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Chapman G, Determan J, Jetter H, Kaushik K, Prakasam R, Kroll KL. Defining cis-regulatory elements and transcription factors that control human cortical interneuron development. iScience 2024; 27:109967. [PMID: 38827400 PMCID: PMC11140214 DOI: 10.1016/j.isci.2024.109967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/08/2024] [Accepted: 05/09/2024] [Indexed: 06/04/2024] Open
Abstract
Although human cortical interneurons (cINs) are a minority population in the cerebral cortex, disruption of interneuron development is a frequent contributor to neurodevelopmental disorders. Here, we utilized a model for deriving cINs from human embryonic stem cells to profile chromatin state changes and generate an atlas of cis-regulatory elements (CREs) controlling human cIN development. We used these data to define candidate transcription factors (TFs) that may bind these CREs to regulate interneuron progenitor specification. Among these were RFX3 and RFX4, risk genes for autism spectrum disorder (ASD) with uncharacterized roles in human neuronal development. Using RFX3 and RFX4 knockdown models, we demonstrated new requirements for both genes in interneuron progenitor specification, with RFX3 deficiency causing precocious neuronal differentiation while RFX4 deficiency instead resulted in cessation of progenitor cell proliferation. Together, this work both defined central features of cis-regulatory control and identified new TF requirements for human interneuron development.
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Affiliation(s)
- Gareth Chapman
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Julianna Determan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Haley Jetter
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Komal Kaushik
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ramachandran Prakasam
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristen L. Kroll
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
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2
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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Kim JK, Hong S, Park J, Kim S. Metabolic and Transcriptomic Changes in the Mouse Brain in Response to Short-Term High-Fat Metabolic Stress. Metabolites 2023; 13:metabo13030407. [PMID: 36984847 PMCID: PMC10051449 DOI: 10.3390/metabo13030407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
The chronic consumption of diets rich in saturated fats leads to obesity and associated metabolic disorders including diabetes and atherosclerosis. Intake of a high-fat diet (HFD) is also recognized to dysregulate neural functions such as cognition, mood, and behavior. However, the effects of short-term high-fat diets on the brain are elusive. Here, we investigated molecular changes in the mouse brain following an acute HFD for 10 days by employing RNA sequencing and metabolomics profiling. Aberrant expressions of 92 genes were detected in the brain tissues of acute HFD-exposed mice. The differentially expressed genes were enriched for various pathways and processes such as superoxide metabolism. In our global metabolomic profiling, a total of 59 metabolites were significantly altered by the acute HFD. Metabolic pathways upregulated from HFD-exposed brain tissues relative to control samples included oxidative stress, oxidized polyunsaturated fatty acids, amino acid metabolism (e.g., branched-chain amino acid catabolism, and lysine metabolism), and the gut microbiome. Acute HFD also elevated levels of N-acetylated amino acids, urea cycle metabolites, and uracil metabolites, further suggesting complex changes in nitrogen metabolism. The observed molecular events in the present study provide a valuable resource that can help us better understand how acute HFD stress impacts brain homeostasis.
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Affiliation(s)
- Ji-Kwang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sehoon Hong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jina Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for the BioCentury, KAIST, Daejeon 34141, Republic of Korea
- KAIST Stem Cell Center, KAIST, Daejeon 34141, Republic of Korea
- Correspondence:
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Chen H, Tu S, Yuan C, Tian F, Zhang Y, Sun Y, Shao Z. HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples. Genome Biol 2022; 23:62. [PMID: 35227282 PMCID: PMC8883642 DOI: 10.1186/s13059-022-02627-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Identifying genomic regions with hypervariable ChIP-seq or ATAC-seq signals across given samples is essential for large-scale epigenetic studies. In particular, the hypervariable regions across tumors from different patients indicate their heterogeneity and can contribute to revealing potential cancer subtypes and the associated epigenetic markers. We present HyperChIP as the first complete statistical tool for the task. HyperChIP uses scaled variances that account for the mean-variance dependence to rank genomic regions, and it increases the statistical power by diminishing the influence of true hypervariable regions on model fitting. A pan-cancer case study illustrates the practical utility of HyperChIP.
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5
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Luo G, Yogeshwar S, Lin L, Mignot EJM. T cell reactivity to regulatory factor X4 in type 1 narcolepsy. Sci Rep 2021; 11:7841. [PMID: 33837283 PMCID: PMC8035403 DOI: 10.1038/s41598-021-87481-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/23/2021] [Indexed: 11/11/2022] Open
Abstract
Type 1 narcolepsy is strongly (98%) associated with human leukocyte antigen (HLA) class II DQA1*01:02/DQB1*06:02 (DQ0602) and highly associated with T cell receptor (TCR) alpha locus polymorphism as well as other immune regulatory loci. Increased incidence of narcolepsy was detected following the 2009 H1N1 pandemic and linked to Pandemrix vaccination, strongly supporting that narcolepsy is an autoimmune disorder. Although recent results suggest CD4+ T cell reactivity to neuropeptide hypocretin/orexin and cross-reactive flu peptide is involved, identification of other autoantigens has remained elusive. Here we study whether autoimmunity directed against Regulatory Factor X4 (RFX4), a protein co-localized with hypocretin, is involved in some cases of narcolepsy. Studying human serum, we found that autoantibodies against RFX4 were rare. Using RFX4 peptides bound to DQ0602 tetramers, antigen RFX4-86, -95, and -60 specific human CD4+ T cells were detected in 4/10 patients and 2 unaffected siblings, but not in others. Following culture with each cognate peptide, enriched autoreactive TCRαβ clones were isolated by single-cell sorting and TCR sequenced. Homologous clones bearing TRBV4-2 and recognizing RFX4-86 in patients and one twin control of patient were identified. These results suggest the involvement of RFX4 CD4+ T cell autoreactivity in some cases of narcolepsy, but also in healthy donors.
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Affiliation(s)
- Guo Luo
- Department of Psychiatry and Behavioral Sciences, Stanford University Center for Sleep Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Selina Yogeshwar
- Department of Psychiatry and Behavioral Sciences, Stanford University Center for Sleep Sciences, Stanford University School of Medicine, Palo Alto, CA, USA.,Division of Biosciences, Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Ling Lin
- Department of Psychiatry and Behavioral Sciences, Stanford University Center for Sleep Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Emmanuel Jean-Marie Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University Center for Sleep Sciences, Stanford University School of Medicine, Palo Alto, CA, USA.
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Loeliger BW, Hanu C, Panyutin IV, Maass-Moreno R, Wakim P, Pritchard WF, Neumann RD, Panyutin IG. Effect of Ionizing Radiation on Transcriptome during Neural Differentiation of Human Embryonic Stem Cells. Radiat Res 2020; 193:460-470. [PMID: 32216708 DOI: 10.1667/rr15535.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human embryonic brain development is highly sensitive to ionizing radiation. However, detailed information on the mechanisms of this sensitivity is not available due to limited experimental data. In this study, differentiation of human embryonic stem cells (hESCs) to neural lineages was used as a model for early embryonic brain development to assess the effect of exposure to low (17 mGy) and high (572 mGy) doses of radiation on gene expression. Transcriptomes were assessed using RNA sequencing during neural differentiation at three time points in control and irradiated samples. The first time point was when the cells were still pluripotent (day 0), the second time point was during the stage of embryoid body formation (day 6), and the third and final time point was during the stage of neural rosette formation (day 10). Analysis of the transcriptomes revealed neurodifferentiation in both the control and irradiated cells. Low-dose irradiation did not result in changes in gene expression at any of the time points, whereas high-dose irradiation resulted in downregulation of some major neurodifferentiation markers on days 6 and 10. Gene ontology analysis showed that pathways related to nervous system development, neurogenesis and generation of neurons were among the most affected. Expression of such key regulators of neuronal development as NEUROG1, ARX, ASCL1, RFX4 and INSM1 was reduced more than twofold. In conclusion, exposure to a 17 mGy low dose of radiation was well tolerated by hESCs while exposure to 572 mGy significantly affected their genetic reprogramming into neuronal lineages.
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Affiliation(s)
| | | | | | | | - Paul Wakim
- Department of Biostatistics and Clinical Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892
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7
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Jeong HY, Kim HJ, Kim CE, Lee S, Choi MC, Kim SH. High expression of RFX4 is associated with tumor progression and poor prognosis in patients with glioblastoma. Int J Neurosci 2020; 131:7-14. [PMID: 32075484 DOI: 10.1080/00207454.2020.1732969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aim: Glioma stem cells (GSCs) have been shown to contribute to tumor development and recurrence, therapeutic resistance, and cellular heterogeneity of glioblastoma multiforme (GBM). Recently, it has been reported that GSCs lose their self-renewal ability and tumorigenic potential upon differentiation. In this study, we identified Regulatory Factor X4 (RFX4) gene to regulate GSCs' survival and self-renewal activity in the GBM patients samples.Materials and methods: We utilized public datasets from the Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Ivy Glioblastoma Atlas Project, and The Human Protein Atlas to screen candidate genes which are associated with the development of GBM and poor patients survival. Small hairpin RNA (shRNA) lentivirus was applied to knockdown RFX4 gene in GSCs.Results: We found that RFX4 mRNA expression among the RFX family was particularly reduced during GSC differentiation. RT-qPCR analysis revealed significant downregulation of RFX4 and stem cell markers (CD15 and CD133) mRNA expressions in primary human GBM-derived GSCs cultured under serum condition. Consistently, GSCs showed significantly elevated RFX4 mRNA expression levels compared to normal astrocytes, NHA, whereas glioma cells did not. Furthermore, analysis of the TCGA data set revealed that RFX4 is highly expressed in GBM, and contributes to the lowering of patient survival. Depletion of RFX4 using shRNA lentivirus in patient GBM-derived GSCs decreased neurosphere formation and cell viability.Conclusion: These results suggest that RFX4 is a potential risk factor for maintaining the stemness of GSCs and making glioma more malignant, and thus, could be a promising target of GBM treatment.
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Affiliation(s)
- Hang Yeon Jeong
- Laboratory of Molecular Biochemistry, Chonnam National University, Gwangju, Republic of Korea
| | - Hyun-Jin Kim
- Laboratory of Molecular Biochemistry, Chonnam National University, Gwangju, Republic of Korea
| | - Cheol-Eun Kim
- Pôle de Formation et de Recherche en Santé (PFRS), Univeristé de Caen Normandie, Caen, France
| | - Seongsoo Lee
- Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea
| | - Moon-Chang Choi
- Department of Biomedical Science, Chosun University, Gwangju, Republic of Korea
| | - Sung-Hak Kim
- Laboratory of Molecular Biochemistry, Chonnam National University, Gwangju, Republic of Korea.,Gwangju Center, Korea Basic Science Institute, Gwangju, Republic of Korea
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Sugiaman-Trapman D, Vitezic M, Jouhilahti EM, Mathelier A, Lauter G, Misra S, Daub CO, Kere J, Swoboda P. Characterization of the human RFX transcription factor family by regulatory and target gene analysis. BMC Genomics 2018; 19:181. [PMID: 29510665 PMCID: PMC5838959 DOI: 10.1186/s12864-018-4564-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology. RFX genes are broadly (RFX1-3, RFX5, RFX7) and specifically (RFX4, RFX6) expressed in different cell types, with high expression in four organ systems: immune system, gastrointestinal tract, reproductive system and nervous system. Tissue type specific expression profiles link defined RFX family members with the target gene batteries they regulate. We experimentally confirmed novel TSS locations and characterized the previously undescribed RFX8 to be lowly expressed. RFX tissue and cell type specificity arises mainly from differences in TSS architecture. RFX transcript isoforms lacking a DNA binding domain (DBD) open up new possibilities for combinatorial target gene regulation. Our results favor a new grouping of the RFX family based on protein domain composition. We uncovered and experimentally confirmed the TFs SP2 and ESR1 as upstream regulators of specific RFX genes. Using TF binding profiles from the JASPAR database, we determined relevant patterns of X-box motif positioning with respect to gene TSS locations of human RFX target genes. CONCLUSIONS The wealth of data we provide will serve as the basis for precisely determining the roles RFX TFs play in human development and disease.
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Affiliation(s)
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen, Denmark
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL partnership, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Sougat Misra
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King's College London, London, UK
- Folkhälsan Institute of Genetics and Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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Sedykh I, Keller AN, Yoon B, Roberson L, Moskvin OV, Grinblat Y. Zebrafish Rfx4 controls dorsal and ventral midline formation in the neural tube. Dev Dyn 2018; 247:650-659. [PMID: 29243319 DOI: 10.1002/dvdy.24613] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 10/13/2017] [Accepted: 12/06/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Rfx winged-helix transcription factors, best known as key regulators of core ciliogenesis, also play ciliogenesis-independent roles during neural development. Mammalian Rfx4 controls neural tube morphogenesis via both mechanisms. RESULTS We set out to identify conserved aspects of rfx4 gene function during vertebrate development and to establish a new genetic model in which to analyze these mechanisms further. To this end, we have generated frame-shift alleles in the zebrafish rfx4 locus using CRISPR/Cas9 mutagenesis. Using RNAseq-based transcriptome analysis, in situ hybridization and immunostaining we identified a requirement for zebrafish rfx4 in the forming midlines of the caudal neural tube. These functions are mediated, least in part, through transcriptional regulation of several zic genes in the dorsal hindbrain and of foxa2 in the ventral hindbrain and spinal cord (floor plate). CONCLUSIONS The midline patterning functions of rfx4 are conserved, because rfx4 regulates transcription of foxa2 and zic2 in zebrafish and in mouse. In contrast, zebrafish rfx4 function is dispensable for forebrain morphogenesis, while mouse rfx4 is required for normal formation of forebrain ventricles in a ciliogenesis-dependent manner. Collectively, this report identifies conserved aspects of rfx4 function and establishes a robust new genetic model for in-depth dissection of these mechanisms. Developmental Dynamics 247:650-659, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Irina Sedykh
- Department of Integrative Biology, University of Wisconsin, Madison, Wisconsin.,Department of Neuroscience, University of Wisconsin, Madison, Wisconsin.,Zoology Ph.D. Program, University of Wisconsin, Madison, Wisconsin
| | - Abigail N Keller
- Department of Integrative Biology, University of Wisconsin, Madison, Wisconsin.,Department of Neuroscience, University of Wisconsin, Madison, Wisconsin
| | - Baul Yoon
- Department of Integrative Biology, University of Wisconsin, Madison, Wisconsin.,Department of Neuroscience, University of Wisconsin, Madison, Wisconsin.,Genetics Ph.D. Training Program, University of Wisconsin, Madison, Wisconsin
| | - Laura Roberson
- Department of Integrative Biology, University of Wisconsin, Madison, Wisconsin.,Department of Neuroscience, University of Wisconsin, Madison, Wisconsin
| | - Oleg V Moskvin
- Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin
| | - Yevgenya Grinblat
- Department of Integrative Biology, University of Wisconsin, Madison, Wisconsin.,Department of Neuroscience, University of Wisconsin, Madison, Wisconsin.,McPherson Eye Research Institute, University of Wisconsin, Madison, Wisconsin
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10
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Lopez-Dee ZP, Chittur SV, Patel H, Chinikaylo A, Lippert B, Patel B, Lawler J, Gutierrez LS. Thrombospondin-1 in a Murine Model of Colorectal Carcinogenesis. PLoS One 2015; 10:e0139918. [PMID: 26461935 PMCID: PMC4603676 DOI: 10.1371/journal.pone.0139918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 09/19/2015] [Indexed: 12/12/2022] Open
Abstract
Colorectal Cancer (CRC) is one of the late complications observed in patients suffering from inflammatory bowel diseases (IBD). Carcinogenesis is promoted by persistent chronic inflammation occurring in IBD. Understanding the mechanisms involved is essential in order to ameliorate inflammation and prevent CRC. Thrombospondin 1 (TSP-1) is a multidomain glycoprotein with important roles in angiogenesis. The effects of TSP-1 in colonic tumor formation and growth were analyzed in a model of inflammation-induced carcinogenesis. WT and TSP-1 deficient mice (TSP-1-/-) of the C57BL/6 strain received a single injection of azoxymethane (AOM) and multiple cycles of dextran sodium sulfate (DSS) to induce chronic inflammation-related cancers. Proliferation and angiogenesis were histologically analyzed in tumors. The intestinal transcriptome was also analyzed using a gene microarray approach. When the area containing tumors was compared with the entire colonic area of each mouse, the tumor burden was decreased in AOM/DSS-treated TSP-1-/- versus wild type (WT) mice. However, these lesions displayed more angiogenesis and proliferation rates when compared with the WT tumors. AOM-DSS treatment of TSP-1-/- mice resulted in significant deregulation of genes involved in transcription, canonical Wnt signaling, transport, defense response, regulation of epithelial cell proliferation and metabolism. Microarray analyses of these tumors showed down-regulation of 18 microRNAs in TSP-1-/- tumors. These results contribute new insights on the controversial role of TSP-1 in cancer and offer a better understanding of the genetics and pathogenesis of CRC.
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Affiliation(s)
- Zenaida P. Lopez-Dee
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Sridar V. Chittur
- Center for Functional Genomics, University of Albany, State University of New York, Renssaeler, New York, United States of America
| | - Hiral Patel
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Aleona Chinikaylo
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Brittany Lippert
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Bhumi Patel
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
| | - Jack Lawler
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Linda S. Gutierrez
- Department of Biology, Wilkes University, Wilkes Barre, Pennsylvania, United States of America
- * E-mail:
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Kistler WS, Baas D, Lemeille S, Paschaki M, Seguin-Estevez Q, Barras E, Ma W, Duteyrat JL, Morlé L, Durand B, Reith W. RFX2 Is a Major Transcriptional Regulator of Spermiogenesis. PLoS Genet 2015; 11:e1005368. [PMID: 26162102 PMCID: PMC4498915 DOI: 10.1371/journal.pgen.1005368] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/17/2015] [Indexed: 11/21/2022] Open
Abstract
Spermatogenesis consists broadly of three phases: proliferation of diploid germ cells, meiosis, and finally extensive differentiation of the haploid cells into effective delivery vehicles for the paternal genome. Despite detailed characterization of many haploid developmental steps leading to sperm, only fragmentary information exists on the control of gene expression underlying these processes. Here we report that the RFX2 transcription factor is a master regulator of genes required for the haploid phase. A targeted mutation of Rfx2 was created in mice. Rfx2-/- mice are perfectly viable but show complete male sterility. Spermatogenesis appears to progress unperturbed through meiosis. However, haploid cells undergo a complete arrest in spermatid development just prior to spermatid elongation. Arrested cells show altered Golgi apparatus organization, leading to a deficit in the generation of a spreading acrosomal cap from proacrosomal vesicles. Arrested cells ultimately merge to form giant multinucleated cells released to the epididymis. Spermatids also completely fail to form the flagellar axoneme. RNA-Seq analysis and ChIP-Seq analysis identified 139 genes directly controlled by RFX2 during spermiogenesis. Gene ontology analysis revealed that genes required for cilium function are specifically enriched in down- and upregulated genes showing that RFX2 allows precise temporal expression of ciliary genes. Several genes required for cell adhesion and cytoskeleton remodeling are also downregulated. Comparison of RFX2-regulated genes with those controlled by other major transcriptional regulators of spermiogenesis showed that each controls independent gene sets. Altogether, these observations show that RFX2 plays a major and specific function in spermiogenesis. Failure of spermatogenesis, which is presumed to often result from genetic defects, is a common cause of male sterility. Although numerous genes associated with defects in male spermatogenesis have been identified, numerous cases of genetic male infertility remain unelucidated. We report here that the transcription factor RFX2 is a master regulator of gene expression programs required for progression through the haploid phase of spermatogenesis. Male RFX2-deficient mice are completely sterile. Spermatogenesis progresses through meiosis, but haploid cells undergo a complete block in development just prior to spermatid elongation. Gene expression profiling and ChIP-Seq analysis revealed that RFX2 controls key pathways implicated in cilium/flagellum formation, as well as genes implicated in microtubule and vesicle associated transport. The set of genes activated by RFX2 in spermatids exhibits virtually no overlap with those controlled by other known transcriptional regulators of spermiogenesis, establishing RFX2 as an essential new player in this developmental process. RFX2-deficient mice should therefore represent a valuable new model for deciphering the regulatory networks that direct sperm formation, and thereby contribute to the identification of causes of human male infertility.
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Affiliation(s)
- W. Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail: (WSK); (BD)
| | - Dominique Baas
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Sylvain Lemeille
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Marie Paschaki
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Queralt Seguin-Estevez
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
| | - Wenli Ma
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Jean-Luc Duteyrat
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Laurette Morlé
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
| | - Bénédicte Durand
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, Villeurbanne, Lyon, France
- * E-mail: (WSK); (BD)
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CMU, Geneva, Switzerland
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12
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Poletti V, Delli Carri A, Malagoli Tagliazucchi G, Faedo A, Petiti L, Mazza EMC, Peano C, De Bellis G, Bicciato S, Miccio A, Cattaneo E, Mavilio F. Genome-Wide Definition of Promoter and Enhancer Usage during Neural Induction of Human Embryonic Stem Cells. PLoS One 2015; 10:e0126590. [PMID: 25978676 PMCID: PMC4433211 DOI: 10.1371/journal.pone.0126590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/06/2015] [Indexed: 11/21/2022] Open
Abstract
Genome-wide mapping of transcriptional regulatory elements is an essential tool for understanding the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of transcription start sites with genome-wide profiling of histones modifications to map active promoters and enhancers in embryonic stem cells (ESCs) induced to neuroepithelial-like stem cells (NESCs). Our analysis showed that most promoters are active in both cell types while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provides a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and of gene expression programs characterizing the transition from a pluripotent to a neural-restricted cell fate.
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Affiliation(s)
- Valentina Poletti
- Division of Genetics and Cell Biology, Scientific Institute H. San Raffaele, Milan, Italy
- Genethon, Evry, France
| | | | | | - Andrea Faedo
- Department of Biosciences, University of Milano, Milan, Italy
| | - Luca Petiti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Imagine Institute, Paris, France
| | - Elena Cattaneo
- Department of Biosciences, University of Milano, Milan, Italy
| | - Fulvio Mavilio
- Genethon, Evry, France
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- * E-mail:
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13
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Jiménez AJ, Domínguez-Pinos MD, Guerra MM, Fernández-Llebrez P, Pérez-Fígares JM. Structure and function of the ependymal barrier and diseases associated with ependyma disruption. Tissue Barriers 2014; 2:e28426. [PMID: 25045600 PMCID: PMC4091052 DOI: 10.4161/tisb.28426] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/03/2014] [Accepted: 03/03/2014] [Indexed: 12/20/2022] Open
Abstract
The neuroepithelium is a germinal epithelium containing progenitor cells that produce almost all of the central nervous system cells, including the ependyma. The neuroepithelium and ependyma constitute barriers containing polarized cells covering the embryonic or mature brain ventricles, respectively; therefore, they separate the cerebrospinal fluid that fills cavities from the developing or mature brain parenchyma. As barriers, the neuroepithelium and ependyma play key roles in the central nervous system development processes and physiology. These roles depend on mechanisms related to cell polarity, sensory primary cilia, motile cilia, tight junctions, adherens junctions and gap junctions, machinery for endocytosis and molecule secretion, and water channels. Here, the role of both barriers related to the development of diseases, such as neural tube defects, ciliary dyskinesia, and hydrocephalus, is reviewed.
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Affiliation(s)
- Antonio J Jiménez
- Department of Cell Biology, Genetics, and Physiology; University of Malaga; Malaga, Spain
| | | | - María M Guerra
- Institute of Anatomy, Histology, and Pathology; Austral University of Chile; Valdivia, Chile
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14
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Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G. The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genet 2013; 9:e1003728. [PMID: 24009522 PMCID: PMC3757057 DOI: 10.1371/journal.pgen.1003728] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 07/03/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. Over 95% of the peaks we measure are conserved to human. Eight of ten (80%) candidates tested using mouse transgenesis drive activity in restricted laminar patterns within the neocortex. GREAT based computational analysis reveals highly significant correlation with genes expressed at E14.5 in key areas for neocortex development, and allows the grouping of enhancers by known biological functions and pathways for further studies. We find that multiple genes are flanked by dozens of candidate enhancers each, including well-known key neocortical genes as well as suspected and novel genes. Nearly a quarter of our candidate enhancers are conserved well beyond mammals. Human and zebrafish regions orthologous to our candidate enhancers are shown to most often function in other aspects of central nervous system development. Finally, we find strong evidence that specific interspersed repeat families have contributed potentially key developmental enhancers via co-option. Our analysis expands the methodologies available for extracting the richness of information found in genome-wide functional maps.
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Affiliation(s)
- Aaron M. Wenger
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Shoa L. Clarke
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - James H. Notwell
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Tisha Chung
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Geetu Tuteja
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Harendra Guturu
- Department of Electrical Engineering, Stanford University, Stanford, California, United States of America
| | - Bruce T. Schaar
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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15
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Role of the subcommissural organ in the pathogenesis of congenital hydrocephalus in the HTx rat. Cell Tissue Res 2013; 352:707-25. [PMID: 23640132 DOI: 10.1007/s00441-013-1615-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 03/08/2013] [Indexed: 01/05/2023]
Abstract
The present investigation was designed to clarify the role of the subcommissural organ (SCO) in the pathogenesis of hydrocephalus occurring in the HTx rat. The brains of non-affected and hydrocephalic HTx rats from embryonic day 15 (E15) to postnatal day 10 (PN10) were processed for electron microscopy, lectin binding and immunocytochemistry by using a series of antibodies. Cerebrospinal fluid (CSF) samples of non-affected and hydrocephalic HTx rats were collected at PN1, PN7 and PN30 and analysed by one- and two-dimensional electrophoresis, immunoblotting and nanoLC-ESI-MS/MS. A distinct malformation of the SCO is present as early as E15. Since stenosis of the Sylvius aqueduct (SA) occurs at E18 and dilation of the lateral ventricles starts at E19, the malformation of the SCO clearly precedes the onset of hydrocephalus. In the affected rats, the cephalic and caudal thirds of the SCO showed high secretory activity with all methods used, whereas the middle third showed no signs of secretion. At E18, the middle non-secretory third of the SCO progressively fused with the ventral wall of SA, resulting in marked aqueduct stenosis and severe hydrocephalus. The abnormal development of the SCO resulted in the permanent absence of Reissner's fibre (RF) and led to changes in the protein composition of the CSF. Since the SCO is the source of a large mass of sialilated glycoproteins that form the RF and of those that remain CSF-soluble, we hypothesize that the absence of this large mass of negatively charged molecules from the SA domain results in SA stenosis and impairs the bulk flow of CSF through the aqueduct.
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16
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Lin M, Pedrosa E, Shah A, Hrabovsky A, Maqbool S, Zheng D, Lachman HM. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders. PLoS One 2011; 6:e23356. [PMID: 21915259 PMCID: PMC3168439 DOI: 10.1371/journal.pone.0023356] [Citation(s) in RCA: 203] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 07/12/2011] [Indexed: 02/01/2023] Open
Abstract
Genome-wide expression analysis using next generation sequencing (RNA-Seq) provides an opportunity for in-depth molecular profiling of fundamental biological processes, such as cellular differentiation and malignant transformation. Differentiating human neurons derived from induced pluripotent stem cells (iPSCs) provide an ideal system for RNA-Seq since defective neurogenesis caused by abnormalities in transcription factors, DNA methylation, and chromatin modifiers lie at the heart of some neuropsychiatric disorders. As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms were seen during the transition from pluripotent stem cells to early differentiating neurons. A number of genes that undergo radical changes in expression during this transition include candidates for schizophrenia (SZ), bipolar disorder (BD) and autism spectrum disorders (ASD) that function as transcription factors and chromatin modifiers, such as POU3F2 and ZNF804A, and genes coding for cell adhesion proteins implicated in these conditions including NRXN1 and NLGN1. In addition, a number of novel lncRNAs were found to undergo dramatic changes in expression, one of which is HOTAIRM1, a regulator of several HOXA genes during myelopoiesis. The increase we observed in differentiating neurons suggests a role in neurogenesis as well. Finally, several lncRNAs that map near SNPs associated with SZ in genome wide association studies also increase during neuronal differentiation, suggesting that these novel transcripts may be abnormally regulated in a subgroup of patients.
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Affiliation(s)
- Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Abhishek Shah
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Anastasia Hrabovsky
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Shahina Maqbool
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Herbert M. Lachman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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17
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Abstract
In animals, RFX transcription factors govern ciliogenesis by binding to an X-box motif in the promoters of ciliogenic genes. In Caenorhabditis elegans, the sole RFX transcription factor (TF) daf-19 null mutant lacks all sensory cilia, fails to express many ciliogenic genes, and is defective in many sensory behaviors, including male mating. The daf-19c isoform is expressed in all ciliated sensory neurons and is necessary and sufficient for activating X-box containing ciliogenesis genes. Here, we describe the daf-19(n4132) mutant that is defective in expression of the sensory polycystic kidney disease (PKD) gene battery and male mating behavior, without affecting expression of ciliogenic genes or ciliogenesis. daf-19(n4132) disrupts expression of a new isoform, daf-19m (for function in male mating). daf-19m is expressed in male-specific PKD and core IL2 neurons via internal promoters and remote enhancer elements located in introns of the daf-19 genomic locus. daf-19m genetically programs the sensory functions of a subset of ciliated neurons, independent of daf-19c. In the male-specific HOB neuron, DAF-19(M) acts downstream of the zinc finger TF EGL-46, indicating that a TF cascade controls the PKD gene battery in this cell-type specific context. We conclude that the RFX TF DAF-19 regulates ciliogenesis via X-box containing ciliogenic genes and controls ciliary specialization by regulating non-X-box containing sensory genes. This study reveals a more extensive role for RFX TFs in generating fully functional cilia.
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18
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Horvath GC, Kistler MK, Kistler WS. RFX2 is a candidate downstream amplifier of A-MYB regulation in mouse spermatogenesis. BMC DEVELOPMENTAL BIOLOGY 2009; 9:63. [PMID: 20003220 PMCID: PMC2797782 DOI: 10.1186/1471-213x-9-63] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 12/09/2009] [Indexed: 11/10/2022]
Abstract
Background Mammalian spermatogenesis involves formation of haploid cells from the male germline and then a complex morphological transformation to generate motile sperm. Focusing on meiotic prophase, some tissue-specific transcription factors are known (A-MYB) or suspected (RFX2) to play important roles in modulating gene expression in pachytene spermatocytes. The current work was initiated to identify both downstream and upstream regulatory connections for Rfx2. Results Searches of pachytene up-regulated genes identified high affinity RFX binding sites (X boxes) in promoter regions of several new genes: Adam5, Pdcl2, and Spag6. We confirmed a strong promoter-region X-box for Alf, a germ cell-specific variant of general transcription factor TFIIA. Using Alf as an example of a target gene, we showed that its promoter is stimulated by RFX2 in transfected cells and used ChIP analysis to show that the promoter is occupied by RFX2 in vivo. Turning to upstream regulation of the Rfx2 promoter, we identified a cluster of three binding sites (MBS) for the MYB family of transcription factors. Because testis is one of the few sites of A-myb expression, and because spermatogenesis arrests in pachytene in A-myb knockout mice, the MBS cluster implicates Rfx2 as an A-myb target. Electrophoretic gel-shift, ChIP, and co-transfection assays all support a role for these MYB sites in Rfx2 expression. Further, Rfx2 expression was virtually eliminated in A-myb knockout testes. Immunohistology on testis sections showed that A-MYB expression is up-regulated only after pachytene spermatocytes have clearly moved away from the tubule wall, which correlates with onset of RFX2 expression, whereas B-MYB expression, by contrast, is prevalent only in earlier spermatocytes and spermatogonia. Conclusion With an expanding list of likely target genes, RFX2 is potentially an important transcriptional regulator in pachytene spermatocytes. Rfx2 itself is a good candidate to be regulated by A-MYB, which is essential for meiotic progression. If Alf is a genuine RFX2 target, then A-myb, Rfx2, and Alf may form part of a transcriptional network that is vital for completion of meiosis and preparation for post-meiotic differentiation.
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Affiliation(s)
- Gary C Horvath
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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19
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El Zein L, Ait-Lounis A, Morlé L, Thomas J, Chhin B, Spassky N, Reith W, Durand B. RFX3 governs growth and beating efficiency of motile cilia in mouse and controls the expression of genes involved in human ciliopathies. J Cell Sci 2009; 122:3180-9. [PMID: 19671664 DOI: 10.1242/jcs.048348] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cilia are cellular organelles that play essential physiological and developmental functions in various organisms. They can be classified into two categories, primary cilia and motile cilia, on the basis of their axonemal architecture. Regulatory factor X (RFX) transcription factors have been shown to be involved in the assembly of primary cilia in Caenorhabditis elegans, Drosophila and mice. Here, we have taken advantage of a novel primary-cell culture system derived from mouse brain to show that RFX3 is also necessary for biogenesis of motile cilia. We found that the growth and beating efficiencies of motile cilia are impaired in multiciliated Rfx3(-/-) cells. RFX3 was required for optimal expression of the FOXJ1 transcription factor, a key player in the differentiation program of motile cilia. Furthermore, we demonstrate for the first time that RFX3 regulates the expression of axonemal dyneins involved in ciliary motility by binding directly to the promoters of their genes. In conclusion, RFX proteins not only regulate genes involved in ciliary assembly, but also genes that are involved in ciliary motility and that are associated with ciliopathies such as primary ciliary dyskinesia in humans.
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20
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Kistler WS, Horvath GC, Dasgupta A, Kistler MK. Differential expression of Rfx1-4 during mouse spermatogenesis. Gene Expr Patterns 2009; 9:515-9. [PMID: 19596083 DOI: 10.1016/j.gep.2009.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 07/02/2009] [Accepted: 07/02/2009] [Indexed: 11/17/2022]
Abstract
The regulatory factor X (RFX) family of transcription factors has been recently implicated in gene regulation during spermatogenesis. However, the relative expression of individual members during this developmental process is not completely characterized, particularly in the case of Rfx4, which has multiple transcript variants in the testis. We used reverse transcriptase-dependent real-time PCR, 5'-RACE cloning, and Western blotting to compare transcripts and protein levels for this family in cell populations from the three major phases of spermatogenesis (mitotic, meiotic, and haploid). Transcripts for Rfx1-4 were present at trace to low levels in spermatogonia prepared from 8-day-old mice. Transcripts for both Rfx2 and Rfx4 were elevated in mid-late pachytene spermatocytes; however, the dominant Rfx4 transcript present begins at a downstream exon and lacks the DNA binding domain. Transcripts for all four genes were elevated in early haploid cells (round spermatids). In these cells Rfx4 transcripts originate primarily from a newly described promoter with intron 1 but are expected to be translationally compromised due to a poorly situated start codon. Western blotting confirmed that RFX2 is greatly elevated beginning in meiosis and also confirmed that full-length RFX4 protein is not prevalent in mouse testis at any stage. These results imply that RFX2 is the most likely X box binding factor to influence novel gene expression during meiosis, that RFX1-3 may all play roles in haploid cells but that RFX4 is much less prevalent than implied by its high transcript levels.
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Affiliation(s)
- W Stephen Kistler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
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21
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Laurençon A, Dubruille R, Efimenko E, Grenier G, Bissett R, Cortier E, Rolland V, Swoboda P, Durand B. Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species. Genome Biol 2008; 8:R195. [PMID: 17875208 PMCID: PMC2375033 DOI: 10.1186/gb-2007-8-9-r195] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 09/14/2007] [Accepted: 09/17/2007] [Indexed: 01/02/2023] Open
Abstract
An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis. Background Regulatory factor X (RFX) transcription factors play a key role in ciliary assembly in nematode, Drosophila and mouse. Using the tremendous advantages of comparative genomics in closely related species, we identified novel genes regulated by dRFX in Drosophila. Results We first demonstrate that a subset of known ciliary genes in Caenorhabditis elegans and Drosophila are regulated by dRFX and have a conserved RFX binding site (X-box) in their promoters in two highly divergent Drosophila species. We then designed an X-box consensus sequence and carried out a genome wide computer screen to identify novel genes under RFX control. We found 412 genes that share a conserved X-box upstream of the ATG in both species, with 83 genes presenting a more restricted consensus. We analyzed 25 of these 83 genes, 16 of which are indeed RFX target genes. Two of them have never been described as involved in ciliogenesis. In addition, reporter construct expression analysis revealed that three of the identified genes encode proteins specifically localized in ciliated endings of Drosophila sensory neurons. Conclusion Our X-box search strategy led to the identification of novel RFX target genes in Drosophila that are involved in sensory ciliogenesis. We also established a highly valuable Drosophila cilia and basal body dataset. These results demonstrate the accuracy of the X-box screen and will be useful for the identification of candidate genes for human ciliopathies, as several human homologs of RFX target genes are known to be involved in diseases, such as Bardet-Biedl syndrome.
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Affiliation(s)
- Anne Laurençon
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Raphaëlle Dubruille
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
- University of Massachusetts Medical School, Department of Neurobiology, Worcester, MA 01605, USA
| | - Evgeni Efimenko
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Guillaume Grenier
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Ryan Bissett
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
- University of Glasgow, Glasgow Biomedical Research Centre, Wellcome Centre for Molecular Parasitology and Infection and Immunity, Glasgow G12 8TA, UK
| | - Elisabeth Cortier
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Vivien Rolland
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, Södertörn University College, School of Life Sciences, S-14189 Huddinge, Sweden
| | - Bénédicte Durand
- Université de Lyon, Lyon, F-69003, France
- Université Lyon 1, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellulaire, Villeurbanne, F-69622, France
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