rs1810636), and 21q22 (rs2236479). Nominally significant findings (P<.05) or findings trending toward significance (P<.1) were observed for five of the six SNPs in the Dutch cohort. CONCLUSION Six SNPs have been identified that are significantly associated with pelvic organ prolapse in high-risk familial case group participants and that provide evidence for a genetic contribution to pelvic organ prolapse. LEVEL OF EVIDENCE II.
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Barbaux S, Gascoin-Lachambre G, Buffat C, Monnier P, Mondon F, Tonanny MB, Pinard A, Auer J, Bessières B, Barlier A, Jacques S, Simeoni U, Dandolo L, Letourneur F, Jammes H, Vaiman D. A genome-wide approach reveals novel imprinted genes expressed in the human placenta. Epigenetics 2012; 7:1079-90. [PMID: 22894909 PMCID: PMC3466192 DOI: 10.4161/epi.21495] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genomic imprinting characterizes genes with a monoallelic expression, which is dependent on the parental origin of each allele. Approximately 150 imprinted genes are known to date, in humans and mice but, though computational searches have tried to extract intrinsic characteristics of these genes to identify new ones, the existing list is probably far from being comprehensive. We used a high-throughput strategy by diverting the classical use of genotyping microarrays to compare the genotypes of mRNA/cDNA vs. genomic DNA to identify new genes presenting monoallelic expression, starting from human placental material. After filtering of data, we obtained a list of 1,082 putative candidate monoallelic SNPs located in more than one hundred candidate genes. Among these, we found known imprinted genes, such as IPW, GRB10, INPP5F and ZNF597, which contribute to validate the approach. We also explored some likely candidates of our list and identified seven new imprinted genes, including ZFAT, ZFAT-AS1, GLIS3, NTM, MAGI2, ZC3H12Cand LIN28B, four of which encode zinc finger transcription factors. They are, however, not imprinted in the mouse placenta, except for Magi2. We analyzed in more details the ZFAT gene, which is paternally expressed in the placenta (as ZFAT-AS1, a non-coding antisense RNA) but biallelic in other tissues. The ZFAT protein is expressed in endothelial cells, as well as in syncytiotrophoblasts. The expression of this gene is, moreover, downregulated in placentas from complicated pregnancies. With this work we increase by about 10% the number of known imprinted genes in humans.
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Doi K, Fujimoto T, Okamura T, Ogawa M, Tanaka Y, Mototani Y, Goto M, Ota T, Matsuzaki H, Kuroki M, Tsunoda T, Sasazuki T, Shirasawa S. ZFAT plays critical roles in peripheral T cell homeostasis and its T cell receptor-mediated response. Biochem Biophys Res Commun 2012; 425:107-12. [PMID: 22828507 DOI: 10.1016/j.bbrc.2012.07.065] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 12/21/2022]
Abstract
ZFAT, originally identified as a candidate susceptibility gene for autoimmune thyroid disease, has been reported to be involved in apoptosis, development and primitive hematopoiesis. Zfat is highly expressed in T- and B-cells in the lymphoid tissues, however, its physiological function in the immune system remains totally unknown. Here, we generated the T cell-specific Zfat-deficient mice and demonstrated that Zfat-deficiency leads to a remarkable reduction in the number of the peripheral T cells. Intriguingly, a reduced expression of IL-7Rα and the impaired responsiveness to IL-7 for the survival were observed in the Zfat-deficient T cells. Furthermore, a severe defect in proliferation and increased apoptosis in the Zfat-deficient T cells following T cell receptor (TCR) stimulation was observed with a reduced IL-2Rα expression as well as a reduced IL-2 production. Thus, our findings reveal that Zfat is a critical regulator in peripheral T cell homeostasis and its TCR-mediated response.
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Affiliation(s)
- Keiko Doi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
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26
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Makvandi-Nejad S, Hoffman GE, Allen JJ, Chu E, Gu E, Chandler AM, Loredo AI, Bellone RR, Mezey JG, Brooks SA, Sutter NB. Four loci explain 83% of size variation in the horse. PLoS One 2012; 7:e39929. [PMID: 22808074 PMCID: PMC3394777 DOI: 10.1371/journal.pone.0039929] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 05/29/2012] [Indexed: 01/09/2023] Open
Abstract
Horse body size varies greatly due to intense selection within each breed. American Miniatures are less than one meter tall at the withers while Shires and Percherons can exceed two meters. The genetic basis for this variation is not known. We hypothesize that the breed population structure of the horse should simplify efforts to identify genes controlling size. In support of this, here we show with genome-wide association scans (GWAS) that genetic variation at just four loci can explain the great majority of horse size variation. Unlike humans, which are naturally reproducing and possess many genetic variants with weak effects on size, we show that horses, like other domestic mammals, carry just a small number of size loci with alleles of large effect. Furthermore, three of our horse size loci contain the LCORL, HMGA2 and ZFAT genes that have previously been found to control human height. The LCORL/NCAPG locus is also implicated in cattle growth and HMGA2 is associated with dog size. Extreme size diversification is a hallmark of domestication. Our results in the horse, complemented by the prior work in cattle and dog, serve to pinpoint those very few genes that have played major roles in the rapid evolution of size during domestication.
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Affiliation(s)
- Shokouh Makvandi-Nejad
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Gabriel E. Hoffman
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Jeremy J. Allen
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Erin Chu
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Esther Gu
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Alyssa M. Chandler
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Ariel I. Loredo
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
- Biology Department, La Sierra University, Riverside, California, United States of America
| | - Rebecca R. Bellone
- Department of Biology, University of Tampa, Tampa, Florida, United States of America
| | - Jason G. Mezey
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Samantha A. Brooks
- Department of Animal Science, Cornell University, Ithaca, New York, United States of America
| | - Nathan B. Sutter
- Department of Clinical Sciences, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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27
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Cao N, Yao ZX. The hemangioblast: from concept to authentication. Anat Rec (Hoboken) 2011; 294:580-8. [PMID: 21370498 DOI: 10.1002/ar.21360] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 01/13/2011] [Indexed: 11/06/2022]
Abstract
The hemangioblast hypothesis has been hotly debated for over a century. Hemangioblasts are defined as multipotent cells that can give rise to both hematopoietic cells and endothelial cells. The existence of hemangioblasts has now been confirmed and many important molecules and several signaling pathways are involved in their generation and differentiation. Fibroblast growth factor, renin-angiotensin system and runt-related transcription factor 1 (Runx1) direct the formation of hemangioblasts through highly selective gene expression patterns. On the other hand, the hemogenic endothelium theory and a newly discovered pattern of hematopoietic/endothelial differentiation make the genesis of hemangioblasts more complicated. But how hemangioblasts are formed and how hematopoietic cells or endothelial cells are derived from remains largely unknown. Here we summarize the current knowledge of the signaling pathways and molecules involved in hemangioblast development and suggest some future clinical applications.
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Affiliation(s)
- Nian Cao
- Department of Physiology, Third Military Medical University, Chongqing, China
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Doi K, Fujimoto T, Koyanagi M, Tsunoda T, Tanaka Y, Yoshida Y, Takashima Y, Kuroki M, Sasazuki T, Shirasawa S. ZFAT is a critical molecule for cell survival in mouse embryonic fibroblasts. Cell Mol Biol Lett 2011; 16:89-100. [PMID: 21225468 PMCID: PMC6275631 DOI: 10.2478/s11658-010-0041-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 12/08/2010] [Indexed: 01/24/2023] Open
Abstract
ZFAT was originally identified as an immune-related transcriptional regulator containing 18 C2H2-type zinc-finger domains and one AT-hook. ZFAT is highly conserved among species and functions as an anti-apoptotic molecule in the lymphoblastic leukemia cell line, MOLT-4. We recently demonstrated that ZFAT is an essential molecule for hematopoietic differentiation in blood islands through the direct regulation of particular transcriptional factors, including Tal1, for endothelial cell assembly, and for the branch point formation of capillary-like structures. However, the molecular mechanisms underlying the anti-apoptotic function of ZFAT remain unknown. Here, we report that ZFAT knockdown by small interfering RNA induced apoptosis in mouse embryonic fibroblasts (MEFs). This response had been similarly observed for MOLT-4 cells. To explore the molecular mechanisms for ZFAT in anti-apoptotic function in both MEFs and MOLT-4 cells, microarray expression analysis and quantitative RT-PCR were done. Of interest was that Bcl-2 and Il6st were identified as commonly down-regulated genes by the depletion of ZFAT for both MEFs and MOLT-4 cells. These results suggest that ZFAT is a critical molecule for cell survival in MEFs and MOLT-4 cells at least in part through the regulation of the apoptosis involved in the BCL-2- and IL6st-mediated pathways. Further elucidation of the molecular functions for ZFAT might shed light on the cellular programs in the mesoderm-derived cells.
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Affiliation(s)
- Keiko Doi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Takahiro Fujimoto
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Midori Koyanagi
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Toshiyuki Tsunoda
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Yoko Tanaka
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Yasuhiro Yoshida
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
| | - Yasuo Takashima
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | - Masahide Kuroki
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
| | | | - Senji Shirasawa
- Department of Cell Biology, Faculty of Medicine, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka, 814-0180 Japan
- Center for Advanced Molecular Medicine, Fukuoka University, Fukuoka, 814-0180 Japan
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