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Blatnik MC, Gallagher TL, Amacher SL. Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1751. [PMID: 35851751 PMCID: PMC9840655 DOI: 10.1002/wrna.1751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.
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Affiliation(s)
- Monica C. Blatnik
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Thomas L. Gallagher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Sharon L. Amacher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
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2
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Carraco G, Martins-Jesus AP, Andrade RP. The vertebrate Embryo Clock: Common players dancing to a different beat. Front Cell Dev Biol 2022; 10:944016. [PMID: 36036002 PMCID: PMC9403190 DOI: 10.3389/fcell.2022.944016] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022] Open
Abstract
Vertebrate embryo somitogenesis is the earliest morphological manifestation of the characteristic patterned structure of the adult axial skeleton. Pairs of somites flanking the neural tube are formed periodically during early development, and the molecular mechanisms in temporal control of this early patterning event have been thoroughly studied. The discovery of a molecular Embryo Clock (EC) underlying the periodicity of somite formation shed light on the importance of gene expression dynamics for pattern formation. The EC is now known to be present in all vertebrate organisms studied and this mechanism was also described in limb development and stem cell differentiation. An outstanding question, however, remains unanswered: what sets the different EC paces observed in different organisms and tissues? This review aims to summarize the available knowledge regarding the pace of the EC, its regulation and experimental manipulation and to expose new questions that might help shed light on what is still to unveil.
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Affiliation(s)
- Gil Carraco
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | | | - Raquel P. Andrade
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas (FMCB), Universidade do Algarve, Campus de Gambelas, Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, Lisbon, Portugal
- *Correspondence: Raquel P. Andrade,
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3
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Xiaoli L, Fengbin H, Shihui H, Xi N, Sheng L, Zhou W, Xueqin R, Jiafu W. Detection of genomic structure variants associated with wrinkled skin in Xiang pig by next generation sequencing. Aging (Albany NY) 2021; 13:24710-24739. [PMID: 34837693 PMCID: PMC8660620 DOI: 10.18632/aging.203711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 08/02/2021] [Indexed: 11/25/2022]
Abstract
Wrinkling is prominent manifestation of aging skin. A mutant phenotype characterized by systemic wrinkles and thickened skin was discovered in Xiang pig populations with incidence about 1-3%. The feature in histological structure was epidermal hyperplasia and thickening, collagen fibers disorder. To uncover genetic mechanisms for the mutant phenotype of Xiang pigs with systemic wrinkle (WXP), a genome-wide of structural variations (SVs) in WXP was described by next generation resequencing, taking Xiang pigs (XP) and European pigs (EUP) as compares. Total of 32,308 SVs were detected from three pig groups and 965 SVs were identified specifically from WXP, involving 481 protein-coding genes. These genes were mainly enriched in nuclear structure, ECM components and immunomodulatory pathways. According to gene function and enrichment analysis, we found that 65 candidate SVs in 59 protein genes were probably related with the systemic wrinkle of WXP. Of these, several genes are reported to be associate with aging, such as EIF4G2, NOLC1, XYLT1, FUT8, MDM2 and so on. The insertion/deletion and duplication variations of SVs in these genes resulted in the loss of stop-codon or frameshift mutation, and aberrant alternative splicing of transcripts. These genes are involved in cell lamin filament, intermediate filament cytoskeleton, supramolecular complex, cell differentiation and regulation of macromolecule metabolic process etc. Our study suggested that the loss of function or aberrant expression of these genes lead to structural disorder of nuclear and the extracellular matrix (ECM) in skin cells, which probably was the genetic mechanisms for the mutant phenotype of systemic skin wrinkle of Xiang pig.
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Affiliation(s)
- Liu Xiaoli
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Hu Fengbin
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Huang Shihui
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Niu Xi
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Li Sheng
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang Zhou
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Ran Xueqin
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Wang Jiafu
- Institute of Agro-Bioengineering, Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Science and College of Animal Science, Guizhou University, Guiyang 550025, China
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4
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Anderson MJ, Magidson V, Kageyama R, Lewandoski M. Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function. eLife 2020; 9:55608. [PMID: 33210601 PMCID: PMC7717904 DOI: 10.7554/elife.55608] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
During vertebrate development, the presomitic mesoderm (PSM) periodically segments into somites, which will form the segmented vertebral column and associated muscle, connective tissue, and dermis. The periodicity of somitogenesis is regulated by a segmentation clock of oscillating Notch activity. Here, we examined mouse mutants lacking only Fgf4 or Fgf8, which we previously demonstrated act redundantly to prevent PSM differentiation. Fgf8 is not required for somitogenesis, but Fgf4 mutants display a range of vertebral defects. We analyzed Fgf4 mutants by quantifying mRNAs fluorescently labeled by hybridization chain reaction within Imaris-based volumetric tissue subsets. These data indicate that FGF4 maintains Hes7 levels and normal oscillatory patterns. To support our hypothesis that FGF4 regulates somitogenesis through Hes7, we demonstrate genetic synergy between Hes7 and Fgf4, but not with Fgf8. Our data indicate that Fgf4 is potentially important in a spectrum of human Segmentation Defects of the Vertebrae caused by defective Notch oscillations.
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Affiliation(s)
- Matthew J Anderson
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, United States
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, United States
| | - Ryoichiro Kageyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Mark Lewandoski
- Genetics of Vertebrate Development Section, Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, United States
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5
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Guo M, Xu C, Chen YZ, Sun QW, Zhao XY, Liu X, Yang Y, Hu YY, Li FF, Liu SL. Associations of CXCL1 gene 5'UTR variations with ovarian cancer. J Ovarian Res 2020; 13:43. [PMID: 32326946 PMCID: PMC7181480 DOI: 10.1186/s13048-020-00640-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are about 2.4 hundred thousand new cases and 1.5 hundred thousand deaths of ovarian cancer (OC) annually in the world. Chronic inflammation is a risk factor for OC. C-X-C motif chemokine ligand 1 (CXCL1) defects may facilitate inflammation and transactivate EGFR in ovarian cancer, but the precise haplotypes associated with the potential diseases remained largely unknown. In this work, we characterized CXCL1 gene variations to elucidate their possible associations with OC. METHODS We analyzed the CXCL1 gene for 300 OC patients with 400 healthy participants as controls. The statistical analyses and Hardy-Weinberg equilibrium tests of the patients and control populations were conducted using the SPSS software (version 19.0) and Plink (version 1.9). RESULTS The variants rs11547681, rs201090116, rs199791199, rs181868085, rs4074 and rs1814092 within or near the CXCL1 gene were characterized. The genetic heterozygosity of rs11547681 and rs4074 was very high. Statistical analysis showed that the variant rs11547681 in the gene was closely associated with the risk of OC in the Chinese Han population, although this variant was not associated with FIGO stages or pathological grades of the patients. CONCLUSIONS Rs11547681 in CXCL1 gene was associated with the risk of OC in the Chinese Han population.
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Affiliation(s)
- Man Guo
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,Department of Gynaecology and Obstetrics of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Chao Xu
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China.,Department of Colorectal Surgery of the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yan-Zhe Chen
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Qi-Wen Sun
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Xin-Ying Zhao
- Department of Blood Dialysis, Heilongjiang Agricultural Reclamation Bureau General Hospital, Harbin, China
| | - Xin Liu
- Fifth Hospital Gynecology the City of Xiamen, Xiamen, Fujian, China
| | - Yi Yang
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Yi-Yan Hu
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China
| | - Fei-Feng Li
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Hegang, Heilongjiang, China.
| | - Shu-Lin Liu
- Genomics Research Center, College of Pharmacy (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, China. .,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Hegang, Heilongjiang, China. .,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada.
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6
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Tietz KT, Gallagher TL, Mannings MC, Morrow ZT, Derr NL, Amacher SL. Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts. Dev Biol 2020; 462:129-140. [PMID: 32246943 DOI: 10.1016/j.ydbio.2020.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 02/18/2020] [Accepted: 03/20/2020] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.
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Affiliation(s)
- Kiel T Tietz
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Thomas L Gallagher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Monica C Mannings
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary T Morrow
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Nicolas L Derr
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Sharon L Amacher
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA; Interdisciplinary Graduate Program in Molecular, Cellular and Developmental Biology, The Ohio State University, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA; Center for Muscle Health and Neuromuscular Disorders, The Ohio State University, Columbus, OH, 43210, USA.
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7
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Saffroy R, Lafaye G, Desterke C, Ortiz-Tudela E, Amirouche A, Innominato P, Pham P, Benyamina A, Lemoine A. Several clock genes polymorphisms are meaningful risk factors in the development and severity of cannabis addiction. Chronobiol Int 2018; 36:122-134. [PMID: 30526093 DOI: 10.1080/07420528.2018.1523797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Circadian rhythms have been related to psychiatric diseases and regulation of dopaminergic transmission, especially in substance abusers. The relationship between them remained enigmatic and no data on the role of clock genes on cannabis dependence have been documented. We aimed at exploring the role of clock gene genotypes as potential predisposing factor to cannabis addiction, using a high throughput mass spectrometry methodology that enables the large-scale analysis of the known relevant polymorphisms of the clock genes. We have conducted a case-control study on 177 Caucasians categorizing between cannabis-addicted subjects and casual consumers based on structured interviews recorded socio-demographic data, AUDIT, Fagerström test, MINI, and medical examinations. Alcohol, opiates, and stimulants' consumption was as exclusion criteria. We report an association between several Single Nucleotide Polymorphism (SNP)s in main circadian genes SNPs, especially the gene locus HES7/PER1 on chromosome 17 and cannabis consumption as well as the development of neuropsychiatric and social disorders. This SNP's signature that may represent a meaningful risk factor in the development of cannabis dependence and its severity requires to be deeply explored in a prospective study.
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Affiliation(s)
- Raphael Saffroy
- a Dpt Biochimie et Oncogénétique, plate-forme Oncomolpath/INCa - F94800 , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,b INSERM UMR-S 1193 , Université Paris-Sud , Villejuif , France
| | - Genevieve Lafaye
- c Dpt Addictologie , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,d INSERM U1178 , Villejuif , France
| | - Christophe Desterke
- e INSERM UMS 33 , University Paris Saclay - UFR Medecine , Villejuif , France
| | - Elisabeth Ortiz-Tudela
- a Dpt Biochimie et Oncogénétique, plate-forme Oncomolpath/INCa - F94800 , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,b INSERM UMR-S 1193 , Université Paris-Sud , Villejuif , France
| | - Ammar Amirouche
- c Dpt Addictologie , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,d INSERM U1178 , Villejuif , France
| | - Pasquale Innominato
- f Cancer Chronotherapy Unit, Cancer Research Centre, Warwick Medical School, Coventry, Warwickshire, United Kingdom & Department of Oncology , Queen Elizabeth Hospital Birmingham NHS Foundation Trust, Birmingham, United Kingdom & INSERM U935 , Villejuif , France
| | - Patrick Pham
- a Dpt Biochimie et Oncogénétique, plate-forme Oncomolpath/INCa - F94800 , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,b INSERM UMR-S 1193 , Université Paris-Sud , Villejuif , France
| | - Amine Benyamina
- c Dpt Addictologie , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,d INSERM U1178 , Villejuif , France
| | - Antoinette Lemoine
- a Dpt Biochimie et Oncogénétique, plate-forme Oncomolpath/INCa - F94800 , AP-HP, GH Paris-Sud, Hôpital Paul Brousse , Villejuif , France.,b INSERM UMR-S 1193 , Université Paris-Sud , Villejuif , France
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8
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Fujino Y, Yamada K, Sugaya C, Ooka Y, Ovara H, Ban H, Akama K, Otosaka S, Kinoshita H, Yamasu K, Mishima Y, Kawamura A. Deadenylation by the CCR4-NOT complex contributes to the turnover of hairy-related mRNAs in the zebrafish segmentation clock. FEBS Lett 2018; 592:3388-3398. [PMID: 30281784 DOI: 10.1002/1873-3468.13261] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/10/2018] [Accepted: 09/23/2018] [Indexed: 01/09/2023]
Abstract
In the zebrafish segmentation clock, hairy/enhancer of split-related genes her1, her7, and hes6 encodes components of core oscillators. Since the expression of cyclic genes proceeds rapidly in the presomitic mesoderm (PSM), these hairy-related mRNAs are subject to strict post-transcriptional regulation. In this study, we demonstrate that inhibition of the CCR4-NOT deadenylase complex lengthens poly(A) tails of hairy-related mRNAs and increases the amount of these mRNAs, which is accompanied by defective somite segmentation. In transgenic embryos, we show that EGFP mRNAs with 3'UTRs of hairy-related genes exhibit turnover similar to endogenous mRNAs. Our results suggest that turnover rates of her1, her7, and hes6 mRNAs are differently regulated by the CCR4-NOT deadenylase complex possibly through their 3'UTRs in the zebrafish PSM.
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Affiliation(s)
- Yuuri Fujino
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Kazuya Yamada
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Chihiro Sugaya
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuko Ooka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Hiroki Ovara
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Hiroyuki Ban
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Shiori Otosaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Hirofumi Kinoshita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuichiro Mishima
- Department of Molecular Biosciences, Faculty of Life Sciences, Kyoto Sangyo University, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Japan
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9
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Lefebvre M, Dieux-Coeslier A, Baujat G, Schaefer E, Judith SO, Bazin A, Pinson L, Attie-Bitach T, Baumann C, Fradin M, Pierquin G, Julia S, Quélin C, Doray B, Berg S, Vincent-Delorme C, Lambert L, Bachmann N, Lacombe D, Isidor B, Laurent N, Joelle R, Blanchet P, Odent S, Kervran D, Leporrier N, Abel C, Segers K, Guiliano F, Ginglinger-Fabre E, Selicorni A, Goldenberg A, El Chehadeh S, Francannet C, Demeer B, Duffourd Y, Thauvin-Robinet C, Verloes A, Cormier-Daire V, Riviere JB, Faivre L, Thevenon J. Diagnostic strategy in segmentation defect of the vertebrae: a retrospective study of 73 patients. J Med Genet 2018; 55:422-429. [DOI: 10.1136/jmedgenet-2017-104939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/02/2018] [Accepted: 01/21/2018] [Indexed: 11/04/2022]
Abstract
BackgroundSegmentation defects of the vertebrae (SDV) are non-specific features found in various syndromes. The molecular bases of SDV are not fully elucidated due to the wide range of phenotypes and classification issues. The genes involved are in the Notch signalling pathway, which is a key system in somitogenesis. Here we report on mutations identified in a diagnosis cohort of SDV. We focused on spondylocostal dysostosis (SCD) and the phenotype of these patients in order to establish a diagnostic strategy when confronted with SDV.Patients and methodsWe used DNA samples from a cohort of 73 patients and performed targeted sequencing of the five known SCD-causing genes (DLL3, MESP2, LFNG, HES7 and TBX6) in the first 48 patients and whole-exome sequencing (WES) in 28 relevant patients.ResultsTen diagnoses, including four biallelic variants in TBX6, two biallelic variants in LFNG and DLL3, and one in MESP2 and HES7, were made with the gene panel, and two diagnoses, including biallelic variants in FLNB and one variant in MEOX1, were made by WES. The diagnostic yield of the gene panel was 10/73 (13.7%) in the global cohort but 8/10 (80%) in the subgroup meeting the SCD criteria; the diagnostic yield of WES was 2/28 (8%).ConclusionAfter negative array CGH, targeted sequencing of the five known SCD genes should only be performed in patients who meet the diagnostic criteria of SCD. The low proportion of candidate genes identified by WES in our cohort suggests the need to consider more complex genetic architectures in cases of SDV.
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10
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Sun CY, Sun C, Cheng R, Shi S, Han Y, Li XQ, Zhi JX, Li FF, Liu SL. Rs2459976 in ZW10 gene associated with congenital heart diseases in Chinese Han population. Oncotarget 2017; 9:3867-3874. [PMID: 29423089 PMCID: PMC5790506 DOI: 10.18632/oncotarget.23240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/01/2017] [Indexed: 11/25/2022] Open
Abstract
Congenital heart diseases (CHD) are a large group of prevalent and complex anatomic malformations of the heart, with the genetic basis remaining largely unknown. Since genes or factors associated with the differentiation of human embryonic stem (HES) cells would affect the development of all embryonic tissues, including cardiac progenitor cells, we postulated their potential roles in CHD. In this study, we focused on ZW10, a kinetochore protein involved in the process of proper chromosome segregation, and conducted comparative studies between CHD patients and normal controls matched in gender and age in Chinese Han populations. We identified three variations in the ZW10 gene, including rs2885987, rs2271261 and rs2459976, which all had high genetic heterozygosity. Association analysis of these genetic variations with CHD showed correlation between rs2459976 and the risk of CHD. We conclude that rs2459976 in the ZW10 gene is associated with CHD in Chinese Han populations.
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Affiliation(s)
- Chao-Yu Sun
- Systemomics Center, College of Pharmacy and Genomics Research Center, State-Province Key Laboratory of Biopharmaceutical Engineering, Harbin Medical University, Harbin, China.,Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Chi Sun
- Systemomics Center, College of Pharmacy and Genomics Research Center, State-Province Key Laboratory of Biopharmaceutical Engineering, Harbin Medical University, Harbin, China.,Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Rui Cheng
- Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Shuai Shi
- Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ying Han
- Systemomics Center, College of Pharmacy and Genomics Research Center, State-Province Key Laboratory of Biopharmaceutical Engineering, Harbin Medical University, Harbin, China.,Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xue-Qi Li
- Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ji-Xin Zhi
- Department of Cardiology, Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Fei-Feng Li
- Systemomics Center, College of Pharmacy and Genomics Research Center, State-Province Key Laboratory of Biopharmaceutical Engineering, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Heilongjiang, China
| | - Shu-Lin Liu
- Systemomics Center, College of Pharmacy and Genomics Research Center, State-Province Key Laboratory of Biopharmaceutical Engineering, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Heilongjiang, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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Wahi K, Friesen S, Coppola V, Cole SE. Putative binding sites for mir-125 family miRNAs in the mouse Lfng 3'UTR affect transcript expression in the segmentation clock, but mir-125a-5p is dispensable for normal somitogenesis. Dev Dyn 2017; 246:740-748. [PMID: 28710810 PMCID: PMC5597482 DOI: 10.1002/dvdy.24552] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 06/21/2017] [Accepted: 07/01/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND In vertebrate embryos, a "segmentation clock" times somitogenesis. Clock-linked genes, including Lunatic fringe (Lfng), exhibit cyclic expression in the presomitic mesoderm (PSM), with a period matching the rate of somite formation. The clock period varies widely across species, but the mechanisms that underlie this variability are not clear. The half-lives of clock components are proposed to influence the rate of clock oscillations, and are tightly regulated in the PSM. Interactions between Lfng and mir-125a-5p in the embryonic chicken PSM promote Lfng transcript instability, but the conservation of this mechanism in other vertebrates has not been tested. Here, we examine whether this interaction affects clock activity in a mammalian species. RESULTS Mutation of mir-125 binding sites in the Lfng 3'UTR leads to persistent, nonoscillatory reporter transcript expression in the caudal-most mouse PSM, although dynamic transcript expression recovers in the central PSM. Despite this, expression of endogenous mir-125a-5p is dispensable for mouse somitogenesis. CONCLUSIONS These results suggest that mir-125a sites in the Lfng 3' untranslated region influence transcript turnover in both mouse and chicken embryos, and support the existence of position-dependent regulatory mechanisms in the PSM. They further suggest the existence of compensatory mechanisms that can rescue the loss of mir-125a-5p in mice. Developmental Dynamics 246:740-748, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kanu Wahi
- Department of Molecular Genetics, College of Arts and Sciences, The Ohio State University, Columbus, Ohio
| | - Sophia Friesen
- Department of Molecular Genetics, College of Arts and Sciences, The Ohio State University, Columbus, Ohio
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio
| | - Susan E Cole
- Department of Molecular Genetics, College of Arts and Sciences, The Ohio State University, Columbus, Ohio
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Pnrc2 regulates 3'UTR-mediated decay of segmentation clock-associated transcripts during zebrafish segmentation. Dev Biol 2017. [PMID: 28648842 DOI: 10.1016/j.ydbio.2017.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Vertebrate segmentation is controlled by the segmentation clock, a molecular oscillator that regulates gene expression and cycles rapidly. The expression of many genes oscillates during segmentation, including hairy/Enhancer of split-related (her or Hes) genes, which encode transcriptional repressors that auto-inhibit their own expression, and deltaC (dlc), which encodes a Notch ligand. We previously identified the tortuga (tor) locus in a zebrafish forward genetic screen for genes involved in cyclic transcript regulation and showed that cyclic transcripts accumulate post-splicing in tor mutants. Here we show that cyclic mRNA accumulation in tor mutants is due to loss of pnrc2, which encodes a proline-rich nuclear receptor co-activator implicated in mRNA decay. Using an inducible in vivo reporter system to analyze transcript stability, we find that the her1 3'UTR confers Pnrc2-dependent instability to a heterologous transcript. her1 mRNA decay is Dicer-independent and likely employs a Pnrc2-Upf1-containing mRNA decay complex. Surprisingly, despite accumulation of cyclic transcripts in pnrc2-deficient embryos, we find that cyclic protein is expressed normally. Overall, we show that Pnrc2 promotes 3'UTR-mediated decay of developmentally-regulated segmentation clock transcripts and we uncover an additional post-transcriptional regulatory layer that ensures oscillatory protein expression in the absence of cyclic mRNA decay.
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Lyons LA, Creighton EK, Alhaddad H, Beale HC, Grahn RA, Rah H, Maggs DJ, Helps CR, Gandolfi B. Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7. BMC Genomics 2016; 17:265. [PMID: 27030474 PMCID: PMC4815086 DOI: 10.1186/s12864-016-2595-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The reduced cost and improved efficiency of whole genome sequencing (WGS) is drastically improving the development of cats as biomedical models. Persian cats are models for Leber's congenital amaurosis (LCA), the most severe and earliest onset form of visual impairment in humans. Cats with innocuous breed-defining traits, such as a bobbed tail, can also be models for somite segmentation and vertebral column development. METHODS The first WGS in cats was conducted on a trio segregating for LCA and the bobbed tail abnormality. Variants were identified using FreeBayes and effects predicted using SnpEff. Variants within a known haplotype block for cat LCA and specific candidate genes for both phenotypes were prioritized by the predicted variant effect on the proteins and concordant segregation within the trio. The efficiency of WGS of a single trio of domestic cats was evaluated. RESULTS A stop gain was identified at position c.577C > T in cat AIPL1, a predicted p.Arg193*. A c.5A > G variant causing a p.V2A was identified in HES7. The variants segregated concordantly in a Persian - Japanese bobtail pedigree. Over 1700 cats from 40 different breeds and populations were genotyped for the AIPL1 variant, defining an allelic frequency in only Persian -related breeds of 1.15%. A sub-set of cats was genotyped for the HES7 variant, supporting the variant as private to the Japanese bobtail breed. Approximately 18 million SNPs were identified for application in cat research. The cat AIPL1 variant would have been considered a high priority variant for evaluation, regardless of a priori knowledge from previous genetic studies. CONCLUSIONS This study represents the first effort of the 99 Lives Cat Genome Sequencing Initiative to identify disease--causing variants in the domestic cat using WGS. The current cat reference assembly is efficient for gene and variant identification. However, as the feline variant database improves, development of cats as biomedical models for human disease will be more efficient, providing an alternative, large animal model for drug and gene therapy trials. Undiagnosed human patients with early-onset blindness should be screened for this AIPL1 variant. The HES7 variant should further calibrate the somite segmentation clock.
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Affiliation(s)
- Leslie A. Lyons
- />Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 1600 E. Rollins Street, Columbia, MO 65211 USA
| | - Erica K. Creighton
- />Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 1600 E. Rollins Street, Columbia, MO 65211 USA
| | - Hasan Alhaddad
- />College of Science, Kuwait University, Safat, 13060 Kuwait
| | | | - Robert A. Grahn
- />Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - HyungChul Rah
- />Graduate School of Health Science Business Convergence, College of Medicine, Chungbuk National University, Chongju, Chungbuk Province 28644 South Korea
| | - David J. Maggs
- />Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California - Davis, Davis, CA 95616 USA
| | - Christopher R. Helps
- />Langford Veterinary Services, University of Bristol, Langford, Bristol, BS40 5DU UK
| | - Barbara Gandolfi
- />Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri - Columbia, E109 Vet Med Building, 1600 E. Rollins Street, Columbia, MO 65211 USA
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The many roles of Notch signaling during vertebrate somitogenesis. Semin Cell Dev Biol 2016; 49:68-75. [DOI: 10.1016/j.semcdb.2014.11.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/23/2014] [Accepted: 11/26/2014] [Indexed: 02/06/2023]
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15
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Li FF, Han Y, Shi S, Li X, Zhu XD, Zhou J, Shao QL, Li XQ, Liu SL. Characterization of Transcriptional Repressor Gene MSX1 Variations for Possible Associations with Congenital Heart Diseases. PLoS One 2015; 10:e0142666. [PMID: 26556783 PMCID: PMC4640503 DOI: 10.1371/journal.pone.0142666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/26/2015] [Indexed: 01/26/2023] Open
Abstract
Background The human heart consists of several cell types with distinct lineage origins. Interactions between these cardiac progenitors are very important for heart formation. The muscle segment homeobox gene family plays a key role in the cell morphogenesis and growth, controlled cellular proliferation, differentiation, and apoptosis, but the relationships between the genetic abnormalities and CHD phenotypes still remain largely unknown. The aim of this work was to evaluate variations in MSX1 and MSX2 for their possible associations with CHD. Methods We sequenced the MSX1 and MSX2 genes for 300 Chinese Han CHD patients and 400 normal controls and identified the variations. The statistical analyses were conducted using Chi-Square Tests as implemented in SPSS (version 19.0). The Hardy-Weinberg equilibrium test of the population was carried out using the online software OEGE. Results Six variations rs4647952, rs2048152, rs4242182, rs61739543, rs111542301 and rs3087539 were identified in the MSX2 gene, but the genetic heterozygosity of those SNPs was very low. In contrast, the genetic heterozygosity of two variations rs3821949 near the 5’UTR and rs12532 within 3’UTR of the MSX1 gene was considerably high. Statistical analyses showed that rs3821949 and rs12532 were associated with the risk of CHD (specifically VSD). Conclusions The SNPs rs3821949 and rs12532 in the MSX1 gene were associated with CHD in Chinese Han populations.
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Affiliation(s)
- Fei-Feng Li
- Genomics Research Center (one of the State-Province Key Laboratory of Biopharmaceutical Engineering, China), Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Heilongjiang, China
| | - Ying Han
- Department of Cardiology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shuai Shi
- Department of Cardiology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xia Li
- Genomics Research Center (one of the State-Province Key Laboratory of Biopharmaceutical Engineering, China), Harbin Medical University, Harbin, China
| | - Xi-Dong Zhu
- Department of Neurology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jing Zhou
- Intensive care unit, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qing-Liang Shao
- Department of Neonatalogy, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xue-Qi Li
- Department of Cardiology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
- * E-mail: (S-LL); (X-QL)
| | - Shu-Lin Liu
- Genomics Research Center (one of the State-Province Key Laboratory of Biopharmaceutical Engineering, China), Harbin Medical University, Harbin, China
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Heilongjiang, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
- * E-mail: (S-LL); (X-QL)
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