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Saul J, Hirose T, Horvitz HR. The transcriptional corepressor CTBP-1 acts with the SOX family transcription factor EGL-13 to maintain AIA interneuron cell identity in Caenorhabditis elegans. eLife 2022; 11:74557. [PMID: 35119366 PMCID: PMC8816384 DOI: 10.7554/elife.74557] [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: 10/10/2021] [Accepted: 01/10/2022] [Indexed: 11/17/2022] Open
Abstract
Cell identity is characterized by a distinct combination of gene expression, cell morphology, and cellular function established as progenitor cells divide and differentiate. Following establishment, cell identities can be unstable and require active and continuous maintenance throughout the remaining life of a cell. Mechanisms underlying the maintenance of cell identities are incompletely understood. Here, we show that the gene ctbp-1, which encodes the transcriptional corepressor C-terminal binding protein-1 (CTBP-1), is essential for the maintenance of the identities of the two AIA interneurons in the nematode Caenorhabditis elegans. ctbp-1 is not required for the establishment of the AIA cell fate but rather functions cell-autonomously and can act in later larval stage and adult worms to maintain proper AIA gene expression, morphology and function. From a screen for suppressors of the ctbp-1 mutant phenotype, we identified the gene egl-13, which encodes a SOX family transcription factor. We found that egl-13 regulates AIA function and aspects of AIA gene expression, but not AIA morphology. We conclude that the CTBP-1 protein maintains AIA cell identity in part by utilizing EGL-13 to repress transcriptional activity in the AIAs. More generally, we propose that transcriptional corepressors like CTBP-1 might be critical factors in the maintenance of cell identities, harnessing the DNA-binding specificity of transcription factors like EGL-13 to selectively regulate gene expression in a cell-specific manner.
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Affiliation(s)
- Josh Saul
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
| | - Takashi Hirose
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
| | - H Robert Horvitz
- Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, United States
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Biallelic in-frame deletion of SOX4 is associated with developmental delay, hypotonia and intellectual disability. Eur J Hum Genet 2022; 30:243-247. [PMID: 34750527 PMCID: PMC8821644 DOI: 10.1038/s41431-021-00968-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 02/03/2023] Open
Abstract
Intellectual disability (ID) represents an extremely heterogeneous group of disorders, characterized by significant limitations in intellectual function and adaptive behavior. Among the monogenic causes, autosomal recessive genes (ARID) are responsible for more than 50% of ID. Here, we report a novel in-frame homozygous deletion variant [c.730_753del; p.(Ala244_Gly251del)] in SOX4 (sex-determining region Y-related high-mobility group box 4), segregating with moderate to severe ID, hypotonia, and developmental delay in a Pakistani family. Our identified variant p.(Ala244_Gly251del) is predicted to remove evolutionarily conserved residues from the interdomain region and may destabilize the protein secondary structure. SOX4 belongs to group C of the SOX transcription regulating family known to be involved in early embryo development. Single-cell RNA data analysis of developing telencephalon revealed highly overlapping expression of SOX4 with SOX11 and DCX, known neurogenesis regulators. Our study expands the mutational landscape of SOX4 and the repertoire of the known genetic causes of ARID.
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Srivastava P, Bamba C, Chopra S, Mandal K. Role of miRNA polymorphism in recurrent pregnancy loss: a systematic review and meta-analysis. Biomark Med 2022; 16:101-115. [PMID: 35026953 DOI: 10.2217/bmm-2021-0568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
There are a plethora of publications on the role of miRNA gene polymorphism and its association with recurrent pregnancy loss (RPL), but a lack of uniformity in the studies available due to the variable subject population, heterogeneity and contrary results of significance. Rigorous data mining was done through PubMed, SCOPUS, Cochrane library, Elsevier and Google Scholar to extract the studies of interest published until June 2021. A total of eight SNPs of miRNAs have been included, where ≥2 studies per SNPs were available. Analysis was done on the basis of pooled odds ratios and 95% CI. This is the first meta-analysis on miRNA SNPs in RPL that suggests that rs11614913, rs3746444 and rs2292832 biomarkers may decrease the risk of RPL under different genetic models.
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Affiliation(s)
- Priyanka Srivastava
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education & Research, Sector-12, Chandigarh, 160012, India
| | - Chitra Bamba
- Genetic Metabolic Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education & Research, Sector-12, Chandigarh, 160012, India
| | - Seema Chopra
- Department of Obstetric & Gynaecology, Post Graduate Institute of Medical Education & Research, Sector-12, Chandigarh, 160012, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Rae Bareli Road, Lucknow, 226014, Uttar Pradesh, India
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Postnatal Sox6 Regulates Synaptic Function of Cortical Parvalbumin-Expressing Neurons. J Neurosci 2021; 41:8876-8886. [PMID: 34503995 PMCID: PMC8549537 DOI: 10.1523/jneurosci.0021-21.2021] [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: 01/05/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022] Open
Abstract
Cortical parvalbumin-expressing (Pvalb+) neurons provide robust inhibition to neighboring pyramidal neurons, crucial for the proper functioning of cortical networks. This class of inhibitory neurons undergoes extensive synaptic formation and maturation during the first weeks after birth and continue to dynamically maintain their synaptic output throughout adulthood. While several transcription factors, such as Nkx2-1, Lhx6, and Sox6, are known to be necessary for the differentiation of progenitors into Pvalb+ neurons, which transcriptional programs underlie the postnatal maturation and maintenance of Pvalb+ neurons' innervation and synaptic function remains largely unknown. Because Sox6 is continuously expressed in Pvalb+ neurons until adulthood, we used conditional knock-out strategies to investigate its putative role in the postnatal maturation and synaptic function of cortical Pvalb+ neurons in mice of both sexes. We found that early postnatal loss of Sox6 in Pvalb+ neurons leads to failure of synaptic bouton growth, whereas later removal in mature Pvalb+ neurons in the adult causes shrinkage of already established synaptic boutons. Paired recordings between Pvalb+ neurons and pyramidal neurons revealed reduced release probability and increased failure rate of Pvalb+ neurons' synaptic output. Furthermore, Pvalb+ neurons lacking Sox6 display reduced expression of full-length tropomyosin-receptor kinase B (TrkB), a key modulator of GABAergic transmission. Once re-expressed in neurons lacking Sox6, TrkB was sufficient to rescue the morphologic synaptic phenotype. Finally, we showed that Sox6 mRNA levels were increased by motor training. Our data thus suggest a constitutive role for Sox6 in the maintenance of synaptic output from Pvalb+ neurons into adulthood. SIGNIFICANCE STATEMENT Cortical parvalbumin-expressing (Pvalb+) inhibitory neurons provide robust inhibition to neighboring pyramidal neurons, crucial for the proper functioning of cortical networks. These inhibitory neurons undergo extensive synaptic formation and maturation during the first weeks after birth and continue to dynamically maintain their synaptic output throughout adulthood. However, it remains largely unknown which transcriptional programs underlie the postnatal maturation and maintenance of Pvalb+ neurons. Here, we show that the transcription factor Sox6 cell-autonomously regulates the synaptic maintenance and output of Pvalb+ neurons until adulthood, leaving unaffected other maturational features of this neuronal population.
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Belinostat resolves skin barrier defects in atopic dermatitis by targeting the dysregulated miR-335:SOX6 axis. J Allergy Clin Immunol 2020; 146:606-620.e12. [DOI: 10.1016/j.jaci.2020.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
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Dehbidi S, Farokhizadeh Z, Karimi MH, Afshari A, Behmanesh M, Sanati MH, Geramizadeh B, Yaghobi R. Evaluation of microRNA Gene Polymorphisms in Liver Transplant Patients with Hepatocellular Carcinoma. HEPATITIS MONTHLY 2020; 20. [DOI: 10.5812/hepatmon.102690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 08/30/2023]
Abstract
Background: Genetic polymorphism in the miRNA sequence might alter miRNA expression and/or maturation, which is associated with the development and progression of hepatocellular carcinoma (HCC) in liver transplant patients. Objectives: Therefore, the prevalence of miRNA-146a G > C (rs2910164), miRNA-499A > G (rs3746444), miRNA-149C > T (rs2292832), and miRNA-196a-2 C > T (rs11614913) gene polymorphisms was evaluated in liver recipients with HCC with or without experiencing graft rejection. Methods: In a cross-sectional study, tissue samples were collected from 60 HCC patients who underwent liver transplant surgery at Namazi Hospital, Shiraz, Iran, in 2013 - 2015. A control group consisting of 120 individuals was randomly selected, as well. The genomic DNA was extracted from collected tissues and blood samples. The miRNA-146a (rs2910164), miRNA-499 (rs3746444), miRNA-149 (rs2292832), and miRNA-196a-2 (rs11614913) gene polymorphisms were evaluated in patients with HCC using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Results: The CC genotype and C allele of the miRNA-146a (rs2910164) polymorphism were significantly associated with the increased risk of transplant rejection in patients with HCC (P = 0.05 and P = 0.05, respectively). The CC genotype and C allele of the miRNA-146a (rs2910164) were also significantly more frequent in male liver transplant patients who experienced acute rejection than in non-rejected ones (P = 0.05 and P = 0.03, respectively). However, no significant association was found between the genotypes and alleles of miRNA-499 (rs3746444), miRNA-149 (rs2292832), and miRNA-196a-2 (rs11614913) polymorphisms and HCC outcomes in liver transplant recipients. Conclusions: The importance of the CC genotype and C allele of the miRNA-146a (rs2910164) polymorphism in increasing the risk of transplant rejection was confirmed, but it needs further studies in larger populations.
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Oliver KF, Wahl AM, Dick M, Toenges JA, Kiser JN, Galliou JM, Moraes JGN, Burns GW, Dalton J, Spencer TE, Neibergs HL. Genomic Analysis of Spontaneous Abortion in Holstein Heifers and Primiparous Cows. Genes (Basel) 2019; 10:genes10120954. [PMID: 31766405 PMCID: PMC6969913 DOI: 10.3390/genes10120954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022] Open
Abstract
Background: The objectives of this study were to identify loci, positional candidate genes, gene-sets, and pathways associated with spontaneous abortion (SA) in cattle and compare these results with previous human SA studies to determine if cattle are a good SA model for humans. Pregnancy was determined at gestation day 35 for Holstein heifers and cows. Genotypes from 43,984 SNPs of 499 pregnant heifers and 498 pregnant cows that calved at full term (FT) were compared to 62 heifers and 28 cows experiencing SA. A genome-wide association analysis, gene-set enrichment analysis–single nucleotide polymorphism, and ingenuity pathway analysis were used to identify regions, pathways, and master regulators associated with SA in heifers, cows, and a combined population. Results: Twenty-three loci and 21 positional candidate genes were associated (p < 1 × 10−5) with SA and one of these (KIR3DS1) has been associated with SA in humans. Eight gene-sets (NES > 3.0) were enriched in SA and one was previously reported as enriched in human SA. Four master regulators (p < 0.01) were associated with SA within two populations. Conclusions: One locus associated with SA was validated and 39 positional candidate and leading-edge genes and 2 gene-sets were enriched in SA in cattle and in humans.
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Affiliation(s)
- Kayleen F. Oliver
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
| | - Alexandria M. Wahl
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
| | - Mataya Dick
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
| | - Jewel A. Toenges
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
| | - Jennifer N. Kiser
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
| | - Justine M. Galliou
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
| | - Joao G. N. Moraes
- Animal Sciences Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO S158A, USA (G.W.B.); (T.E.S.)
| | - Gregory W. Burns
- Animal Sciences Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO S158A, USA (G.W.B.); (T.E.S.)
| | - Joseph Dalton
- Department of Animal and Veterinary Sciences, University of Idaho, Caldwell, ID 1904 E, USA;
| | - Thomas E. Spencer
- Animal Sciences Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO S158A, USA (G.W.B.); (T.E.S.)
| | - Holly L. Neibergs
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA 646310, USA; (K.F.O.); (A.M.W.); (M.D.); (J.A.T.); (J.N.K.); (J.M.G.)
- Correspondence: ; Tel.: +1-1509-335-6491
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Alipour M, Abtin M, Hosseinzadeh A, Maleki M. Association between miR-146a C > G, miR-149 T > C, miR-196a2 T > C, and miR-499 A > G polymorphisms and susceptibility to idiopathic recurrent pregnancy loss. J Assist Reprod Genet 2019; 36:2237-2244. [PMID: 31605260 DOI: 10.1007/s10815-019-01573-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/23/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND A growing body of evidence suggests that microRNAs play fundamental regulatory roles in embryo implantation and maintenance of pregnancy. The aim of this study was to investigate the possible association between miR-146a C > G, miR-149 T > C, miR-196a2 T > C, and miR-499 A > G polymorphisms and genetic susceptibility to recurrent pregnancy loss (RPL). MATERIAL AND METHODS One hundred and twenty women with a history of two or more unexplained consecutive miscarriages and 90 ethnically matched healthy women with a history of at least two successful pregnancy outcomes and without a history of miscarriage were enrolled in a case-control study. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. RESULTS Our findings showed that the prevalence of miR-149 T > C polymorphism in RPL patients was significantly higher than those in healthy controls (p < 0.05). We also found that the presence of miR-149 C and miR-499 G alleles was significantly associated with susceptibility to RPL (p < 0.05). The miR-146a CC/miR-499 GG, miR-149 TC/miR-499 AG, and miR-196a2 TT/miR-499 GG combined genotypes were associated with the high risk of RPL (p < 0.05). CONCLUSION This study suggests that miR-149 T > C polymorphism and the presence of miR-149 C, and miR-499 G alleles are a genetic determinant for the risk of idiopathic RPL.
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Affiliation(s)
- Meysam Alipour
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Maryam Abtin
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asghar Hosseinzadeh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Maleki
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
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Liang Z, Xu J, Gu C. Novel role of the SRY-related high-mobility-group box D gene in cancer. Semin Cancer Biol 2019; 67:83-90. [PMID: 31356865 DOI: 10.1016/j.semcancer.2019.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/28/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022]
Abstract
The SRY-related high-mobility-group box (Sox) gene family encodes a set of transcription factors and is defined by the presence of highly conserved domains. The Sox gene can be divided into 10 groups (A-J). The SoxD subpopulation consists of Sox5, Sox6, Sox13 and Sox23, which are involved in the transcriptional regulation of developmental processes, including embryonic development, nerve growth and cartilage formation. Recently, the SoxD gene family was recognized as important transcriptional regulators associated with many types of cancer. In addition, Sox5 and Sox6 are representatives of the D subfamily, and there are many related studies; however, there are few reports on Sox13 and Sox23. In this review, we first introduce the structures of the SoxD genes. Next, we summarize the latest research progress on SoxD in various types of cancer. Finally, we discuss the potential direction of future SoxD research. In general, the information reviewed here may contribute to future experimental design and increase the potential of SoxD as a cancer treatment target.
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Affiliation(s)
- Zhenxing Liang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East, Zhengzhou 450052, China.
| | - Jing Xu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East, Zhengzhou 450052, China
| | - Chunhu Gu
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, 127 Changle West Road, Xi'an 710032, China.
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Sox13 is a novel early marker for hair follicle development. Biochem Biophys Res Commun 2019; 509:862-868. [PMID: 30638933 DOI: 10.1016/j.bbrc.2018.12.163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 12/25/2018] [Indexed: 12/16/2022]
Abstract
Sox13, a group D member of the Sry-related high-mobility group box (Sox) transcription factor family, is expressed in various tissues including the hair follicle. However, its spatiotemporal expression patterns in the hair follicle and its role in hair development remain to be elucidated. To address these questions, we generated Sox13-LacZ-knock-in mice (Sox13LacZ/+), in which the LacZ reporter gene was inserted in-frame into exon 2, which contains the translation initiation codon. X-gal staining in Sox13LacZ/+ embryos revealed that Sox13 is initially expressed in the epithelial portion of the placode, and subsequently in the hair germ and the hair peg during early hair follicle development. In postnatal catagen and anagen, Sox13 was detected in the epithelial sheath, whereas in telogen, Sox13 was localized in the bulge region, where hair follicle stem cells reside. Immunohistochemistry with an anti-β-galactosidase antibody and anti-hair keratin antibodies that specifically mark the different layers of the hair follicle revealed that Sox13 was predominantly expressed in the outer root sheath in anagen. However, the integumentary structures of Sox13LacZ/LacZ mice were grossly and histologically indistinguishable from those of wild type mice. These results suggest that although Sox13 is dispensable for epidermal and adnexal development, Sox13 is a useful marker for early hair follicle development.
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Blevins MA, Zhang C, Zhang L, Li H, Li X, Norris DA, Huang M, Zhao R. CPP-E1A fusion peptides inhibit CtBP-mediated transcriptional repression. Mol Oncol 2018; 12:1358-1373. [PMID: 29879296 PMCID: PMC6068344 DOI: 10.1002/1878-0261.12330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/17/2018] [Accepted: 05/18/2018] [Indexed: 12/29/2022] Open
Abstract
The carboxyl‐terminal binding proteins (CtBP) are transcriptional corepressors that regulate the expression of multiple epithelial‐specific and pro‐apoptotic genes. Overexpression of CtBP occurs in many human cancers where they promote the epithelial‐to‐mesenchymal transition, stem cell‐like features, and cell survival, while knockdown of CtBP in tumor cells results in p53‐independent apoptosis. CtBPs are recruited to their target genes by binding to a conserved PXDLS peptide motif present in multiple DNA‐binding transcription factors. Disrupting the interaction between CtBP and its transcription factor partners may be a means of altering CtBP‐mediated transcriptional repression and a potential approach for cancer therapies. However, small molecules targeting protein–protein interactions have traditionally been difficult to identify. In this study, we took advantage of the fact that CtBP binds to a conserved peptide motif to explore the feasibility of using peptides containing the PXDLS motif fused to cell‐penetrating peptides (CPP) to inhibit CtBP function. We demonstrate that these peptides disrupt the ability of CtBP to interact with its protein partner, E1A, in an AlphaScreen assay. Moreover, these peptides can enter both lung carcinoma and melanoma cells, disrupt the interaction between CtBP and a transcription factor partner, and inhibit CtBP‐mediated transcriptional repression. Finally, the constitutive expression of one such peptide, Pep1‐E1A‐WT, in a melanoma cell line reverses CtBP‐mediated oncogenic phenotypes including proliferation, migration, and sphere formation and limits tumor growth in vivo. Together, our results suggest that CPP‐fused PXDLS‐containing peptides can potentially be developed into a research tool or therapeutic agent targeting CtBP‐mediated transcriptional events in various biological pathways.
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Affiliation(s)
- Melanie A Blevins
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Caiguo Zhang
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Hong Li
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - David A Norris
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Mingxia Huang
- Department of Dermatology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
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Exploring digenic inheritance in arrhythmogenic cardiomyopathy. BMC MEDICAL GENETICS 2017; 18:145. [PMID: 29221435 PMCID: PMC5723071 DOI: 10.1186/s12881-017-0503-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 11/23/2017] [Indexed: 12/21/2022]
Abstract
Background Arrhythmogenic cardiomyopathy (ACM) is an inherited genetic disorder, characterized by the substitution of heart muscle with fibro-fatty tissue and severe ventricular arrhythmias, often leading to heart failure and sudden cardiac death. ACM is considered a monogenic disorder, but the low penetrance of mutations identified in patients suggests the involvement of additional genetic or environmental factors. Methods We used whole exome sequencing to investigate digenic inheritance in two ACM families where previous diagnostic tests have revealed a PKP2 mutation in all affected and some healthy individuals. In family members with PKP2 mutations we determined all genes that harbor variants in affected but not in healthy carriers or vice versa. We computationally prioritized the most likely candidates, focusing on known ACM genes and genes related to PKP2 through protein interactions, functional relationships, or shared biological processes. Results We identified four candidate genes in family 1, namely DAG1, DAB2IP, CTBP2 and TCF25, and eleven candidate genes in family 2. The most promising gene in the second family is TTN, a gene previously associated with ACM, in which the affected individual harbors two rare deleterious-predicted missense variants, one of which is located in the protein’s only serine kinase domain. Conclusions In this study we report genes that might act as digenic players in ACM pathogenesis, on the basis of co-segregation with PKP2 mutations. Validation in larger cohorts is still required to prove the utility of this model. Electronic supplementary material The online version of this article (10.1186/s12881-017-0503-7) contains supplementary material, which is available to authorized users.
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Amin-Beidokhti M, Mirfakhraie R, Zare-Karizi S, Karamoddin F. The role of parental microRNA alleles in recurrent pregnancy loss: an association study. Reprod Biomed Online 2016; 34:325-330. [PMID: 28012790 DOI: 10.1016/j.rbmo.2016.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/13/2016] [Accepted: 12/08/2016] [Indexed: 01/19/2023]
Abstract
The medical evaluation of recurrent pregnancy loss (RPL), the occurrence of two or more consecutive pregnancy losses prior to 20th week of gestation, is mainly focused on maternal factors. However, paternally expressed genes may also play a role in implantation and placenta quality. This study aimed to investigate the possible association between parental miR-196a2C>T and miR-499aT>C polymorphisms and RPL in a case-control study including 200 RPL couples and 400 healthy men and women. Genotyping was performed using Tetra-ARMS-PCR and PCR-RFLP for miR-196a2C>T and miR-499aT>C polymorphisms, respectively. In men, the association was observed between miR-499a and RPL under dominant (P = 0.006; odds ratio [OR] = 2.36; 95% confidence interval [CI], 1.28-4.37), recessive (P < 0.0001; OR = 2.89; 95% CI, 1.92-4.36) and additive (P < 0.001; OR = 2.77; 95% CI, 1.52-5.10) models. In women, the association was found between miR-196a2 and RPL under recessive (P = 0.02; OR = 2.19; 95% CI, 1.16-4.14) and additive (P = 0.03; OR = 1.53; 95% CI, 1.04-2.27) models. Hence, evidence was provided for association of genetic variation in parental microRNA polymorphisms with RPL. Further studies are required to validate the significance of the studied genetic variations in diverse ethnic populations.
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Affiliation(s)
- Mona Amin-Beidokhti
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shohreh Zare-Karizi
- Department of Biology, Varamin Islamic Azad University, Pishva-Varamin, Iran
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Cho SH, Chung KW, Kim JO, Jang H, Yoo JK, Choi Y, Ko JJ, Kim JH, Nishi Y, Yanase T, Lee WS, Kim NK. Association of miR-146aC>G, miR-149C>T, miR-196a2T>C, and miR-499A>G polymorphisms with risk of recurrent implantation failure in Korean women. Eur J Obstet Gynecol Reprod Biol 2016; 202:14-9. [PMID: 27156151 DOI: 10.1016/j.ejogrb.2016.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 03/25/2016] [Accepted: 04/02/2016] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the association of microRNA polymorphisms (miR-146aC>G, miR-149T>C, miR-196a2T>C, and miR-499A>G) in Korean patients with recurrent implantation failure (RIF). METHODS We conducted a case-control study of 354 Korean women: 120 patients with RIF and 234 healthy controls with at least one live birth and no history of pregnancy loss. RESULTS The combined miR-146aCG+GG/miR-196a2CC genotype was more frequent in patients than in controls (P<0.05), and apparently conferred increased susceptibility. Conversely, genotype-based multifactor dimensionality reduction analysis, revealed that the G-T-T-A (miR-146a/-149/-196a2/-499) and G-T-T inferred genotypes (miR-146a/-149/-196a2) were significantly less frequent in patients, which suggested potential protective effects. The expression of miR-146a for the GG homozygote was significantly lower (P<0.05) than expression of the CC homozygote from both the pre, mature and sequences of miR-146a-3p (P<0.05 each). The expression of miR-196a2 for the CC homozygote was also lower than the TT homozygote from the mature sequence of miR-196a2-3p (P<0.05). CONCLUSIONS These results suggest that the polymorphisms in miR-146a and miR-196a2 could alter their target mRNA expression. Our findings suggest that expression levels of miR-146aC>G, miR-196a2T>C and putative gene-gene interaction between miR-146a, miR-196a2, miR-149 may be involved in RIF development in Korean women.
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Affiliation(s)
- Sung Hwan Cho
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea; Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Seongnam, 463-712, South Korea
| | - Ki Wha Chung
- Department of Biological Science, College of Natural Science, Kongju National University, Gongju, South Korea
| | - Jung Oh Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea
| | - Hyogeun Jang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea
| | - Jung Ki Yoo
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea
| | - Youngsok Choi
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea
| | - Jung Jae Ko
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea
| | - Ji Hyang Kim
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Yoshihiro Nishi
- Department of Endocrinology and Diabetes, School of Medicine, Fukuoka University, 814-0180, Japan
| | - Toshihiko Yanase
- Department of Endocrinology and Diabetes, School of Medicine, Fukuoka University, 814-0180, Japan
| | - Woo Sik Lee
- Fertility Center of CHA Gangnam Medical Center, CHA University, Gangnam, 135-081, South Korea.
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 463-400, South Korea; Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Seongnam, 463-712, South Korea.
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Olaya-Sánchez D, Sánchez-Guardado LÓ, Ohta S, Chapman SC, Schoenwolf GC, Puelles L, Hidalgo-Sánchez M. Fgf3 and Fgf16 expression patterns define spatial and temporal domains in the developing chick inner ear. Brain Struct Funct 2016; 222:131-149. [PMID: 26995070 DOI: 10.1007/s00429-016-1205-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/19/2016] [Indexed: 11/26/2022]
Abstract
The inner ear is a morphologically complex sensory structure with auditory and vestibular functions. The developing otic epithelium gives rise to neurosensory and non-sensory elements of the adult membranous labyrinth. Extrinsic and intrinsic signals manage the patterning and cell specification of the developing otic epithelium by establishing lineage-restricted compartments defined in turn by differential expression of regulatory genes. FGF3 and FGF16 are excellent candidates to govern these developmental events. Using the chick inner ear, we show that Fgf3 expression is present in the borders of all developing cristae. Strong Fgf16 expression was detected in a portion of the developing vertical and horizontal pouches, whereas the cristae show weaker or undetected Fgf16 expression at different developmental stages. Concerning the rest of the vestibular sensory elements, both the utricular and saccular maculae were Fgf3 positive. Interestingly, strong Fgf16 expression delimited these Fgf16-negative sensory patches. The Fgf3-negative macula neglecta and the Fgf3-positive macula lagena were included within weakly Fgf16-expressing areas. Therefore, different FGF-mediated mechanisms might regulate the specification of the anterior (utricular and saccular) and posterior (neglecta and lagena) maculae. In the developing cochlear duct, dynamic Fgf3 and Fgf16 expression suggests their cooperation in the early specification and later cell differentiation in the hearing system. The requirement of Fgf3 and Fgf16 genes in endolymphatic apparatus development and neurogenesis are discussed. Based on these observations, FGF3 and FGF16 seem to be key signaling pathways that control the inner ear plan by defining epithelial identities within the developing otic epithelium.
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Affiliation(s)
- Daniel Olaya-Sánchez
- Department of Cell Biology, School of Science, University of Extremadura, Avda. de Elvas s/n, 06071, Badajoz, Spain
| | - Luis Óscar Sánchez-Guardado
- Department of Cell Biology, School of Science, University of Extremadura, Avda. de Elvas s/n, 06071, Badajoz, Spain
| | - Sho Ohta
- Department of Neurobiology and Anatomy, University of Utah, 2R066 School of Medicine, 30 N. 1900 E., Salt Lake City, UT, 84132-3401, USA
| | - Susan C Chapman
- Department of Biological Sciences, Clemson University, 340 Long Hall, Clemson, SC, 29634, USA
| | - Gary C Schoenwolf
- Department of Neurobiology and Anatomy, University of Utah, 2R066 School of Medicine, 30 N. 1900 E., Salt Lake City, UT, 84132-3401, USA
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, 30100, Murcia, Spain
| | - Matías Hidalgo-Sánchez
- Department of Cell Biology, School of Science, University of Extremadura, Avda. de Elvas s/n, 06071, Badajoz, Spain.
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Genetic variation in Micro-RNA genes of host genome affects clinical manifestation of symptomatic Human Cytomegalovirus infection. Hum Immunol 2015; 76:765-9. [PMID: 26429309 DOI: 10.1016/j.humimm.2015.09.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 07/31/2015] [Accepted: 09/27/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Micro-RNAs are implicated in various physiological and pathologic processes. In this study, we tested whether Micro-RNA gene variants of host-genome affect clinical manifestation of symptomatic HCMV infection. METHODOLOGY HCMV infection was detected by fluorescent PCR and immuno-histochemistry. The detection of genetic variants of four studied Micro-RNA tag-SNPs was done through PCR-RFLP assay and validated with DNA sequencing. RESULTS We observed an increased risk ranged from 3-folds to 5-folds among symptomatic HCMV cases for mutant genotype of rs2910164 (crude OR=3.11, p=0.009 and adjusted OR=3.25, p=0.007), rs11614913 (crude OR=3.20, p=0.006 and adjusted OR=3.48, p=0.004) and rs3746444 (crude OR=4.91, p=0.002 and adjusted OR=5.28, p=0.002) tag-SNPs. Interestingly, all the tag-SNPs that were significant after multiple comparisons at a FDR of 5% in symptomatic HCMV cases remained significant even after bootstrap analysis, providing internal validation to these results. Multifactor Dimensionality Reduction (MDR) analysis revealed 5-folds increased risk for symptomatic HCMV cases under the four-factor model (rs2910164, rs2292832, rs11614913 and rs3746444). CONCLUSIONS These results suggest that Micro-RNA gene variants of host-genome may affect clinical manifestation of symptomatic HCMV infection.
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17
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Jungke P, Hammer J, Hans S, Brand M. Isolation of Novel CreERT2-Driver Lines in Zebrafish Using an Unbiased Gene Trap Approach. PLoS One 2015; 10:e0129072. [PMID: 26083735 PMCID: PMC4471347 DOI: 10.1371/journal.pone.0129072] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 05/04/2015] [Indexed: 01/01/2023] Open
Abstract
Gene manipulation using the Cre/loxP-recombinase system has been successfully employed in zebrafish to study gene functions and lineage relationships. Recently, gene trapping approaches have been applied to produce large collections of transgenic fish expressing conditional alleles in various tissues. However, the limited number of available cell- and tissue-specific Cre/CreERT2-driver lines still constrains widespread application in this model organism. To enlarge the pool of existing CreERT2-driver lines, we performed a genome-wide gene trap screen using a Tol2-based mCherry-T2a-CreERT2 (mCT2aC) gene trap vector. This cassette consists of a splice acceptor and a mCherry-tagged variant of CreERT2 which enables simultaneous labeling of the trapping event, as well as CreERT2 expression from the endogenous promoter. Using this strategy, we generated 27 novel functional CreERT2-driver lines expressing in a cell- and tissue-specific manner during development and adulthood. This study summarizes the analysis of the generated CreERT2-driver lines with respect to functionality, expression, integration, as well as associated phenotypes. Our results significantly enlarge the existing pool of CreERT2-driver lines in zebrafish and combined with Cre-dependent effector lines, the new CreERT2-driver lines will be important tools to manipulate the zebrafish genome.
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Affiliation(s)
- Peggy Jungke
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Juliane Hammer
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Stefan Hans
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
| | - Michael Brand
- Biotechnology Center and Center for Regenerative Therapies Dresden, Dresden University of Technology, Fetscherstrasse 105, 01307 Dresden, Germany
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KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome. Blood 2015; 125:2405-17. [PMID: 25724378 DOI: 10.1182/blood-2014-08-590968] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/21/2015] [Indexed: 12/14/2022] Open
Abstract
We describe a case of severe neonatal anemia with kernicterus caused by compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents. One of the mutations is novel. This is the first described case of a KLF1-null human. The phenotype of severe nonspherocytic hemolytic anemia, jaundice, hepatosplenomegaly, and marked erythroblastosis is more severe than that present in congenital dyserythropoietic anemia type IV as a result of dominant mutations in the second zinc-finger of KLF1. There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching. We performed RNA-seq on circulating erythroblasts and found that human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell-cycle regulators, and blood group antigens. We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis. We also identify new roles for KLF1 in autophagy, global transcriptional control, and RNA splicing. We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis.
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19
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Pniewska E, Sokolowska M, Kupryś-Lipińska I, Kacprzak D, Kuna P, Pawliczak R. Exacerbating factors induce different gene expression profiles in peripheral blood mononuclear cells from asthmatics, patients with chronic obstructive pulmonary disease and healthy subjects. Int Arch Allergy Immunol 2015; 165:229-43. [PMID: 25634111 DOI: 10.1159/000370067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 11/21/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite several common phenotypic features, chronic obstructive pulmonary disease (COPD) and severe asthma differ with regard to their causative factors and pathophysiology. Both diseases may be exacerbated by environmental factors, however, the molecular profiles of disease episodes have not been comprehensively studied. We identified differences in gene and protein expression profiles expressed by peripheral blood mononuclear cells (PBMC) of COPD patients, patients with atopic asthma and healthy subjects when challenged with exacerbating factors in vitro: lipopolysaccharide (LPS), house dust mite (HDM) and cat allergen. METHODS PBMC isolated from patients with severe atopic asthma and COPD, as well as healthy subjects were stimulated with rDer p 1 DG, rFel d 1 DG and LPS. The changes in the expression of 47 genes belonging to five groups (phospholipase A2, eicosanoids, transcription factors, cytokines and airway remodeling) were studied using TaqMan low density array cards. Immunoblotting was used to study relative protein expression. RESULTS rDer p 1 significantly up-regulated the expression of PLA2G4A, PLA2G6, PLA2G15, CYSLTR1, LB4R2, PTGS1, PTGS2, FOXP1, GATA3, HDAC2, IREB2, PPARG, STAT4, TSLP and CHI3L1 genes in asthmatics in comparison to healthy subjects. LPS induced significant expression of ANXA1 and LTA4H in asthmatics when compared to COPD patients and healthy subjects. SOX6,STAT4 and IL1RL1 were induced in COPD after LPS stimulation. Analysis of protein expression revealed a pattern similar to mRNA expression. CONCLUSIONS LPS-induced exacerbation of asthma and COPD is characterized by differential expression of selected genes in PBMC. HDM allergen changed the expression profile of inflammatory genes between patients with asthma of atopic origin and healthy controls.
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Affiliation(s)
- Ewa Pniewska
- Division of Allergology, Immunology and Dermatology, Department of Immunopathology, Faculty of Biomedical Sciences and Postgraduate Training, Medical University of Lodz, Lodz, Poland
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20
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Chill HH, Dior UP, Kogan L, Revel A. microRNAs and Endometrial Pathophysiology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 887:143-55. [PMID: 26662990 DOI: 10.1007/978-3-319-22380-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Embryo implantation requires a reciprocal interaction between the blastocyst and endometrium and is associated with complex regulatory mechanisms. Since their discovery, microRNAs became prominent candidates providing missing links for many biological pathways. In recent years, microRNAs were implicated as one of the important players in regulation of various biological and physiological endometrial related processes. This chapter aims to present recent knowledge pertaining to the diverse aspects of microRNAs in the embryo-endometrial relationship. We will focus on the role of microRNAs in decidualization and their part in natural and stimulated cycles. Next, we will present recent studies deliberating the role of microRNAs in recurrent pregnancy loss and in the important phenomenon of recurrent implantation failure. Lastly, demonstrating an important aspect of embryo implantation and invasion, we will outline few microRNA related shared pathways of implantation and carcinogenesis.
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Affiliation(s)
- Henry H Chill
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel.
| | - Uri P Dior
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel
| | - Liron Kogan
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel
| | - Ariel Revel
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel
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21
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Abstract
Micro-RNAs (miRNAs) regulate diverse cellular processes such as cell differentiation, proliferation and apoptosis. Mutation in miRNAs results in various pathological conditions such as inflammation, viral infections, neurodegeneration, autoimmunity, and so on. We have evaluated the association of miR-146aC > G (rs2910164), miR-149T > C (rs2292832), miR-196a2T > C (rs11614913), and miR-499A > G (rs3746444) among patients with recurrent miscarriage (RM) and controls from North India. All the 200 patients with RM reported to experience at least 3 unexplained miscarriages before 20th week of gestation. Three hundred fertile women with no history of RMs were taken as controls. Both patients and controls were genotyped by the polymerase chain reaction amplification followed by restriction fragment length polymorphism. Variant alleles and genotypes of miR-499 A > G (Single Nucleotide Polymorphism Database [dbSNP] ID rs3746444) were found to be significant risks associated with patients having RM (odds ratio [OR] = 1.98; 95% confidence interval [CI] = 1.40-2.81; P value = .0001) and controls (OR = 3.64; 95% CI = 1.33-9.94; P value = .0109). A significant susceptible effect was found at allelic level in miR-196aT > C (dbSNP ID rs11614913) and miR-499 A > G (dbSNP ID rs3746444).
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Affiliation(s)
- Farah Parveen
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Suraksha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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22
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Kamachi Y, Kondoh H. Sox proteins: regulators of cell fate specification and differentiation. Development 2013; 140:4129-44. [PMID: 24086078 DOI: 10.1242/dev.091793] [Citation(s) in RCA: 417] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sox transcription factors play widespread roles during development; however, their versatile funtions have a relatively simple basis: the binding of a Sox protein alone to DNA does not elicit transcriptional activation or repression, but requires binding of a partner transcription factor to an adjacent site on the DNA. Thus, the activity of a Sox protein is dependent upon the identity of its partner factor and the context of the DNA sequence to which it binds. In this Primer, we provide an mechanistic overview of how Sox family proteins function, as a paradigm for transcriptional regulation of development involving multi-transcription factor complexes, and we discuss how Sox factors can thus regulate diverse processes during development.
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Affiliation(s)
- Yusuke Kamachi
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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23
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Xu Y, Gu L, Pan Y, Li R, Gao T, Song G, Nie Z, Chen L, Wang S, He B. Different effects of three polymorphisms in MicroRNAs on cancer risk in Asian population: evidence from published literatures. PLoS One 2013; 8:e65123. [PMID: 23750236 PMCID: PMC3672198 DOI: 10.1371/journal.pone.0065123] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 04/22/2013] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-protein-coding RNAs, which have emerged as integrated and important post-transcriptional regulators of gene expression. It has been demonstrated that single nucleotide polymorphisms (SNPs) exist in protein-coding genes. Accumulated studies have evaluated the association of miRNA SNPs with cancer risk, especially in Asian population, which included a series of related studies. However, the results remain controversial for the different genetic backgrounds, living habits and environment exposed. To evaluate the relationship between SNPs in miRNAs and cancer risk, 21 studies focused on Asian population were enrolled for the pooled analysis for three polymorphisms rs2910164, rs11614913, rs3746444 in three miRNAs miR-146aG>C, miR-196a2C>T, miR-499A>G using odds ratios (ORs) with 95% confidence intervals (CIs). For rs2910164 polymorphism, C allele was observed association with decreased overall cancer risk. In addition, subgroup analysis revealed of rs2910164 C allele decreased hepatocellular carcinoma (HCC), cervical cancer and prostate cancer risk among Chinese population. For rs11614913 polymorphism, TT genotype was observed to be associated with decreased cancer risk, especially for cancer type of colorectal cancer (CRC), lung cancer and country of Korea, North India. Whereas, rs3746444 G allele was an increased cancer risk factor in Chinese population, especially for breast cancer. In conclusion, this meta-analysis indicated that rs2910164 C allele was associated with decreased cancer risk in Chinese population. However, the association varied from different cancer types. Furthermore, TT genotype of rs11614913 was associated with decreased cancer risk. While different cancer types and countries contributed to different effects. Whereas, rs3746444 G allele was a risk factor in Chinese population, and the association varied from different cancer types.
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Affiliation(s)
- Yeqiong Xu
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ling Gu
- Department of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Yuqin Pan
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Rui Li
- Department of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Tianyi Gao
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Guoqi Song
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenlin Nie
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Liping Chen
- Department of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Shukui Wang
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- * E-mail: (BSH); (SKW)
| | - Bangshun He
- The Central Laboratory of Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- * E-mail: (BSH); (SKW)
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C-Terminal Binding Protein: A Molecular Link between Metabolic Imbalance and Epigenetic Regulation in Breast Cancer. Int J Cell Biol 2013; 2013:647975. [PMID: 23762064 PMCID: PMC3671672 DOI: 10.1155/2013/647975] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/14/2013] [Accepted: 04/15/2013] [Indexed: 12/21/2022] Open
Abstract
The prevalence of obesity has given rise to significant global concerns as numerous population-based studies demonstrate an incontrovertible association between obesity and breast cancer. Mechanisms proposed to account for this linkage include exaggerated levels of carbohydrate substrates, elevated levels of circulating mitogenic hormones, and inflammatory cytokines that impinge on epithelial programming in many tissues. Moreover, recently many scientists have rediscovered the observation, first described by Otto Warburg nearly a century ago, that most cancer cells undergo a dramatic metabolic shift in energy utilization and expenditure that fuels and supports the cellular expansion associated with malignant proliferation. This shift in substrate oxidation comes at the cost of sharp changes in the levels of the high energy intermediate, nicotinamide adenine dinucleotide (NADH). In this review, we discuss a novel example of how shifts in the concentration and flux of substrates metabolized and generated during carbohydrate metabolism represent components of a signaling network that can influence epigenetic regulatory events in the nucleus. We refer to this regulatory process as "metabolic transduction" and describe how the C-terminal binding protein (CtBP) family of NADH-dependent nuclear regulators represents a primary example of how cellular metabolic status can influence epigenetic control of cellular function and fate.
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Jeon YJ, Kim SY, Rah H, Choi DH, Cha SH, Yoon TK, Lee WS, Shim SH, Kim NK. Association of themiR-146aC>G,miR-149T>C,miR-196a2T>C, andmiR-499A>G Polymorphisms with Risk of Spontaneously Aborted Fetuses. Am J Reprod Immunol 2012; 68:408-17. [DOI: 10.1111/aji.12005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 07/12/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
| | | | | | - Dong Hee Choi
- Department of Obstetrics and Gynecology; CHA Bundang Medical Center; CHA University; Seongnam; Korea
| | - Sun Hee Cha
- Department of Obstetrics and Gynecology; CHA Bundang Medical Center; CHA University; Seongnam; Korea
| | - Tae Ki Yoon
- Fertility Center of CHA Gangnam Medical Center; CHA University; Seoul; Korea
| | - Woo Sik Lee
- Fertility Center of CHA Gangnam Medical Center; CHA University; Seoul; Korea
| | - Sung Han Shim
- Fertility Center of CHA Gangnam Medical Center; CHA University; Seoul; Korea
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Rah H, Jeon YJ, Shim SH, Cha SH, Choi DH, Kwon H, Kim JH, Shin JE, Kim NK. Association of miR-146aC>G, miR-196a2T>C, and miR-499A>G polymorphisms with risk of premature ovarian failure in Korean women. Reprod Sci 2012; 20:60-8. [PMID: 22872486 DOI: 10.1177/1933719112450341] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We investigated whether microRNA (miRNA) polymorphisms (miR-146aC>G, miR-196a2T>C, and miR-499A>G) confer risk of premature ovarian failure (POF) in Korean women. DNA samples from 136 patients with POF and 234 controls were genotyped for the 3 miRNA single-nucleotide polymorphisms by polymerase chain reaction-restriction fragment length polymorphism. The miR-146aCG/miR-196a2TC combined genotype was less frequent in patients than in controls (P < .05), conferring less susceptibility. Using haplotype-based multifactor dimensionality reduction analysis, the C-C-A and G-T-A inferred haplotypes (miR-146a/miR-196a2/miR-499) were less frequent in patients, suggesting protective effects (P < .05 for each), whereas the C-T-A and G-C-A haplotypes were more frequent in patients (P < .05 for each). The C-T and G-C haplotypes (miR-146a/miR-196a2) were more frequent in patients, whereas the C-C and G-T haplotypes were less frequent in patients (P < .05 for each). However, none of the 3 miRNA polymorphisms alone was associated with POF risk. Our findings suggest that putative gene-gene interaction between miR-146 and miR-196a2 may be involved in POF development.
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Affiliation(s)
- HyungChul Rah
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
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Kim YH, Shin JY, Na W, Kim J, Ju BG, Kim WS. Regulation of XFGF8 gene expression through SRY (sex-determining region Y)-box 2 in developing Xenopus embryos. Reprod Fertil Dev 2012; 24:769-77. [DOI: 10.1071/rd10332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 08/03/2011] [Indexed: 11/23/2022] Open
Abstract
Fibroblast growth factors (FGFs) function as mitogens and morphogens during vertebrate development. In the present study, to characterise the regulatory mechanism of FGF8 gene expression in developing Xenopus embryos the upstream region of the Xenopus FGF8 (XFGF8) gene was isolated. The upstream region of the XFGF8 gene contains two putative binding sites for the SRY (sex-determining region Y)-box 2 (SOX2) transcription factor. A reporter assay with serially deleted constructs revealed that the putative SOX2-binding motif may be a critical cis-element for XFGF8 gene activation in developing Xenopus embryos. Furthermore, Xenopus SOX2 (XSOX2) physically interacted with the SOX2-binding motif within the upstream region of the XFGF8 gene in vitro and in vivo. Depletion of endogenous XSOX2 resulted in loss of XFGF8 gene expression in midbrain–hindbrain junction, auditory placode, lens placode and forebrain in developing Xenopus embryos. Collectively, our results suggest that XSOX2 directly upregulates XFGF8 gene expression in the early embryonic development of Xenopus.
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Jeon YJ, Choi YS, Rah H, Kim SY, Choi DH, Cha SH, Shin JE, Shim SH, Lee WS, Kim NK. Association study of microRNA polymorphisms with risk of idiopathic recurrent spontaneous abortion in Korean women. Gene 2011; 494:168-73. [PMID: 22222140 DOI: 10.1016/j.gene.2011.12.026] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 12/02/2011] [Accepted: 12/17/2011] [Indexed: 12/18/2022]
Abstract
AIM The aim of this study was to investigate the association of microRNA polymorphisms (miR-146aC>G, miR-149T>C, miR-196a2T>C, and miR-499A>G) in Korean patients with recurrent spontaneous abortion (RSA). METHODS We conducted a case-control study of 564 Korean women: 330 patients with at least two unexplained consecutive pregnancy losses and 234 healthy controls with at least one live birth and no history of pregnancy loss. RESULTS RSA patients exhibited significantly different frequencies of the miR-196a2CC (TT+TC vs. CC; adjusted odds ratio [AOR], 1.587; 95% confidence interval [CI], 1.042–2.417) and miR-499AG+GG genotypes (AOR, 1.587; 95% CI, 1.096–2.298) [corrected] compared with the control group. The combination of miR-196a2CC and miR-499AG+GG showed synergistic effects (AOR, 3.541; 95% CI, 1.645–7.624). CONCLUSION miR-196a2CC, miR-499AG+GG, and the miR-196a2CC/miR-499AG+GG combination are significantly associated with idiopathic RSA in Korean women.
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Affiliation(s)
- Young Joo Jeon
- Institute for Clinical Research, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
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Min KT, Kim JW, Jeon YJ, Jang MJ, Chong SY, Oh D, Kim NK. Association of the miR-146aC>G, 149C>T, 196a2C>T, and 499A>G polymorphisms with colorectal cancer in the Korean population. Mol Carcinog 2011; 51 Suppl 1:E65-73. [PMID: 22161766 DOI: 10.1002/mc.21849] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 11/04/2011] [Accepted: 11/09/2011] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are small, 18- to 22-nucleotide non-coding RNAs that regulate target gene expression. Although recent studies focused on various diseases that harbor the miR-146aC>G (rs2910164), 149C>T (rs2292832), 196a2C>T (rs11614913), and 499A>G (rs3746444) polymorphisms, the role of miRNA genetic variants in colorectal cancer is still unknown. The present study aimed to evaluate the role of four miRNA polymorphisms in patients with colorectal cancer. We enrolled 446 colorectal cancer patients and 502 control subjects from the Korean population. We found a significantly increased colorectal cancer risk with the miR-196a2CC genotype compared with the TT/CT genotype (AOR = 1.50; 95% CI = 1.11-2.04; P = 0.01; FDR-P = 0.04). In the stratified analyses, we observed both weak and strong association data. We found stronger associations of the miR-196a2 variants in the non-diabetic and rectal cancer groups than other stratified groups. Our data suggest that the miRNA variants could affect the development of colorectal cancer in the Korean population.
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Affiliation(s)
- Kyung Tae Min
- Institute for Clinical Research, School of Medicine, CHA University, Seongnam, South Korea
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30
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An CI, Dong Y, Hagiwara N. Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6. BMC DEVELOPMENTAL BIOLOGY 2011; 11:59. [PMID: 21985497 PMCID: PMC3239296 DOI: 10.1186/1471-213x-11-59] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 10/10/2011] [Indexed: 01/06/2023]
Abstract
Background Sox6 is a multi-faceted transcription factor involved in the terminal differentiation of many different cell types in vertebrates. It has been suggested that in mice as well as in zebrafish Sox6 plays a role in the terminal differentiation of skeletal muscle by suppressing transcription of slow fiber specific genes. In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-seq analyses to identify Sox6 target genes in mouse fetal myotubes and generated muscle-specific Sox6 knockout (KO) mice to determine the Sox6 null muscle phenotype in adult mice. Results We have identified 1,066 Sox6 binding sites using mouse fetal myotubes. The Sox6 binding sites were found to be associated with slow fiber-specific, cardiac, and embryonic isoform genes that are expressed in the sarcomere as well as transcription factor genes known to play roles in muscle development. The concurrently performed RNA polymerase II (Pol II) ChIP-seq analysis revealed that 84% of the Sox6 peak-associated genes exhibited little to no binding of Pol II, suggesting that the majority of the Sox6 target genes are transcriptionally inactive. These results indicate that Sox6 directly regulates terminal differentiation of muscle by affecting the expression of sarcomere protein genes as well as indirectly through influencing the expression of transcription factors relevant to muscle development. Gene expression profiling of Sox6 KO skeletal and cardiac muscle revealed a significant increase in the expression of the genes associated with Sox6 binding. In the absence of the Sox6 gene, there was dramatic upregulation of slow fiber-specific, cardiac, and embryonic isoform gene expression in Sox6 KO skeletal muscle and fetal isoform gene expression in Sox6 KO cardiac muscle, thus confirming the role Sox6 plays as a transcriptional suppressor in muscle development. Conclusions Our present data indicate that during development, Sox6 functions as a transcriptional suppressor of fiber type-specific and developmental isoform genes to promote functional specification of muscle which is critical for optimum muscle performance and health.
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Affiliation(s)
- Chung-Il An
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, One Shields Avenue, Davis, California 95616, USA
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31
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Hagiwara N. Sox6, jack of all trades: a versatile regulatory protein in vertebrate development. Dev Dyn 2011; 240:1311-21. [PMID: 21495113 DOI: 10.1002/dvdy.22639] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2011] [Indexed: 12/27/2022] Open
Abstract
Approximately 20,000 genes are encoded in our genome, one tenth of which are thought to be transcription factors. Considering the complexity and variety of cell types generated during development, many transcription factors likely play multiple roles. Uncovering the versatile roles of Sox6 in vertebrate development sheds some light on how an organism efficiently utilizes the limited resources of transcription factors. The structure of the Sox6 gene itself may dictate its functional versatility. First, Sox6 contains no known regulatory domains; instead, it utilizes various cofactors. Second, Sox6 has a long 3'-UTR that contains multiple microRNA targets, thus its protein level is duly adjusted by cell type-specific microRNAs. Just combining these two characteristics alone makes Sox6 extremely versatile. To date, Sox6 has been reported to regulate differentiation of tissues of mesoderm, ectoderm, and endoderm origins, making Sox6 a truly multifaceted transcription factor.
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Affiliation(s)
- Nobuko Hagiwara
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, California 95616, USA.
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Cantu' C, Grande V, Alborelli I, Cassinelli L, Cantu' I, Colzani MT, Ierardi R, Ronzoni L, Cappellini MD, Ferrari G, Ottolenghi S, Ronchi A. A highly conserved SOX6 double binding site mediates SOX6 gene downregulation in erythroid cells. Nucleic Acids Res 2010; 39:486-501. [PMID: 20852263 PMCID: PMC3025548 DOI: 10.1093/nar/gkq819] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Sox6 transcription factor plays critical roles in various cell types, including erythroid cells. Sox6-deficient mice are anemic due to impaired red cell maturation and show inappropriate globin gene expression in definitive erythrocytes. To identify new Sox6 target genes in erythroid cells, we used the known repressive double Sox6 consensus within the εy-globin promoter to perform a bioinformatic genome-wide search for similar, evolutionarily conserved motifs located within genes whose expression changes during erythropoiesis. We found a highly conserved Sox6 consensus within the Sox6 human gene promoter itself. This sequence is bound by Sox6 in vitro and in vivo, and mediates transcriptional repression in transient transfections in human erythroleukemic K562 cells and in primary erythroblasts. The binding of a lentiviral transduced Sox6FLAG protein to the endogenous Sox6 promoter is accompanied, in erythroid cells, by strong downregulation of the endogenous Sox6 transcript and by decreased in vivo chromatin accessibility of this region to the PstI restriction enzyme. These observations suggest that the negative Sox6 autoregulation, mediated by the double Sox6 binding site within its own promoter, may be relevant to control the Sox6 transcriptional downregulation that we observe in human erythroid cultures and in mouse bone marrow cells in late erythroid maturation.
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Affiliation(s)
- Claudio Cantu'
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy.
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Xu J, Sankaran VG, Ni M, Menne TF, Puram RV, Kim W, Orkin SH. Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev 2010; 24:783-98. [PMID: 20395365 DOI: 10.1101/gad.1897310] [Citation(s) in RCA: 283] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The developmental switch from human fetal (gamma) to adult (beta) hemoglobin represents a clinically important example of developmental gene regulation. The transcription factor BCL11A is a central mediator of gamma-globin silencing and hemoglobin switching. Here we determine chromatin occupancy of BCL11A at the human beta-globin locus and other genomic regions in vivo by high-resolution chromatin immunoprecipitation (ChIP)-chip analysis. BCL11A binds the upstream locus control region (LCR), epsilon-globin, and the intergenic regions between gamma-globin and delta-globin genes. A chromosome conformation capture (3C) assay shows that BCL11A reconfigures the beta-globin cluster by modulating chromosomal loop formation. We also show that BCL11A and the HMG-box-containing transcription factor SOX6 interact physically and functionally during erythroid maturation. BCL11A and SOX6 co-occupy the human beta-globin cluster along with GATA1, and cooperate in silencing gamma-globin transcription in adult human erythroid progenitors. These findings collectively demonstrate that transcriptional silencing of gamma-globin genes by BCL11A involves long-range interactions and cooperation with SOX6. Our findings provide insight into the mechanism of BCL11A action and new clues for the developmental gene regulatory programs that function at the beta-globin locus.
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Affiliation(s)
- Jian Xu
- Children's Hospital Boston, Massachusetts 02115, USA
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34
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Sankaran VG, Xu J, Orkin SH. Advances in the understanding of haemoglobin switching. Br J Haematol 2010; 149:181-94. [PMID: 20201948 DOI: 10.1111/j.1365-2141.2010.08105.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The study of haemoglobin switching has represented a focus in haematology due in large part to the clinical relevance of the fetal to adult haemoglobin switch for developing targeted approaches to ameliorate the severity of the beta-haemoglobinopathies. Additionally, the process by which this switch occurs represents an important paradigm for developmental gene regulation. In this review, we provide an overview of both the embryonic primitive to definitive switch in haemoglobin expression, as well as the fetal to adult switch that is unique to humans and old world monkeys. We discuss the nature of these switches and models of their regulation. The factors that have been suggested to regulate this process are then discussed. With the increased understanding and discovery of molecular regulators of haemoglobin switching, such as BCL11A, new avenues of research may lead ultimately to novel therapeutic, mechanism-based approaches to fetal haemoglobin reactivation in patients.
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Affiliation(s)
- Vijay G Sankaran
- Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
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35
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Chew LJ, Gallo V. The Yin and Yang of Sox proteins: Activation and repression in development and disease. J Neurosci Res 2010; 87:3277-87. [PMID: 19437544 DOI: 10.1002/jnr.22128] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The general view of development consists of the acquisition of committed/differentiated phenotypes following a period of self-renewal and progenitor expansion. Lineage specification and progression are phenomena of antagonistic events, silencing tissue-specific gene expression in precursors to allow self-renewal and multipotentiality, and subsequently suppressing proliferation and embryonic gene expression to promote the restricted expression of tissue-specific genes during maturation. The high mobility group-containing Sox family of transcription factors constitutes one of the earliest classes of genes to be expressed during embryonic development. These proteins not only are indispensable for progenitor cell specification but also are critical for terminal differentiation of multiple cell types in a wide variety of lineages. Sox transcription factors are now known to induce or repress progenitor cell characteristics and cell proliferation or to activate the expression of tissue-specific genes. Sox proteins fulfill their diverse functions in developmental regulation by distinct molecular mechanisms. Not surprisingly, in addition to DNA binding and bending, Sox transcription factors also interact with different protein partners to function as coactivators or corepressors of downstream target genes. Here we seek to provide an overview of the current knowledge of Sox gene functional mechanisms, in an effort to understand their roles in both development and pathology.
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Affiliation(s)
- Li-Jin Chew
- Center for Neuroscience Research, Children's National Medical Center, Washington, DC, USA
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36
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Tarleton HP, Lemischka IR. Delayed differentiation in embryonic stem cells and mesodermal progenitors in the absence of CtBP2. Mech Dev 2009; 127:107-19. [PMID: 19825414 DOI: 10.1016/j.mod.2009.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 10/02/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
Abstract
Mammalian embryonic stem cells (ESCs) are characterized by an ability to self-renew and give rise to each of the three germ layers. ESCs are a pluripotential source of numerous primitive progenitors and committed lineages and can make stoichiometric decisions leading to either asymmetric or symmetric cell division. Several genes have been identified as essential for maintenance of self-renewal, but few non-lineage specific genes have been identified as essential for differentiation. We selected the chromatin factor Ctbp2 from microarray data for its enriched expression in stem cells, in comparison to committed progenitors. RNA interference (RNAi) was used to knockdown gene expression in mouse ESCs and the potential for transduced cells to self-renew and differentiate was assessed in ESC and mesodermal assays. Here, we demonstrate an important role for Ctbp2 in stem cell maintenance and regulation of differentiation using an in vitro system. The knockdown of Ctbp2 increases the prevalence of ESCs in culture, delays differentiation induced by LIF withdrawal, and introduces developmental changes in mesodermal differentiation. A model is presented for the importance of Ctbp2 in maintaining a balance in decisions to self-renewal and differentiate.
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Affiliation(s)
- Heather P Tarleton
- Molecular Cancer Epidemiology, Department of Epidemiology, School of Public Health, University of California, Los Angeles, CA 90095, USA.
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37
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Lefebvre V. The SoxD transcription factors--Sox5, Sox6, and Sox13--are key cell fate modulators. Int J Biochem Cell Biol 2009; 42:429-32. [PMID: 19647094 DOI: 10.1016/j.biocel.2009.07.016] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 07/02/2009] [Accepted: 07/23/2009] [Indexed: 01/14/2023]
Abstract
Sox5, Sox6, and Sox13 constitute the group D of sex-determining region (Sry)-related transcription factors. They are highly conserved in the family-specific high-mobility-group (HMG) box DNA-binding domain and in a group-specific coiled-coil domain. The latter mediates SoxD protein dimerization and thereby preferential binding to pairs of DNA recognition sites. The SoxD genes have overlapping expression and cell-autonomously control discrete lineages. Sox5 and Sox6 redundantly enhance chondrogenesis, but retard gliogenesis. Sox5 hinders melanogenesis, promotes neural crest generation, and controls the pace of neurogenesis. Sox6 promotes erythropoiesis, and Sox13 modulates T cell specification and is an autoimmune antigen. SoxD proteins enhance transactivation by Sox9 in chondrocytes, but antagonize Sox9 and other SoxE proteins in oligodendrocytes and melanocytes, and also repress transcription through various mechanisms in several other lineages. While their biological and molecular functions remain incompletely understood, the SoxD proteins have thus already proven that they critically modulate cell fate in major lineages.
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Affiliation(s)
- Véronique Lefebvre
- Department of Cell Biology and Orthopaedic Research Center, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.
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38
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Weisinger K, Wilkinson DG, Sela-Donenfeld D. Inhibition of BMPs by follistatin is required for FGF3 expression and segmental patterning of the hindbrain. Dev Biol 2008; 324:213-25. [PMID: 18823972 DOI: 10.1016/j.ydbio.2008.09.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 09/04/2008] [Accepted: 09/05/2008] [Indexed: 10/21/2022]
Abstract
A network of molecular interactions is required in the developing vertebrate hindbrain for the formation and anterior-posterior patterning of the rhombomeres. FGF signaling is required in this network to upregulate the expression of the Krox20 and Kreisler segmentation genes, but little is known of how FGF gene expression is regulated in the hindbrain. We show that the dynamic expression of FGF3 in chick hindbrain segments and boundaries is similar to that of the BMP antagonist, follistatin. Consistent with a regulatory relationship between BMP signaling and FGF3 expression, we find that an increase in BMP activity due to blocking of follistatin translation by morpholino antisense oligonucleotides or overexpression of BMP results in strong inhibition of FGF3 expression. Conversely, addition of follistatin leads to an increase in the level of FGF3 expression. Furthermore, the segmental inhibition of BMP activity by follistatin is required for the expression of Krox20, Hoxb1 and EphA4 in the hindbrain. In addition, we show that the maintenance of FGF3 gene expression requires FGF activity, suggestive of an autoregulatory loop. These results reveal an antagonistic relationship between BMP activity and FGF3 expression that is required for correct segmental gene expression in the chick hindbrain, in which follistatin enables FGF3 expression by inhibiting BMP activity.
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Affiliation(s)
- Karen Weisinger
- Koret School of Veterinary Medicine, Hebrew University, Faculty of Agriculture, Food and Environmental Quality Sciences, P.O. Box 12, Rehovot 76100, Israel
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39
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Stolt CC, Lommes P, Hillgärtner S, Wegner M. The transcription factor Sox5 modulates Sox10 function during melanocyte development. Nucleic Acids Res 2008; 36:5427-40. [PMID: 18703590 PMCID: PMC2553580 DOI: 10.1093/nar/gkn527] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The transcription factor Sox5 has previously been shown in chicken to be expressed in early neural crest cells and neural crest-derived peripheral glia. Here, we show in mouse that Sox5 expression also continues after neural crest specification in the melanocyte lineage. Despite its continued expression, Sox5 has little impact on melanocyte development on its own as generation of melanoblasts and melanocytes is unaltered in Sox5-deficient mice. Loss of Sox5, however, partially rescued the strongly reduced melanoblast generation and marker gene expression in Sox10 heterozygous mice arguing that Sox5 functions in the melanocyte lineage by modulating Sox10 activity. This modulatory activity involved Sox5 binding and recruitment of CtBP2 and HDAC1 to the regulatory regions of melanocytic Sox10 target genes and direct inhibition of Sox10-dependent promoter activation. Both binding site competition and recruitment of corepressors thus help Sox5 to modulate the activity of Sox10 in the melanocyte lineage.
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Affiliation(s)
- C Claus Stolt
- Institut für Biochemie, Emil-Fischer-Zentrum, Universität Erlangen, Fahrstrasse 17, D-91054 Erlangen, Germany
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40
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Hagiwara N, Yeh M, Liu A. Sox6 is required for normal fiber type differentiation of fetal skeletal muscle in mice. Dev Dyn 2007; 236:2062-76. [PMID: 17584907 DOI: 10.1002/dvdy.21223] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Sox6, a member of the Sox family of transcription factors, is highly expressed in skeletal muscle. Despite its abundant expression, the role of Sox6 in muscle development is not well understood. We hypothesize that, in fetal muscle, Sox6 functions as a repressor of slow fiber type-specific genes. In the wild-type mouse, differentiation of fast and slow fibers becomes apparent during late fetal stages (after approximately embryonic day 16). However, in the Sox6 null-p(100H) mutant mouse, all fetal muscle fibers maintain slow fiber characteristics, as evidenced by expression of the slow myosin heavy chain MyHC-beta. Knockdown of Sox6 expression in wild-type myotubes results in a significant increase in MyHC-beta expression, supporting our hypothesis. Analysis of the MyHC-beta promoter revealed a Sox consensus sequence that likely functions as a negative cis-regulatory element. Together, our results suggest that Sox6 plays a critical role in the fiber type differentiation of fetal skeletal muscle.
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Affiliation(s)
- Nobuko Hagiwara
- University of California, Davis, Division of Cardiovascular Medicine/Rowe Program in Human Genetics, Davis, California 95616, USA.
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41
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Gunasekera AM, Myrick A, Militello KT, Sims JS, Dong CK, Gierahn T, Le Roch K, Winzeler E, Wirth DF. Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum. Mol Biochem Parasitol 2007; 153:19-30. [PMID: 17307259 DOI: 10.1016/j.molbiopara.2007.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 11/29/2006] [Accepted: 01/10/2007] [Indexed: 10/23/2022]
Abstract
Control of gene expression is poorly understood in the Plasmodium system, where relatively few homologues to known eukaryotic transcription factors have been uncovered. Recent evidence suggests that the parasite may utilize a combinatorial mode of gene regulation, with multiple cis-acting sequences contributing to overall activity at individual promoters [1]. To further probe this mechanism of control, we first searched for over-represented sequence motifs among gene clusters sharing similar expression profiles in Plasmodium falciparum. More specifically, we applied bioinformatic tools to a previously characterized micro-array data set from drug-treated asexual stage cultures (Gunasekera et al., submitted). Cluster analysis of 600 drug responsive genes identified only a single 5' motif, GAGAGAA. Two additional 5' motifs, ACTATAAAGA and TGCAC, were also shared among loci displaying patterns of coordinate expression across varying asexual growth stages. Secondly and most importantly, the functional relevance of each motif was tested in two independent assays-transient transfection and gel-retardation experiments. The GAGAGAA and TGCAC motifs were both active in the former. The GAGAGAA and ACTATAAAGA elements formed specific RNA-protein, but not DNA-protein complexes in gel shift assays, suggesting a key level of control at the RNA level. This is the first report of functionally characterized motifs in P. falciparum that were uncovered following clustering analysis of its asexual stage transcriptome. Together, both the bioinformatic and functional data reported here imply that multiple forms of gene regulation, including post-transcriptional control, may be important in the malarial system.
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Affiliation(s)
- Anusha M Gunasekera
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Harvard University, Boston, MA, USA
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42
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Stolt CC, Schlierf A, Lommes P, Hillgärtner S, Werner T, Kosian T, Sock E, Kessaris N, Richardson WD, Lefebvre V, Wegner M. SoxD Proteins Influence Multiple Stages of Oligodendrocyte Development and Modulate SoxE Protein Function. Dev Cell 2006; 11:697-709. [PMID: 17084361 DOI: 10.1016/j.devcel.2006.08.011] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 05/18/2006] [Accepted: 08/17/2006] [Indexed: 11/21/2022]
Abstract
The myelin-forming oligodendrocytes are an excellent model to study transcriptional regulation of specification events, lineage progression, and terminal differentiation in the central nervous system. Here, we show that the group D Sox transcription factors Sox5 and Sox6 jointly and cell-autonomously regulate several stages of oligodendrocyte development in the mouse spinal cord. They repress specification and terminal differentiation and influence migration patterns. As a consequence, oligodendrocyte precursors and terminally differentiating oligodendrocytes appear precociously in spinal cords deficient for both Sox proteins. Sox5 and Sox6 have opposite functions than the group E Sox proteins Sox9 and Sox10, which promote oligodendrocyte specification and terminal differentiation. Both genetic as well as molecular evidence suggests that Sox5 and Sox6 directly interfere with the function of group E Sox proteins. Our studies reveal a complex regulatory network between different groups of Sox proteins that is essential for proper progression of oligodendrocyte development.
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Affiliation(s)
- C Claus Stolt
- Institut für Biochemie, Emil-Fischer-Zentrum, Universität Erlangen, D-91054 Erlangen, Germany
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43
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Quinlan KGR, Verger A, Kwok A, Lee SHY, Perdomo J, Nardini M, Bolognesi M, Crossley M. Role of the C-terminal binding protein PXDLS motif binding cleft in protein interactions and transcriptional repression. Mol Cell Biol 2006; 26:8202-13. [PMID: 16940173 PMCID: PMC1636740 DOI: 10.1128/mcb.00445-06] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
C-terminal binding proteins (CtBPs) are multifunctional proteins that can mediate gene repression. CtBPs contain a cleft that binds Pro-X-Asp-Leu-Ser (PXDLS) motifs. PXDLS motifs occur in numerous transcription factors and in effectors of gene repression, such as certain histone deacetylases. CtBPs have been depicted as bridging proteins that self-associate and link PXDLS-containing transcription factors to PXDLS-containing chromatin-modifying enzymes. CtBPs also recruit effectors that do not contain recognizable PXDLS motifs. We have investigated the importance of the PXDLS binding cleft to CtBP's interactions with various partner proteins and to its ability to repress transcription. We used CtBP cleft mutant and cleft-filled fusion derivatives to distinguish between partner proteins that bind in the cleft and elsewhere on the CtBP surface. Functional assays demonstrate that CtBP mutants that carry defective clefts retain repression activity when fused to heterologous DNA-binding domains. This result suggests that the cleft is not essential for recruiting effectors. In contrast, when tested in the absence of a fused DNA-binding domain, disruption of the cleft abrogates repression activity. These results demonstrate that the PXDLS binding cleft is functionally important but suggest that it is primarily required for localization of the CtBP complex to promoter-bound transcription factors.
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Affiliation(s)
- Kate G R Quinlan
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia
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44
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Hagiwara N, Ma B, Ly A. Slow and fast fiber isoform gene expression is systematically altered in skeletal muscle of the Sox6 mutant, p100H. Dev Dyn 2006; 234:301-11. [PMID: 16124007 DOI: 10.1002/dvdy.20535] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We have previously demonstrated that p100H mutant mice, which lack a functional Sox6 gene, exhibit skeletal and cardiac muscle degeneration and develop cardiac conduction abnormalities soon after birth. To understand the role of Sox6 in skeletal muscle development, we identified muscle-specific genes differentially expressed between wild-type and p100H mutant skeletal muscles and investigated their temporal expression in the mutant muscle. We found that, in the mutant skeletal muscle, slow fiber and cardiac isoform genes are expressed at significantly higher levels, whereas fast fiber isoform genes are expressed at significantly lower levels than wild-type. Onset of this aberrant fiber type-specific gene expression in the mutant coincides with the beginning of the secondary myotube formation, at embryonic day 15-16 in mice. Together with our earlier report, demonstrating early postnatal muscle defects in the Sox6 null-p100H mutant, the present results suggest that Sox6 likely plays an important role in muscle development.
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Affiliation(s)
- Nobuko Hagiwara
- University of California, Davis, Division of Cardiovascular Medicine, Rowe Program in Genetics, Davis, CA 95616, USA
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Yi Z, Cohen-Barak O, Hagiwara N, Kingsley PD, Fuchs DA, Erickson DT, Epner EM, Palis J, Brilliant MH. Sox6 directly silences epsilon globin expression in definitive erythropoiesis. PLoS Genet 2006; 2:e14. [PMID: 16462943 PMCID: PMC1359074 DOI: 10.1371/journal.pgen.0020014] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Accepted: 12/20/2005] [Indexed: 11/19/2022] Open
Abstract
Sox6 is a member of the Sox transcription factor family that is defined by the conserved high mobility group (HMG) DNA binding domain, first described in the testis determining gene, Sry. Previous studies have suggested that Sox6 plays a role in the development of the central nervous system, cartilage, and muscle. In the Sox6-deficient mouse, p100H, epsilony globin is persistently expressed, and increased numbers of nucleated red cells are present in the fetal circulation. Transfection assays in GM979 (erythroleukemic) cells define a 36-base pair region of the epsilony proximal promoter that is critical for Sox6 mediated repression. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assays demonstrate that Sox6 acts as a repressor by directly binding to the epsilony promoter. The normal expression of Sox6 in wild-type fetal liver and the ectopic expression of epsilony in p100H homozygous fetal liver demonstrate that Sox6 functions in definitive erythropoiesis. The present study shows that Sox6 is required for silencing of epsilony globin in definitive erythropoiesis and suggests a role for Sox6 in erythroid cell maturation. Thus, Sox6 regulation of epsilony globin might provide a novel therapeutical target in the treatment of hemoglobinopathies such as sickle cell anemia and thalassemia.
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Affiliation(s)
- Zanhua Yi
- Department of Pediatrics, University of Arizona, College of Medicine, Tucson, Arizona, United States of America
| | - Orit Cohen-Barak
- Department of Pediatrics, University of Arizona, College of Medicine, Tucson, Arizona, United States of America
| | - Nobuko Hagiwara
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of California Davis, Davis, California, United States of America
| | - Paul D Kingsley
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Deborah A Fuchs
- Department of Pathology, University of Arizona, College of Medicine, Tucson, Arizona, United States of America
| | - Drew T Erickson
- Department of Pediatrics, University of Arizona, College of Medicine, Tucson, Arizona, United States of America
| | - Elliot M Epner
- Department of Hematology & Oncology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - James Palis
- Department of Pediatrics, Center for Pediatric Biomedical Research, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Murray H Brilliant
- Department of Pediatrics, University of Arizona, College of Medicine, Tucson, Arizona, United States of America
- * To whom correspondence should be addressed. E-mail:
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Fernández-Lloris R, Osses N, Jaffray E, Shen LN, Vaughan OA, Girwood D, Bartrons R, Rosa JL, Hay RT, Ventura F. Repression of SOX6 transcriptional activity by SUMO modification. FEBS Lett 2006; 580:1215-21. [PMID: 16442531 DOI: 10.1016/j.febslet.2006.01.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Revised: 12/22/2005] [Accepted: 01/12/2006] [Indexed: 11/22/2022]
Abstract
SOX6 plays key functions in several developmental processes, including neurogenesis and skeleton formation. In this report, we show that SOX6 is modified in vitro and in vivo by small ubiquitin-related modifier (SUMO) on two distinct sites. Mutation of both sites abolished SOX6 sumoylation and increased SOX6 transcriptional activity. SUMO dependent repression of SOX6 transcription was promoted by UBC9 whereas siRNA to UBC9, cotransfection of inactive UBC9 or a SUMO protease increased SOX6 transcriptional activity. Furthermore, co-expression of SOX6 with SUMO2 results in the appearance of SOX6 in a punctate nuclear pattern that colocalized with promyelocytic leukemia protein, which was partially abolished by mutations in SOX6 sumoylation sites.
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Affiliation(s)
- R Fernández-Lloris
- Departament de Ciències Fisiològiques II, IDIBELL, Campus de Bellvitge, Universitat de Barcelona, C/Feixa Llarga s/n, 08907 L'Hospitalet de Llobregat, Spain
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47
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Abstract
Sox proteins are transcriptional regulators with a high-mobility-group domain as sequence-specific DNA-binding domain. For function, they generally require other transcription factors as partner proteins. Sox proteins furthermore affect DNA topology and may shape the conformation of enhancer-bound multiprotein complexes as architectural proteins. Recent studies suggest that Sox proteins are tightly regulated in their expression by many signalling pathways, and that their transcriptional activity is subject to post-translational modification and sequestration mechanisms. Sox proteins are thus ideally suited to perform their many different functions as transcriptional regulators throughout mammalian development. Their unique properties also cause Sox proteins to escape detection in many standard transcription assays. In melanocytes, studies have so far focused on the Sox10 protein which functions both during melanocyte specification and at later times in the melanocyte lineage. During specification, Sox10 activates the Mitf gene as the key regulator of melanocyte development. At later stages, it ensures cell-type specific expression of melanocyte genes such as Dopachrome tautomerase. Both activities require cooperation with transcriptional partner proteins such as Pax-3, CREB and eventually Mitf. If predictions can be made from other cell lineages, further functions of Sox proteins in melanocytes may still lie ahead.
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Affiliation(s)
- Michael Wegner
- Institut für Biochemie, Universität Erlangen-Nürnberg, D-91054 Erlangen, Germany.
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Maruyama M, Ichisaka T, Nakagawa M, Yamanaka S. Differential Roles for Sox15 and Sox2 in Transcriptional Control in Mouse Embryonic Stem Cells. J Biol Chem 2005; 280:24371-9. [PMID: 15863505 DOI: 10.1074/jbc.m501423200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sox family transcription factors play essential roles in cell differentiation, development, and sex determination. Sox2 was previously thought to be the sole Sox protein expressed in mouse embryonic stem (ES) cells. Sox2 associates with Oct3/4 to maintain self-renewal of ES cells. In the current study, digital differential display identified transcripts for an additional Sox family member, Sox15, enriched in mouse ES cells. Reverse transcription-PCR confirmed that Sox15 expression is highest in undifferentiated ES cells and repressed upon differentiation. Sox15 is expressed at low levels in several tissues, including testis and muscle. In vitro studies showed that Sox15, like Sox2, associated with Oct3/4 on DNA sequences containing the octamer motif and Sox-binding site. Gel mobility shift assays and SELEX analyses showed that Sox15 binds similar DNA sequences as Sox2 but with weaker affinity. In contrast to the early embryonic lethality observed in Sox2-null mice, Sox15-null ES cells and mice were grossly normal. DNA microarray analyses revealed that Otx2, Ctgf, Ebaf, and Hrc are dysregulated in Sox15-null ES cells, however. Chromatin immunoprecipitation showed that Sox15, but not Sox2, bound to a Sox consensus binding site within the Hrc gene. Taken together, these data demonstrate differential roles for Sox15 and Sox2 in transcriptional control in mouse ES cells.
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Affiliation(s)
- Masayoshi Maruyama
- Department of Stem Cell Biology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
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Scheel JR, Ray J, Gage FH, Barlow C. Quantitative analysis of gene expression in living adult neural stem cells by gene trapping. Nat Methods 2005; 2:363-70. [PMID: 15846364 DOI: 10.1038/nmeth755] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2005] [Accepted: 03/21/2005] [Indexed: 12/27/2022]
Abstract
The potential of neural stem cells (NSCs) for the treatment of neurodegenerative diseases makes the identification and characterization of genes involved in neural stem cell responses therapeutically important. Although technologies exist for measuring gene expression in cells, they often provide only a representative expression profile specific to a stimulus and time. We developed a complementary technology based on a retroviral-vector gene-trap approach that uses beta-lactamase-induced disruption of fluorescence resonance energy transfer in the fluorophore CCF-2/AM. A library of 'tagged' adult rat NSCs was generated by transduction with gene-trap virus produced from a single-integrant packaging cell line that allowed us to quantitatively analyze dynamic gene expression changes in real time in living NSCs. Using this library we identified previously unknown genes regulated by oxidative stress, indomethacin and factors that induce differentiation, and show that one of the trapped genes, Sox6, is sufficient to induce astrocytic differentiation when overexpressed.
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Affiliation(s)
- John R Scheel
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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50
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Ohuchi H, Yasue A, Ono K, Sasaoka S, Tomonari S, Takagi A, Itakura M, Moriyama K, Noji S, Nohno T. Identification ofcis-element regulating expression of the mouseFgf10 gene during inner ear development. Dev Dyn 2005; 233:177-87. [PMID: 15765517 DOI: 10.1002/dvdy.20319] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Fibroblast growth factor (FGF) signaling is crucial for the induction and growth of the ear, a sensory organ that involves intimate tissue interactions. Here, we report the abnormality of Fgf10 null ear and the identification of a cis-regulatory element directing otic expression of Fgf10. In Fgf10 null inner ears, we found that the initial development of semicircular, vestibular, and cochlear divisions is roughly normal, after which there are abnormalities of semicircular canal/cristae and vestibular development. The mutant semicircular disks remain without canal formation by the perinatal stage. To elucidate regulation of the Fgf10 expression during inner ear development, we isolated a 6.6-kb fragment of its 5'-upstream region and examined its transcriptional activity with transgenic mice, using a lacZ-reporter system. From comparison of the mouse sequences of the 6.6-kb fragment with corresponding sequences of the human and chicken Fgf10, we identified a 0.4-kb enhancer sequence that drives Fgf10 expression in the developing inner ear. The enhancer sequences have motifs for many homeodomain-containing proteins (e.g., Prx, Hox, Nkx), in addition to POU-domain factors (e.g., Brn3), zinc-finger transcription factors (e.g., GATA-binding factors), TCF/LEF-1, and a SMAD-interacting protein. Thus, FGF10 signaling is dispensable for specification of otic compartment identity but is required for hollowing the semicircular disk. Furthermore, the analysis of a putative inner ear enhancer of Fgf10 has disclosed a complicated regulation of Fgf10 during inner ear development by numerous transcription factors and signaling pathways.
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Affiliation(s)
- Hideyo Ohuchi
- Department of Biological Science and Technology, Faculty of Engineering, University of Tokushima, 2-1 Minami-Jyosanjima-cho, Tokushima City 770-8506, Japan.
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