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Aouci R, Fontaine A, Vion A, Belz L, Levi G, Narboux-Nême N. The Antidepressant Action of Fluoxetine Involves the Inhibition of Dlx5/6 in Cortical GABAergic Neurons through a TrkB-Dependent Pathway. Cells 2024; 13:1262. [PMID: 39120293 PMCID: PMC11311550 DOI: 10.3390/cells13151262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
Major depressive disorder (MDD) is a complex and devastating illness that affects people of all ages. Despite the large use of antidepressants in current medical practice, neither their mechanisms of action nor the aetiology of MDD are completely understood. Experimental evidence supports the involvement of Parvalbumin-positive GABAergic neurons (PV-neurons) in the pathogenesis of MDD. DLX5 and DLX6 (DLX5/6) encode two homeodomain transcription factors involved in cortical GABAergic differentiation and function. In the mouse, the level of expression of these genes is correlated with the cortical density of PV-neurons and with anxiety-like behaviours. The same genomic region generates the lncRNA DLX6-AS1, which, in humans, participates in the GABAergic regulatory module downregulated in schizophrenia and ASD. Here, we show that the expression levels of Dlx5/6 in the adult mouse brain are correlated with the immobility time in the forced swim test, which is used to measure depressive-like behaviours. We show that the administration of the antidepressant fluoxetine (Flx) to normal mice induces, within 24 h, a rapid and stable reduction in Dlx5, Dlx6 and Dlx6-AS1 expression in the cerebral cortex through the activation of the TrkB-CREB pathway. Experimental Dlx5 overexpression counteracts the antidepressant effects induced by Flx treatment. Our findings show that one of the short-term effects of Flx administration is the reduction in Dlx5/6 expression in GABAergic neurons, which, in turn, has direct consequences on PV expression and on behavioural profiles. Variants in the DLX5/6 regulatory network could be implicated in the predisposition to depression and in the variability of patients' response to antidepressant treatment.
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Affiliation(s)
| | | | | | | | | | - Nicolas Narboux-Nême
- Molecular Physiology and Adaption, UMR7221 CNRS, Museum National d’Histoire Naturelle, 75005 Paris, France; (R.A.); (A.F.); (L.B.); (G.L.)
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2
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Rubenstein JL, Nord AS, Ekker M. DLX genes and proteins in mammalian forebrain development. Development 2024; 151:dev202684. [PMID: 38819455 PMCID: PMC11190439 DOI: 10.1242/dev.202684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The vertebrate Dlx gene family encode homeobox transcription factors that are related to the Drosophila Distal-less (Dll) gene and are crucial for development. Over the last ∼35 years detailed information has accrued about the redundant and unique expression and function of the six mammalian Dlx family genes. DLX proteins interact with general transcriptional regulators, and co-bind with other transcription factors to enhancer elements with highly specific activity in the developing forebrain. Integration of the genetic and biochemical data has yielded a foundation for a gene regulatory network governing the differentiation of forebrain GABAergic neurons. In this Primer, we describe the discovery of vertebrate Dlx genes and their crucial roles in embryonic development. We largely focus on the role of Dlx family genes in mammalian forebrain development revealed through studies in mice. Finally, we highlight questions that remain unanswered regarding vertebrate Dlx genes despite over 30 years of research.
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Affiliation(s)
- John L. Rubenstein
- UCSF Department of Psychiatry and Behavioral Sciences, Department of UCSF Weill Institute for Neurosciences, Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alex S. Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and 20 Behavioral Sciences, Center for Neuroscience, University of California Davis, Davis, CA 95618, USA
| | - Marc Ekker
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
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3
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Fleck K, Luria V, Garag N, Karger A, Hunter T, Marten D, Phu W, Nam KM, Sestan N, O’Donnell-Luria AH, Erceg J. Functional associations of evolutionarily recent human genes exhibit sensitivity to the 3D genome landscape and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585403. [PMID: 38559085 PMCID: PMC10980080 DOI: 10.1101/2024.03.17.585403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome organization is intricately tied to regulating genes and associated cell fate decisions. In this study, we examine the positioning and functional significance of human genes, grouped by their evolutionary age, within the 3D organization of the genome. We reveal that genes of different evolutionary origin have distinct positioning relationships with both domains and loop anchors, and remarkably consistent relationships with boundaries across cell types. While the functional associations of each group of genes are primarily cell type-specific, such associations of conserved genes maintain greater stability across 3D genomic features and disease than recently evolved genes. Furthermore, the expression of these genes across various tissues follows an evolutionary progression, such that RNA levels increase from young genes to ancient genes. Thus, the distinct relationships of gene evolutionary age, function, and positioning within 3D genomic features contribute to tissue-specific gene regulation in development and disease.
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Affiliation(s)
- Katherine Fleck
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Nitanta Garag
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA 02115
| | - Trevor Hunter
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
| | - Daniel Marten
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - William Phu
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
| | - Kee-Myoung Nam
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06510
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510
| | - Anne H. O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jelena Erceg
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030
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4
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Gillespie B, Panthi S, Sundram S, Hill RA. The impact of maternal immune activation on GABAergic interneuron development: A systematic review of rodent studies and their translational implications. Neurosci Biobehav Rev 2024; 156:105488. [PMID: 38042358 DOI: 10.1016/j.neubiorev.2023.105488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
Mothers exposed to infections during pregnancy disproportionally birth children who develop autism and schizophrenia, disorders associated with altered GABAergic function. The maternal immune activation (MIA) model recapitulates this risk factor, with many studies also reporting disruptions to GABAergic interneuron expression, protein, cellular density and function. However, it is unclear if there are species, sex, age, region, or GABAergic subtype specific vulnerabilities to MIA. Furthermore, to fully comprehend the impact of MIA on the GABAergic system a synthesised account of molecular, cellular, electrophysiological and behavioural findings was required. To this end we conducted a systematic review of GABAergic interneuron changes in the MIA model, focusing on the prefrontal cortex and hippocampus. We reviewed 102 articles that revealed robust changes in a number of GABAergic markers that present as gestationally-specific, region-specific and sometimes sex-specific. Disruptions to GABAergic markers coincided with distinct behavioural phenotypes, including memory, sensorimotor gating, anxiety, and sociability. Findings suggest the MIA model is a valid tool for testing novel therapeutics designed to recover GABAergic function and associated behaviour.
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Affiliation(s)
- Brendan Gillespie
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Sandesh Panthi
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Suresh Sundram
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rachel A Hill
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia.
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Liao T, Xu X, Wu J, Xie Y, Yan J. Increased expression levels of DLX5 inhibit the development of the nervous system. Int J Dev Neurosci 2023; 83:728-739. [PMID: 37767888 DOI: 10.1002/jdn.10300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/29/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
INTRODUCTION Preeclampsia is a hypertensive disorder of pregnancy. DLX5 plays an important role in the migration and differentiation of subglobus pallidus precursor cells. METHODS We established a zebrafish line expressing high levels of DLX5 and investigated changes in behavior and development of the nervous system. RESULTS The ratios of brain volume area to whole body area at 96 hpf zebrafish in the experimental group (gRNA + CasRx) were significantly lower than the WT group and the negative control group (casRx) (P < 0.01). Behavioral trajectory distances and movement speeds exhibited by the 6th day of development in zebrafish in the experimental group (gRNA + CasRx) were significantly shorter (P < 0.01) and lower (P < 0.05) than the negative control group (gRNA + CasRx), respectively. CONCLUSIONS Data suggested that the increased expression levels of DLX5 can inhibit brain volume development and behavioral activities in zebrafish. Maybe the high expression levels of DLX5 in the pathological state of preeclampsia can inhibit the development of the nervous system in offspring.
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Affiliation(s)
- Tingting Liao
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Xia Xu
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Junzi Wu
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Yi Xie
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Jianying Yan
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Maternity and Child Health Hospital, Fuzhou, China
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6
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López-Tobón A, Shyti R, Villa CE, Cheroni C, Fuentes-Bravo P, Trattaro S, Caporale N, Troglio F, Tenderini E, Mihailovich M, Skaros A, Gibson WT, Cuomo A, Bonaldi T, Mercurio C, Varasi M, Osborne L, Testa G. GTF2I dosage regulates neuronal differentiation and social behavior in 7q11.23 neurodevelopmental disorders. SCIENCE ADVANCES 2023; 9:eadh2726. [PMID: 38019906 PMCID: PMC10686562 DOI: 10.1126/sciadv.adh2726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023]
Abstract
Copy number variations at 7q11.23 cause neurodevelopmental disorders with shared and opposite manifestations. Deletion causes Williams-Beuren syndrome featuring hypersociability, while duplication causes 7q11.23 microduplication syndrome (7Dup), frequently exhibiting autism spectrum disorder (ASD). Converging evidence indicates GTF2I as key mediator of the cognitive-behavioral phenotypes, yet its role in cortical development and behavioral hallmarks remains largely unknown. We integrated proteomic and transcriptomic profiling of patient-derived cortical organoids, including longitudinally at single-cell resolution, to dissect 7q11.23 dosage-dependent and GTF2I-specific disease mechanisms. We observed dosage-dependent impaired dynamics of neural progenitor proliferation, transcriptional imbalances, and highly specific alterations in neuronal output, leading to precocious excitatory neuron production in 7Dup, which was rescued by restoring physiological GTF2I levels. Transgenic mice with Gtf2i duplication recapitulated progenitor proliferation and neuronal differentiation defects alongside ASD-like behaviors. Consistently, inhibition of lysine demethylase 1 (LSD1), a GTF2I effector, was sufficient to rescue ASD-like phenotypes in transgenic mice, establishing GTF2I-LSD1 axis as a molecular pathway amenable to therapeutic intervention in ASD.
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Affiliation(s)
- Alejandro López-Tobón
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Reinald Shyti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Carlo Emanuele Villa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Cristina Cheroni
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Patricio Fuentes-Bravo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicolò Caporale
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Flavia Troglio
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Erika Tenderini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Marija Mihailovich
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Adrianos Skaros
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - William T. Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Ciro Mercurio
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Mario Varasi
- Experimental Therapeutics Program, FIRC Institute of Molecular Oncology Foundation (IFOM), 20139 Milan, Italy
| | - Lucy Osborne
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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7
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Liu A, Wang N, Xie G, Li Y, Yan X, Li X, Zhu Z, Li Z, Yang J, Meng F, Dou M, Chen W, Ma N, Jiang Y, Gao Y, Wang Y. GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes. Genome Res 2023; 33:1673-1689. [PMID: 37884342 PMCID: PMC10691551 DOI: 10.1101/gr.277784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/23/2023] [Indexed: 10/28/2023]
Abstract
Ultraconserved elements (UCEs) are the most conserved regions among the genomes of evolutionarily distant species and are thought to play critical biological functions. However, some UCEs rapidly evolved in specific lineages, and whether they contributed to adaptive evolution is still controversial. Here, using an increased number of sequenced genomes with high taxonomic coverage, we identified 2191 mammalian UCEs and 5938 avian UCEs from 95 mammal and 94 bird genomes, respectively. Our results show that these UCEs are functionally constrained and that their adjacent genes are prone to widespread expression with low expression diversity across tissues. Functional enrichment of mammalian and avian UCEs shows different trends indicating that UCEs may contribute to adaptive evolution of taxa. Focusing on lineage-specific accelerated evolution, we discover that the proportion of fast-evolving UCEs in nine mammalian and 10 avian test lineages range from 0.19% to 13.2%. Notably, up to 62.1% of fast-evolving UCEs in test lineages are much more likely to result from GC-biased gene conversion (gBGC). A single cervid-specific gBGC region embracing the uc.359 allele significantly alters the expression of Nova1 and other neural-related genes in the rat brain. Combined with the altered regulatory activity of ancient gBGC-induced fast-evolving UCEs in eutherians, our results provide evidence that synergy between gBGC and selection shaped lineage-specific substitution patterns, even in the most constrained regulatory elements. In summary, our results show that gBGC played an important role in facilitating lineage-specific accelerated evolution of UCEs, and further support the idea that a combination of multiple evolutionary forces shapes adaptive evolution.
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Affiliation(s)
- Anguo Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nini Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, and Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University Hospital Cologne, Cologne 50931, Germany
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xixi Yan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenliang Zhu
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuohui Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Yang
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fanxin Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingle Dou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weihuang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nange Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
- Center for Functional Genomics, Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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8
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Singh A, Kaileh M, De S, Mazan-Mamczarz K, Bayarsaihan D, Sen R, Roy AL. Transcription factor TFII-I fine tunes innate properties of B lymphocytes. Front Immunol 2023; 14:1067459. [PMID: 36756127 PMCID: PMC9900109 DOI: 10.3389/fimmu.2023.1067459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/04/2023] [Indexed: 01/24/2023] Open
Abstract
The ubiquitously expressed transcription factor TFII-I is a multifunctional protein with pleiotropic roles in gene regulation. TFII-I associated polymorphisms are implicated in Sjögren's syndrome and Lupus in humans and, germline deletion of the Gtf2i gene in mice leads to embryonic lethality. Here we report a unique role for TFII-I in homeostasis of innate properties of B lymphocytes. Loss of Gtf2i in murine B lineage cells leads to an alteration in transcriptome, chromatin landscape and associated transcription factor binding sites, which exhibits myeloid-like features and coincides with enhanced sensitivity to LPS induced gene expression. TFII-I deficient B cells also show increased switching to IgG3, a phenotype associated with inflammation. These results demonstrate a role for TFII-I in maintaining immune homeostasis and provide clues for GTF2I polymorphisms associated with B cell dominated autoimmune diseases in humans.
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Affiliation(s)
- Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics & Genomics, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics & Genomics, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, United States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
| | - Ananda L Roy
- Laboratory of Molecular Biology and Immunology, National Institutes of Health, National Institute on Aging, Baltimore, MD, United States
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9
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Baruah C, Nath P, Barah P. LncRNAs in neuropsychiatric disorders and computational insights for their prediction. Mol Biol Rep 2022; 49:11515-11534. [PMID: 36097122 DOI: 10.1007/s11033-022-07819-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 12/06/2022]
Abstract
Long non-coding RNAs (lncRNAs) are 200 nucleotide extended transcripts that do not encode proteins or possess limited coding ability. LncRNAs epigenetically control several biological functions such as gene regulation, transcription, mRNA splicing, protein interaction, and genomic imprinting. Over the years, drastic progress in understanding the role of lncRNAs in diverse biological processes has been made. LncRNAs are reported to show tissue-specific expression patterns suggesting their potential as novel candidate biomarkers for diseases. Among all other non-coding RNAs, lncRNAs are highly expressed within the brain-enriched or brain-specific regions of the neural tissues. They are abundantly expressed in the neocortex and pre-mature frontal regions of the brain. LncRNAs are co-expressed with the protein-coding genes and have a significant role in the evolution of functions of the brain. Any deregulation in the lncRNAs contributes to disruptions in normal brain functions resulting in multiple neurological disorders. Neuropsychiatric disorders such as schizophrenia, bipolar disease, autism spectrum disorders, and anxiety are associated with the abnormal expression and regulation of lncRNAs. This review aims to highlight the understanding of lncRNAs concerning normal brain functions and their deregulation associated with neuropsychiatric disorders. We have also provided a survey on the available computational tools for the prediction of lncRNAs, their protein coding potentials, and sub-cellular locations, along with a section on existing online databases with known lncRNAs, and their interactions with other molecules.
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Affiliation(s)
- Cinmoyee Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India
| | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, 784028, Napaam, Sonitpur, Assam, India.
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10
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Aouci R, El Soudany M, Maakoul Z, Fontaine A, Kurihara H, Levi G, Narboux-Nême N. Dlx5/6 Expression Levels in Mouse GABAergic Neurons Regulate Adult Parvalbumin Neuronal Density and Anxiety/Compulsive Behaviours. Cells 2022; 11:cells11111739. [PMID: 35681437 PMCID: PMC9179869 DOI: 10.3390/cells11111739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Neuronal circuits integrating Parvalbumin-positive GABAergic inhibitory interneurons (PV) are essential for normal brain function and are often altered in psychiatric conditions. During development, Dlx5 and Dlx6 (Dlx5/6) genes are involved in the differentiation of PV-interneurons. In the adult, Dlx5/6 continue to be expressed at low levels in most telencephalic GABAergic neurons, but their importance in determining the number and distribution of adult PV-interneurons is unknown. Previously, we have shown that targeted deletion of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in altered behavioural and metabolic profiles. Here we evaluate the consequences of targeted Dlx5/6 gene dosage alterations in adult GABAergic neurons. We compare the effects on normal brain of homozygous and heterozygous (Dlx5/6VgatCre and Dlx5/6VgatCre/+ mice) Dlx5/6 deletions to those of Dlx5 targeted overexpression (GABAergicDlx5/+ mice). We find a linear correlation between Dlx5/6 allelic dosage and the density of PV-positive neurons in the adult prelimbic cortex and in the hippocampus. In parallel, we observe that Dlx5/6 expression levels in GABAergic neurons are also linearly associated with the intensity of anxiety and compulsivity-like behaviours. Our findings reinforce the notion that regulation of Dlx5/6 expression is involved in individual cognitive variability and, possibly, in the genesis of certain neuropsychiatric conditions.
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Affiliation(s)
- Rym Aouci
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Team BBC, Département AVIV, Muséum National d’Histoire Naturelle, UMR-7221, 7 rue Cuvier, 75005 Paris, France; (R.A.); (M.E.S.); (Z.M.); (A.F.); (G.L.)
| | - Mey El Soudany
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Team BBC, Département AVIV, Muséum National d’Histoire Naturelle, UMR-7221, 7 rue Cuvier, 75005 Paris, France; (R.A.); (M.E.S.); (Z.M.); (A.F.); (G.L.)
| | - Zakaria Maakoul
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Team BBC, Département AVIV, Muséum National d’Histoire Naturelle, UMR-7221, 7 rue Cuvier, 75005 Paris, France; (R.A.); (M.E.S.); (Z.M.); (A.F.); (G.L.)
| | - Anastasia Fontaine
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Team BBC, Département AVIV, Muséum National d’Histoire Naturelle, UMR-7221, 7 rue Cuvier, 75005 Paris, France; (R.A.); (M.E.S.); (Z.M.); (A.F.); (G.L.)
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan;
| | - Giovanni Levi
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Team BBC, Département AVIV, Muséum National d’Histoire Naturelle, UMR-7221, 7 rue Cuvier, 75005 Paris, France; (R.A.); (M.E.S.); (Z.M.); (A.F.); (G.L.)
| | - Nicolas Narboux-Nême
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Team BBC, Département AVIV, Muséum National d’Histoire Naturelle, UMR-7221, 7 rue Cuvier, 75005 Paris, France; (R.A.); (M.E.S.); (Z.M.); (A.F.); (G.L.)
- Correspondence: ; Tel.: +33-140-798-027
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11
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Levi G, de Lombares C, Giuliani C, Iannuzzi V, Aouci R, Garagnani P, Franceschi C, Grimaud-Hervé D, Narboux-Nême N. DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution. Mol Biol Evol 2021; 38:4748-4764. [PMID: 34132815 PMCID: PMC8557472 DOI: 10.1093/molbev/msab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.
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Affiliation(s)
- Giovanni Levi
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Camille de Lombares
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Vincenzo Iannuzzi
- Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Italy
| | - Rym Aouci
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky University, Nizhniy Novgorod, Russia
| | - Dominique Grimaud-Hervé
- Histoire Naturelle de l’Homme Préhistorique, CNRS UMR 7194, Département H&E, Muséum National d'Histoire Naturelle, Paris, France
| | - Nicolas Narboux-Nême
- Physiologie Moléculaire et Adaptation, CNRS UMR7221, Département AVIV, Muséum National d'Histoire Naturelle, Paris, France
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12
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Fazel Darbandi S, Esau C, Lesage-Pelletier C, Monis S, Poitras L, Yu M, Perin S, Hatch G, Ekker M. Increased Sociability in Mice Lacking Intergenic Dlx Enhancers. Front Neurosci 2021; 15:718948. [PMID: 34671237 PMCID: PMC8520905 DOI: 10.3389/fnins.2021.718948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
The Dlx homeodomain transcription factors play important roles in the differentiation and migration of GABAergic interneuron precursors. The mouse and human genomes each have six Dlx genes organized into three convergently transcribed bigene clusters (Dlx1/2, Dlx3/4, and Dlx5/6) with cis-regulatory elements (CREs) located in the intergenic region of each cluster. Amongst these, the I56i and I12b enhancers from the Dlx1/2 and Dlx5/6 locus, respectively, are active in the developing forebrain. I56i is also a binding site for GTF2I, a transcription factor whose function is associated with increased sociability and Williams-Beuren syndrome. In determining the regulatory roles of these CREs on forebrain development, we have generated mutant mouse-lines where Dlx forebrain intergenic enhancers have been deleted (I56i(-/-), I12b(-/-)). Loss of Dlx intergenic enhancers impairs expression of Dlx genes as well as some of their downstream targets or associated genes including Gad2 and Evf2. The loss of the I56i enhancer resulted in a transient decrease in GABA+ cells in the developing forebrain. The intergenic enhancer mutants also demonstrate increased sociability and learning deficits in a fear conditioning test. Characterizing mice with mutated Dlx intergenic enhancers will help us to further enhance our understanding of the role of these Dlx genes in forebrain development.
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Affiliation(s)
| | - Crystal Esau
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | | | - Simon Monis
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Luc Poitras
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Man Yu
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Sofia Perin
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Gary Hatch
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
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13
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Santos-Terra J, Deckmann I, Fontes-Dutra M, Schwingel GB, Bambini-Junior V, Gottfried C. Transcription factors in neurodevelopmental and associated psychiatric disorders: A potential convergence for genetic and environmental risk factors. Int J Dev Neurosci 2021; 81:545-578. [PMID: 34240460 DOI: 10.1002/jdn.10141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/23/2021] [Accepted: 07/02/2021] [Indexed: 12/16/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are a heterogeneous and highly prevalent group of psychiatric conditions marked by impairments in the nervous system. Their onset occurs during gestation, and the alterations are observed throughout the postnatal life. Although many genetic and environmental risk factors have been described in this context, the interactions between them challenge the understanding of the pathways associated with NDDs. Transcription factors (TFs)-a group of over 1,600 proteins that can interact with DNA, regulating gene expression through modulation of RNA synthesis-represent a point of convergence for different risk factors. In addition, TFs organize critical processes like angiogenesis, blood-brain barrier formation, myelination, neuronal migration, immune activation, and many others in a time and location-dependent way. In this review, we summarize important TF alterations in NDD and associated disorders, along with specific impairments observed in animal models, and, finally, establish hypotheses to explain how these proteins may be critical mediators in the context of genome-environment interactions.
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Affiliation(s)
- Júlio Santos-Terra
- Translational Research Group in Autism Spectrum Disorders (GETTEA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Autism Wellbeing And Research Development (AWARD) Institute, BR-UK-CA, Preston, UK
| | - Iohanna Deckmann
- Translational Research Group in Autism Spectrum Disorders (GETTEA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Autism Wellbeing And Research Development (AWARD) Institute, BR-UK-CA, Preston, UK
| | - Mellanie Fontes-Dutra
- Translational Research Group in Autism Spectrum Disorders (GETTEA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Autism Wellbeing And Research Development (AWARD) Institute, BR-UK-CA, Preston, UK
| | - Gustavo Brum Schwingel
- Translational Research Group in Autism Spectrum Disorders (GETTEA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Autism Wellbeing And Research Development (AWARD) Institute, BR-UK-CA, Preston, UK
| | - Victorio Bambini-Junior
- Translational Research Group in Autism Spectrum Disorders (GETTEA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Autism Wellbeing And Research Development (AWARD) Institute, BR-UK-CA, Preston, UK.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Preston, UK
| | - Carmem Gottfried
- Translational Research Group in Autism Spectrum Disorders (GETTEA), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,School of Pharmacology and Biomedical Sciences, University of Central Lancashire, Autism Wellbeing And Research Development (AWARD) Institute, BR-UK-CA, Preston, UK
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14
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Kozel BA, Barak B, Ae Kim C, Mervis CB, Osborne LR, Porter M, Pober BR. Williams syndrome. Nat Rev Dis Primers 2021; 7:42. [PMID: 34140529 PMCID: PMC9437774 DOI: 10.1038/s41572-021-00276-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 11/09/2022]
Abstract
Williams syndrome (WS) is a relatively rare microdeletion disorder that occurs in as many as 1:7,500 individuals. WS arises due to the mispairing of low-copy DNA repetitive elements at meiosis. The deletion size is similar across most individuals with WS and leads to the loss of one copy of 25-27 genes on chromosome 7q11.23. The resulting unique disorder affects multiple systems, with cardinal features including but not limited to cardiovascular disease (characteristically stenosis of the great arteries and most notably supravalvar aortic stenosis), a distinctive craniofacial appearance, and a specific cognitive and behavioural profile that includes intellectual disability and hypersociability. Genotype-phenotype evidence is strongest for ELN, the gene encoding elastin, which is responsible for the vascular and connective tissue features of WS, and for the transcription factor genes GTF2I and GTF2IRD1, which are known to affect intellectual ability, social functioning and anxiety. Mounting evidence also ascribes phenotypic consequences to the deletion of BAZ1B, LIMK1, STX1A and MLXIPL, but more work is needed to understand the mechanism by which these deletions contribute to clinical outcomes. The age of diagnosis has fallen in regions of the world where technological advances, such as chromosomal microarray, enable clinicians to make the diagnosis of WS without formally suspecting it, allowing earlier intervention by medical and developmental specialists. Phenotypic variability is considerable for all cardinal features of WS but the specific sources of this variability remain unknown. Further investigation to identify the factors responsible for these differences may lead to mechanism-based rather than symptom-based therapies and should therefore be a high research priority.
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Affiliation(s)
- Beth A. Kozel
- Translational Vascular Medicine Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, USA
| | - Boaz Barak
- The Sagol School of Neuroscience and The School of Psychological Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Chong Ae Kim
- Department of Pediatrics, Universidade de São Paulo, São Paulo, Brazil
| | - Carolyn B. Mervis
- Department of Psychological and Brain Sciences, University of Louisville, Louisville, USA
| | - Lucy R. Osborne
- Department of Medicine, University of Toronto, Ontario, Canada
| | - Melanie Porter
- Department of Psychology, Macquarie University, Sydney, Australia
| | - Barbara R. Pober
- Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Boston, USA
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15
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Hoffmann A, Spengler D. Single-Cell Transcriptomics Supports a Role of CHD8 in Autism. Int J Mol Sci 2021; 22:3261. [PMID: 33806835 PMCID: PMC8004931 DOI: 10.3390/ijms22063261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/16/2022] Open
Abstract
Chromodomain helicase domain 8 (CHD8) is one of the most frequently mutated and most penetrant genes in the autism spectrum disorder (ASD). Individuals with CHD8 mutations show leading symptoms of autism, macrocephaly, and facial dysmorphisms. The molecular and cellular mechanisms underpinning the early onset and development of these symptoms are still poorly understood and prevent timely and more efficient therapies of patients. Progress in this area will require an understanding of "when, why and how cells deviate from their normal trajectories". High-throughput single-cell RNA sequencing (sc-RNAseq) directly quantifies information-bearing RNA molecules that enact each cell's biological identity. Here, we discuss recent insights from sc-RNAseq of CRISPR/Cas9-editing of Chd8/CHD8 during mouse neocorticogenesis and human cerebral organoids. Given that the deregulation of the balance between excitation and inhibition (E/I balance) in cortical and subcortical circuits is thought to represent a major etiopathogenetic mechanism in ASD, we focus on the question of whether, and to what degree, results from current sc-RNAseq studies support this hypothesis. Beyond that, we discuss the pros and cons of these approaches and further steps to be taken to harvest the full potential of these transformative techniques.
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Affiliation(s)
| | - Dietmar Spengler
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany;
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16
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Sumiyama K, Tanave A. The regulatory landscape of the
Dlx
gene system in branchial arches: Shared characteristics among
Dlx
bigene clusters and evolution. Dev Growth Differ 2020; 62:355-362. [DOI: 10.1111/dgd.12671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/18/2020] [Accepted: 04/28/2020] [Indexed: 01/09/2023]
Affiliation(s)
- Kenta Sumiyama
- Laboratory for Mouse Genetic EngineeringRIKEN Center for Biosystems Dynamics Research Suita Osaka Japan
| | - Akira Tanave
- Laboratory for Mouse Genetic EngineeringRIKEN Center for Biosystems Dynamics Research Suita Osaka Japan
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17
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McCole RB, Erceg J, Saylor W, Wu CT. Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization. Cell Rep 2019; 24:479-488. [PMID: 29996107 DOI: 10.1016/j.celrep.2018.06.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/09/2018] [Accepted: 06/07/2018] [Indexed: 12/23/2022] Open
Abstract
This study explores the relationship between three-dimensional genome organization and ultraconserved elements (UCEs), an enigmatic set of DNA elements that are perfectly conserved between the reference genomes of distantly related species. Examining both human and mouse genomes, we interrogate the relationship of UCEs to three features of chromosome organization derived from Hi-C studies. We find that UCEs are enriched within contact domains and, further, that the subset of UCEs within domains shared across diverse cell types are linked to kidney-related and neuronal processes. In boundaries, UCEs are generally depleted, with those that do overlap boundaries being overrepresented in exonic UCEs. Regarding loop anchors, UCEs are neither overrepresented nor underrepresented, but those present in loop anchors are enriched for splice sites. Finally, as the relationships between UCEs and human Hi-C features are conserved in mouse, our findings suggest that UCEs contribute to interspecies conservation of genome organization and, thus, genome stability.
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Affiliation(s)
- Ruth B McCole
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Wren Saylor
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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18
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Demin KA, Meshalkina DA, Volgin AD, Yakovlev OV, de Abreu MS, Alekseeva PA, Friend AJ, Lakstygal AM, Zabegalov K, Amstislavskaya TG, Strekalova T, Bao W, Kalueff AV. Developing zebrafish experimental animal models relevant to schizophrenia. Neurosci Biobehav Rev 2019; 105:126-133. [DOI: 10.1016/j.neubiorev.2019.07.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/20/2019] [Accepted: 07/27/2019] [Indexed: 12/18/2022]
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19
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Meng Y, He Y, Zhang J, Xie Q, Yang M, Chen Y, Wu Y. Association of GTF2I gene polymorphisms with renal involvement of systemic lupus erythematosus in a Chinese population. Medicine (Baltimore) 2019; 98:e16716. [PMID: 31374066 PMCID: PMC6709260 DOI: 10.1097/md.0000000000016716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The purposes of the study was to validate the relationship between General transcription factor II-I (GTF2I) genetic variants and kidney involvements of systemic lupus erythematosus (SLE) patients in a Chinese Han population.Samples from 400 SLE patients and 400 age- and sex-matched healthy controls were collected and genotyped by improved multiplex ligation detection reaction technique. The relationship between gene polymorphism of rs117026326, rs73366469, and susceptibility, progression of SLE were analyzed.The present study provided evidence that rs117026326 and rs73366469 were both associated with SLE susceptibility (both C vs T: P < .001). The analysis of dominant, recessive disease model provided us with further validation (P < .001). Both gene polymorphisms are associated with a triad of disease manifestations among SLE patients. Patients carrying genotype TT of rs117026326 had lower 24-hour urinary total protein (24 hours UTP, g/24 hours), 24-hour urinary protein level (g/L·24 hours), lower frequency of the proteinuria and lupus nephritis (LN). Patients carrying genotype TT at rs73366469 had higher 24-hour urinary protein level, higher frequency of the proteinuria, LN and positive anti-dsDNA than those with other genotypes.This study identified the involvement of GTF2I gene polymorphisms in development of SLE, particularly in renal involvement.
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Affiliation(s)
- Yanming Meng
- Department of Laboratory Medicine and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan
| | - Yao He
- Department of Laboratory Medicine and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan
| | - Junlong Zhang
- Department of Laboratory Medicine and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan
| | - Qibing Xie
- Department of Rheumatology, West China Hospital, Sichuan University
| | - Min Yang
- Department of Rheumatology, West China Hospital, Sichuan University
| | - Yuning Chen
- Department of Medical Laboratory, Xindu District People's Hospital of Chengdu, Chengdu, China
| | - Yongkang Wu
- Department of Laboratory Medicine and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan
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20
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Pla R, Stanco A, Howard MA, Rubin AN, Vogt D, Mortimer N, Cobos I, Potter GB, Lindtner S, Price JD, Nord AS, Visel A, Schreiner CE, Baraban SC, Rowitch DH, Rubenstein JLR. Dlx1 and Dlx2 Promote Interneuron GABA Synthesis, Synaptogenesis, and Dendritogenesis. Cereb Cortex 2018; 28:3797-3815. [PMID: 29028947 PMCID: PMC6188538 DOI: 10.1093/cercor/bhx241] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 11/14/2022] Open
Abstract
The postnatal functions of the Dlx1&2 transcription factors in cortical interneurons (CINs) are unknown. Here, using conditional Dlx1, Dlx2, and Dlx1&2 knockouts (CKOs), we defined their roles in specific CINs. The CKOs had dendritic, synaptic, and survival defects, affecting even PV+ CINs. We provide evidence that DLX2 directly drives Gad1, Gad2, and Vgat expression, and show that mutants had reduced mIPSC amplitude. In addition, the mutants formed fewer GABAergic synapses on excitatory neurons and had reduced mIPSC frequency. Furthermore, Dlx1/2 CKO had hypoplastic dendrites, fewer excitatory synapses, and reduced excitatory input. We provide evidence that some of these phenotypes were due to reduced expression of GRIN2B (a subunit of the NMDA receptor), a high confidence Autism gene. Thus, Dlx1&2 coordinate key components of CIN postnatal development by promoting their excitability, inhibitory output, and survival.
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Affiliation(s)
- Ramon Pla
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Amelia Stanco
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - MacKenzie A Howard
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Anna N Rubin
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Daniel Vogt
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Niall Mortimer
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Inma Cobos
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Gregory Brian Potter
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Susan Lindtner
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - James D Price
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
| | - Alex S Nord
- Departments of Neurobiology, Physiology, and Behavior and Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, USA
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Christoph E Schreiner
- Department of Otolaryngology and Center for Integrative Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | - Scott C Baraban
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David H Rowitch
- Departments of Pediatrics and Neurological Surgery, Eli and Edyth Broad Institute for Stem Cell Research and Regenerative Medicine, University of California San Francisco, San Francisco, CA, USA
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program and the Nina Ireland Laboratory of Developmental Neurobiology, University of California San Francisco, San Francisco, CA, USA
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21
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Murphy E, Benítez-Burraco A. Toward the Language Oscillogenome. Front Psychol 2018; 9:1999. [PMID: 30405489 PMCID: PMC6206218 DOI: 10.3389/fpsyg.2018.01999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Language has been argued to arise, both ontogenetically and phylogenetically, from specific patterns of brain wiring. We argue that it can further be shown that core features of language processing emerge from particular phasal and cross-frequency coupling properties of neural oscillations; what has been referred to as the language ‘oscillome.’ It is expected that basic aspects of the language oscillome result from genetic guidance, what we will here call the language ‘oscillogenome,’ for which we will put forward a list of candidate genes. We have considered genes for altered brain rhythmicity in conditions involving language deficits: autism spectrum disorders, schizophrenia, specific language impairment and dyslexia. These selected genes map on to aspects of brain function, particularly on to neurotransmitter function. We stress that caution should be adopted in the construction of any oscillogenome, given the range of potential roles particular localized frequency bands have in cognition. Our aim is to propose a set of genome-to-language linking hypotheses that, given testing, would grant explanatory power to brain rhythms with respect to language processing and evolution.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom.,Department of Psychology, University of Westminster, London, United Kingdom
| | - Antonio Benítez-Burraco
- Department of Spanish Language, Linguistics and Literary Theory, University of Seville, Seville, Spain
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22
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Wang P, Mokhtari R, Pedrosa E, Kirschenbaum M, Bayrak C, Zheng D, Lachman HM. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells. Mol Autism 2017; 8:11. [PMID: 28321286 PMCID: PMC5357816 DOI: 10.1186/s13229-017-0124-1] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/15/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND CHD8 (chromodomain helicase DNA-binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is one of the most commonly mutated genes in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities and influence cancer cell proliferation. We previously reported an RNA-seq analysis carried out on neural progenitor cells (NPCs) and monolayer neurons derived from induced pluripotent stem (iPS) cells that were heterozygous for CHD8 knockout (KO) alleles generated using CRISPR-Cas9 gene editing. A significant number of ASD and SZ candidate genes were among those that were differentially expressed in a comparison of heterozygous KO lines (CHD8+/-) vs isogenic controls (CHD8+/-), including the SZ and bipolar disorder (BD) candidate gene TCF4, which was markedly upregulated in CHD8+/- neuronal cells. METHODS In the current study, RNA-seq was carried out on CHD8+/- and isogenic control (CHD8+/+) cerebral organoids, which are 3-dimensional structures derived from iPS cells that model the developing human telencephalon. RESULTS TCF4 expression was, again, significantly upregulated. Pathway analysis carried out on differentially expressed genes (DEGs) revealed an enrichment of genes involved in neurogenesis, neuronal differentiation, forebrain development, Wnt/β-catenin signaling, and axonal guidance, similar to our previous study on NPCs and monolayer neurons. There was also significant overlap in our CHD8+/- DEGs with those found in a transcriptome analysis carried out by another group using cerebral organoids derived from a family with idiopathic ASD. Remarkably, the top DEG in our respective studies was the non-coding RNA DLX6-AS1, which was markedly upregulated in both studies; DLX6-AS1 regulates the expression of members of the DLX (distal-less homeobox) gene family. DLX1 was also upregulated in both studies. DLX genes code for transcription factors that play a key role in GABAergic interneuron differentiation. Significant overlap was also found in a transcriptome study carried out by another group using iPS cell-derived neurons from patients with BD, a condition characterized by dysregulated WNT/β-catenin signaling in a subgroup of affected individuals. CONCLUSIONS Overall, the findings show that distinct ASD, SZ, and BD candidate genes converge on common molecular targets-an important consideration for developing novel therapeutics in genetically heterogeneous complex traits.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
| | - Ryan Mokhtari
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Michael Kirschenbaum
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
| | - Can Bayrak
- Erciyes University School of Medicine, Kayseri, Turkey
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Psychiatry and Behavioral Sciences, Erciyes University School of Medicine, Kayseri, Turkey
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY USA
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23
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Role of Splice Variants of Gtf2i, a Transcription Factor Localizing at Postsynaptic Sites, and Its Relation to Neuropsychiatric Diseases. Int J Mol Sci 2017; 18:ijms18020411. [PMID: 28212274 PMCID: PMC5343945 DOI: 10.3390/ijms18020411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/01/2017] [Accepted: 02/09/2017] [Indexed: 12/17/2022] Open
Abstract
We previously reported that various mRNAs were associated with postsynaptic density (PSD) purified from rat forebrain. Among the thousands of PSD-associated mRNAs, we highlight the biology of the general transcription factor II-I (Gtf2i) mRNA, focusing on the significance of its versatile splicing for targeting its own mRNA into dendrites, regulation of translation, and the effects of Gtf2i expression level as well as its relationship with neuropsychiatric disorders.
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24
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Benítez-Burraco A, Lattanzi W, Murphy E. Language Impairments in ASD Resulting from a Failed Domestication of the Human Brain. Front Neurosci 2016; 10:373. [PMID: 27621700 PMCID: PMC5002430 DOI: 10.3389/fnins.2016.00373] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders entailing social and cognitive deficits, including marked problems with language. Numerous genes have been associated with ASD, but it is unclear how language deficits arise from gene mutation or dysregulation. It is also unclear why ASD shows such high prevalence within human populations. Interestingly, the emergence of a modern faculty of language has been hypothesized to be linked to changes in the human brain/skull, but also to the process of self-domestication of the human species. It is our intention to show that people with ASD exhibit less marked domesticated traits at the morphological, physiological, and behavioral levels. We also discuss many ASD candidates represented among the genes known to be involved in the “domestication syndrome” (the constellation of traits exhibited by domesticated mammals, which seemingly results from the hypofunction of the neural crest) and among the set of genes involved in language function closely connected to them. Moreover, many of these genes show altered expression profiles in the brain of autists. In addition, some candidates for domestication and language-readiness show the same expression profile in people with ASD and chimps in different brain areas involved in language processing. Similarities regarding the brain oscillatory behavior of these areas can be expected too. We conclude that ASD may represent an abnormal ontogenetic itinerary for the human faculty of language resulting in part from changes in genes important for the “domestication syndrome” and, ultimately, from the normal functioning of the neural crest.
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Affiliation(s)
| | - Wanda Lattanzi
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore Rome, Italy
| | - Elliot Murphy
- Division of Psychology and Language Sciences, University College London London, UK
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25
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Murphy E, Benítez-Burraco A. Language deficits in schizophrenia and autism as related oscillatory connectomopathies: An evolutionary account. Neurosci Biobehav Rev 2016; 83:742-764. [PMID: 27475632 DOI: 10.1016/j.neubiorev.2016.07.029] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/23/2016] [Accepted: 07/25/2016] [Indexed: 01/28/2023]
Abstract
Schizophrenia (SZ) and autism spectrum disorders (ASD) are characterised by marked language deficits, but it is not clear how these arise from gene mutations associated with the disorders. Our goal is to narrow the gap between SZ and ASD and, ultimately, give support to the view that they represent abnormal (but related) ontogenetic itineraries for the human faculty of language. We will focus on the distinctive oscillatory profiles of the SZ and ASD brains, in turn using these insights to refine our understanding of how the brain implements linguistic computations by exploring a novel model of linguistic feature-set composition. We will argue that brain rhythms constitute the best route to interpreting language deficits in both conditions and mapping them to neural dysfunction and risk alleles of the genes. Importantly, candidate genes for SZ and ASD are overrepresented among the gene sets believed to be important for language evolution. This translational effort may help develop an understanding of the aetiology of SZ and ASD and their high prevalence among modern populations.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom.
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26
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Warnefors M, Hartmann B, Thomsen S, Alonso CR. Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. Mol Biol Evol 2016; 33:2294-306. [PMID: 27247329 PMCID: PMC4989106 DOI: 10.1093/molbev/msw101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa.
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Affiliation(s)
- Maria Warnefors
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Britta Hartmann
- Institute of Human Genetics, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University Medical Center Freiburg, Freiburg, Germany
| | - Stefan Thomsen
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Claudio R Alonso
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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27
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Becker M, Guadalupe T, Franke B, Hibar DP, Renteria ME, Stein JL, Thompson PM, Francks C, Vernes SC, Fisher SE. Early developmental gene enhancers affect subcortical volumes in the adult human brain. Hum Brain Mapp 2016; 37:1788-800. [PMID: 26890892 DOI: 10.1002/hbm.23136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 12/30/2015] [Accepted: 01/26/2016] [Indexed: 11/08/2022] Open
Abstract
Genome-wide association screens aim to identify common genetic variants contributing to the phenotypic variability of complex traits, such as human height or brain morphology. The identified genetic variants are mostly within noncoding genomic regions and the biology of the genotype-phenotype association typically remains unclear. In this article, we propose a complementary targeted strategy to reveal the genetic underpinnings of variability in subcortical brain volumes, by specifically selecting genomic loci that are experimentally validated forebrain enhancers, active in early embryonic development. We hypothesized that genetic variation within these enhancers may affect the development and ultimately the structure of subcortical brain regions in adults. We tested whether variants in forebrain enhancer regions showed an overall enrichment of association with volumetric variation in subcortical structures of >13,000 healthy adults. We observed significant enrichment of genomic loci that affect the volume of the hippocampus within forebrain enhancers (empirical P = 0.0015), a finding which robustly passed the adjusted threshold for testing of multiple brain phenotypes (cutoff of P < 0.0083 at an alpha of 0.05). In analyses of individual single nucleotide polymorphisms (SNPs), we identified an association upstream of the ID2 gene with rs7588305 and variation in hippocampal volume. This SNP-based association survived multiple-testing correction for the number of SNPs analyzed but not for the number of subcortical structures. Targeting known regulatory regions offers a way to understand the underlying biology that connects genotypes to phenotypes, particularly in the context of neuroimaging genetics. This biology-driven approach generates testable hypotheses regarding the functional biology of identified associations. Hum Brain Mapp 37:1788-1800, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Martin Becker
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Tulio Guadalupe
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Barbara Franke
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Derrek P Hibar
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina Del Rey, California
| | - Miguel E Renteria
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jason L Stein
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina Del Rey, California.,Department of Neurology, Neurogenetics Program, UCLA School of Medicine, Los Angeles, California
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina Del Rey, California
| | - Clyde Francks
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Simon E Fisher
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
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28
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Proudfoot A, Axelrod HL, Geralt M, Fletterick RJ, Yumoto F, Deacon AM, Elsliger MA, Wilson IA, Wüthrich K, Serrano P. Dlx5 Homeodomain:DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome. J Mol Biol 2016; 428:1130-1141. [PMID: 26829219 DOI: 10.1016/j.jmb.2016.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/20/2016] [Accepted: 01/24/2016] [Indexed: 12/18/2022]
Abstract
The Dlx5 homeodomain is a transcription factor related to the Drosophila distal-less gene that is associated with breast and lung cancer, lymphoma, Rett syndrome and osteoporosis in humans. Mutations in the DLX5 gene have been linked to deficiencies in craniofacial and limb development in higher eukaryotes, including split hand and foot malformation 1 in humans. Our characterization of a Dlx5 homeodomain:(CGACTAATTAGTCG)2 complex by NMR spectroscopy paved the way for determination of its crystal structure at 1.85Å resolution that enabled rationalization of the effects of disease-related mutations on the protein function. A Q186H mutation linked to split hand and foot malformation 1 likely affects affinity of DNA binding by disrupting water-mediated interactions with the DNA major groove. A more subtle effect is implicated for the Q178P mutation, which is not in direct contact with the DNA. Our data indicate that these mutations diminish the ability of the Dlx5 homeodomain to recognize and bind target DNAs, and they likely destabilize the formation of functional complexes.
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Affiliation(s)
- Andrew Proudfoot
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Herbert L Axelrod
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Michael Geralt
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robert J Fletterick
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Fumiaki Yumoto
- Department of Biochemistry and Biophysics, University of California San Francisco, 600 16th Street, San Francisco, CA 94158, USA
| | - Ashley M Deacon
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Marc-André Elsliger
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Institute of Molecular Biology and Biophysics, ETH Zürich, CH 8093, Zürich, Switzerland
| | - Pedro Serrano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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29
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Merelo V, Durand D, Lescallette AR, Vrana KE, Hong LE, Faghihi MA, Bellon A. Associating schizophrenia, long non-coding RNAs and neurostructural dynamics. Front Mol Neurosci 2015; 8:57. [PMID: 26483630 PMCID: PMC4588008 DOI: 10.3389/fnmol.2015.00057] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/10/2015] [Indexed: 01/10/2023] Open
Abstract
Several lines of evidence indicate that schizophrenia has a strong genetic component. But the exact nature and functional role of this genetic component in the pathophysiology of this mental illness remains a mystery. Long non-coding RNAs (lncRNAs) are a recently discovered family of molecules that regulate gene transcription through a variety of means. Consequently, lncRNAs could help us bring together apparent unrelated findings in schizophrenia; namely, genomic deficiencies on one side and neuroimaging, as well as postmortem results on the other. In fact, the most consistent finding in schizophrenia is decreased brain size together with enlarged ventricles. This anomaly appears to originate from shorter and less ramified dendrites and axons. But a decrease in neuronal arborizations cannot explain the complex pathophysiology of this psychotic disorder; however, dynamic changes in neuronal structure present throughout life could. It is well recognized that the structure of developing neurons is extremely plastic. This structural plasticity was thought to stop with brain development. However, breakthrough discoveries have shown that neuronal structure retains some degree of plasticity throughout life. What the neuroscientific field is still trying to understand is how these dynamic changes are regulated and lncRNAs represent promising candidates to fill this knowledge gap. Here, we present evidence that associates specific lncRNAs with schizophrenia. We then discuss the potential role of lncRNAs in neurostructural dynamics. Finally, we explain how dynamic neurostructural modifications present throughout life could, in theory, reconcile apparent unrelated findings in schizophrenia.
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Affiliation(s)
- Veronica Merelo
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miller School of Medicine Miami, FL, USA
| | - Dante Durand
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miller School of Medicine Miami, FL, USA
| | - Adam R Lescallette
- Penn State Hershey Medical Center, Department of Pharmacology Hershey, PA, USA ; Penn State Hershey Medical Center, Department of Psychiatry Hershey, PA, USA
| | - Kent E Vrana
- Penn State Hershey Medical Center, Department of Pharmacology Hershey, PA, USA
| | - L Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine Baltimore, MD, USA
| | - Mohammad Ali Faghihi
- Center for Therapeutic Innovation, Department of Psychiatry and Behavioral Sciences University of Miami, Miller School of Medicine Miami, FL, USA
| | - Alfredo Bellon
- Penn State Hershey Medical Center, Department of Pharmacology Hershey, PA, USA ; Penn State Hershey Medical Center, Department of Psychiatry Hershey, PA, USA
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30
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Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, Clark BS, Thompson J, Yates JR, Kingston RE, Kohtz JD. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 2015; 142:2641-52. [PMID: 26138476 DOI: 10.1242/dev.126318] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/09/2015] [Indexed: 01/12/2023]
Abstract
Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in the developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA-BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity are promiscuous, suggesting that context is a crucial factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model in which RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin-Siris syndrome, a human intellectual disability disorder, localize to the BRG1 RNA-binding and DLX1-binding domains.
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Affiliation(s)
- Ivelisse Cajigas
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - David E Leib
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Jesse Cochrane
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Hao Luo
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Kelsey R Swyter
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Sean Chen
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Brian S Clark
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | | | - John R Yates
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert E Kingston
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Jhumku D Kohtz
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
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31
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Nord AS. Learning about mammalian gene regulation from functional enhancer assays in the mouse. Genomics 2015; 106:178-184. [PMID: 26079655 DOI: 10.1016/j.ygeno.2015.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/06/2015] [Accepted: 06/08/2015] [Indexed: 01/29/2023]
Abstract
Enhancer biology is emerging as a critical area of research that informs studies of evolution, development, and disease. From early experiments that defined and mapped the first enhancers to recent enhancer models of human disease, functional experiments in the mouse have played a central role in revealing enhancer biology. Three decades of in vivo enhancer studies in mouse have laid the groundwork for the current understanding of mammalian enhancers, demonstrating the developmental and tissue-specific activity of enhancers and illuminating general features of enhancer evolution and function. Recent studies offer an emerging perspective on the importance of chromosomal context, combinatorial enhancer activity, and the functional consequences of enhancer sequence variation. This review describes the basic principles of functional testing in mouse, summarizes the contributions these studies have made to our understanding of enhancer biology, and describes limitations and future outlook of in vivo mouse enhancer studies.
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Affiliation(s)
- Alex S Nord
- Center for Neuroscience, Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, University of California, Davis, CA, USA; Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, Davis, CA, USA.
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Shirai Y, Watanabe M, Sakagami H, Suzuki T. Novel splice variants in the 5'UTR of Gtf2i expressed in the rat brain: alternative 5'UTRs and differential expression in the neuronal dendrites. J Neurochem 2015; 134:578-89. [PMID: 25913238 DOI: 10.1111/jnc.13136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
General transcription factor II-I (Gtf2i) is a transcription factor and one of the genes implicated in Willams-Beuren syndrome, an autism spectrum disorder. In this study, we investigated splice variants of the Gtf2i gene in both the 5'untranslated region (5'UTR) and the coding region. To search for novel 5'UTRs of Gtf2i, we utilized the cap analysis gene expression database of the mouse. We identified seven novel Gtf2i transcripts with alternatively spliced 5'UTRs in the rat brain. We also identified four novel splice variants in the coding sequence of Gtf2i. Furthermore, we identified a selective usage of certain types of 5'UTR by coding variants. In situ hybridization demonstrated a differential pattern of expression of Gtf2i mRNAs with alternatively spliced 5'UTRs among neuronal cells, and the localization of one of the variants in neuronal dendrites in the rat brain. Immunohistochemistry also demonstrated a distribution of Gtf2i-immunoreactivity in the dendrites. These results suggest multiple pathways of expression of Gtf2i gene in the brain. The expression patterns may be under the control of alternative promoters coupled to the alternative splicing in the coding region. Differential localization of mRNA to neuronal dendrites suggests spatiotemporal-specific translation at the post-synaptic sites that is involved in transfer of synaptic activity to expression of specific sets of genes in the nucleus. Gtf2i is a transcription factor and implicated in Willams-Beuren syndrome. We identified seven novel Gtf2i transcripts with alternatively spliced 5'UTRs in the rat brain. In situ hybridization demonstrated a differential expression of Gtf2i mRNAs with different 5'UTRs in somas and dendrites of neuronal cells. Differential localization of mRNA to neuronal dendrites suggests spatiotemporal-specific translation at the postsynaptic sites. The scheme shows genomic structure showing the positions of the potential transcription start tags (rDEC695, rDEC3D7, rDEC1D3, rDEC104, rDEC072 and rDEBE25). Newly identified exons (1.1-1.6) are shown with the white boxes. The distances from rDEC695-5'end are indicated in bp.
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Affiliation(s)
- Yoshinori Shirai
- Department of Neuroplasticity, Institute of Pathogenesis and Disease Prevention, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hiroyuki Sakagami
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - Tatsuo Suzuki
- Department of Neuroplasticity, Institute of Pathogenesis and Disease Prevention, Shinshu University Graduate School of Medicine, Matsumoto, Japan.,Department of Biological Sciences for Intractable Neurological Diseases, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Japan
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Nord AS, Pattabiraman K, Visel A, Rubenstein JLR. Genomic perspectives of transcriptional regulation in forebrain development. Neuron 2015; 85:27-47. [PMID: 25569346 PMCID: PMC4438709 DOI: 10.1016/j.neuron.2014.11.011] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The forebrain is the seat of higher-order brain functions, and many human neuropsychiatric disorders are due to genetic defects affecting forebrain development, making it imperative to understand the underlying genetic circuitry. Recent progress now makes it possible to begin fully elucidating the genomic regulatory mechanisms that control forebrain gene expression. Herein, we discuss the current knowledge of how transcription factors drive gene expression programs through their interactions with cis-acting genomic elements, such as enhancers; how analyses of chromatin and DNA modifications provide insights into gene expression states; and how these approaches yield insights into the evolution of the human brain.
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Affiliation(s)
- Alex S Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA.
| | - Kartik Pattabiraman
- Department of Psychiatry, Rock Hall, University of California, San Francisco, San Francisco, CA 94158-2324, USA
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - John L R Rubenstein
- Department of Psychiatry, Rock Hall, University of California, San Francisco, San Francisco, CA 94158-2324, USA
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Huang D, Ovcharenko I. Identifying causal regulatory SNPs in ChIP-seq enhancers. Nucleic Acids Res 2015; 43:225-36. [PMID: 25520196 PMCID: PMC4288203 DOI: 10.1093/nar/gku1318] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/19/2023] Open
Abstract
Thousands of non-coding SNPs have been linked to human diseases in the past. The identification of causal alleles within this pool of disease-associated non-coding SNPs is largely impossible due to the inability to accurately quantify the impact of non-coding variation. To overcome this challenge, we developed a computational model that uses ChIP-seq intensity variation in response to non-coding allelic change as a proxy to the quantification of the biological role of non-coding SNPs. We applied this model to HepG2 enhancers and detected 4796 enhancer SNPs capable of disrupting enhancer activity upon allelic change. These SNPs are significantly over-represented in the binding sites of HNF4 and FOXA families of liver transcription factors and liver eQTLs. In addition, these SNPs are strongly associated with liver GWAS traits, including type I diabetes, and are linked to the abnormal levels of HDL and LDL cholesterol. Our model is directly applicable to any enhancer set for mapping causal regulatory SNPs.
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Affiliation(s)
- Di Huang
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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McCole RB, Fonseka CY, Koren A, Wu CT. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells. PLoS Genet 2014; 10:e1004646. [PMID: 25340765 PMCID: PMC4207606 DOI: 10.1371/journal.pgen.1004646] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/04/2014] [Indexed: 12/17/2022] Open
Abstract
Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.
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Affiliation(s)
- Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Biological and Biomedical Sciences PhD program, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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Lossie AC, Muir WM, Lo CL, Timm F, Liu Y, Gray W, Zhou FC. Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice. Front Genet 2014; 5:173. [PMID: 24966868 PMCID: PMC4052096 DOI: 10.3389/fgene.2014.00173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/22/2014] [Indexed: 12/12/2022] Open
Abstract
Maternal alcohol consumption inflicts a multitude of phenotypic consequences that range from undetectable changes to severe dysmorphology. Using tightly controlled murine studies that deliver precise amounts of alcohol at discrete developmental stages, our group and other labs demonstrated in prior studies that the C57BL/6 and DBA/2 inbred mouse strains display differential susceptibility to the teratogenic effects of alcohol. Since the phenotypic diversity extends beyond the amount, dosage and timing of alcohol exposure, it is likely that an individual's genetic background contributes to the phenotypic spectrum. To identify the genomic signatures associated with these observed differences in alcohol-induced dysmorphology, we conducted a microarray-based transcriptome study that also interrogated the genomic signatures between these two lines based on genetic background and alcohol exposure. This approach is called a gene x environment (GxE) analysis; one example of a GxE interaction would be a gene whose expression level increases in C57BL/6, but decreases in DBA/2 embryos, following alcohol exposure. We identified 35 candidate genes exhibiting GxE interactions. To identify cis-acting factors that mediated these interactions, we interrogated the proximal promoters of these 35 candidates and found 241 single nucleotide variants (SNVs) in 16 promoters. Further investigation indicated that 186 SNVs (15 promoters) are predicted to alter transcription factor binding. In addition, 62 SNVs created, removed or altered the placement of a CpG dinucleotide in 13 of the proximal promoters, 53 of which overlapped putative transcription factor binding sites. These 53 SNVs are also our top candidates for future studies aimed at examining the effects of alcohol on epigenetic gene regulation.
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Affiliation(s)
- Amy C Lossie
- Department of Animal Sciences, Purdue University West Lafayette, IN, USA
| | - William M Muir
- Department of Animal Sciences, Purdue University West Lafayette, IN, USA ; Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
| | - Chiao-Ling Lo
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Floyd Timm
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Molecular and Medical Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Whitney Gray
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Feng C Zhou
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA ; Stark Neuroscience Research Institute, Indiana University School of Medicine Indianapolis, IN, USA
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Kim DS, Ross PJ, Zaslavsky K, Ellis J. Optimizing neuronal differentiation from induced pluripotent stem cells to model ASD. Front Cell Neurosci 2014; 8:109. [PMID: 24782713 PMCID: PMC3990101 DOI: 10.3389/fncel.2014.00109] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/25/2014] [Indexed: 01/01/2023] Open
Abstract
Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder characterized by deficits in social communication, and restricted and repetitive patterns of behavior. Despite its high prevalence, discovery of pathophysiological mechanisms underlying ASD has lagged due to a lack of appropriate model systems. Recent advances in induced pluripotent stem cell (iPSC) technology and neural differentiation techniques allow for detailed functional analyses of neurons generated from living individuals with ASD. Refinement of cortical neuron differentiation methods from iPSCs will enable mechanistic studies of specific neuronal subpopulations that may be preferentially impaired in ASD. In this review, we summarize recent accomplishments in differentiation of cortical neurons from human pluripotent stems cells and efforts to establish in vitro model systems to study ASD using personalized neurons.
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Affiliation(s)
- Dae-Sung Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada
| | - P Joel Ross
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada
| | - Kirill Zaslavsky
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada ; Department of Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada ; Department of Molecular Genetics, University of Toronto Toronto, ON, Canada
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38
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Boeckx C, Benítez-Burraco A. The shape of the human language-ready brain. Front Psychol 2014; 5:282. [PMID: 24772099 PMCID: PMC3983487 DOI: 10.3389/fpsyg.2014.00282] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/17/2014] [Indexed: 12/14/2022] Open
Abstract
Our core hypothesis is that the emergence of our species-specific language-ready brain ought to be understood in light of the developmental changes expressed at the levels of brain morphology and neural connectivity that occurred in our species after the split from Neanderthals–Denisovans and that gave us a more globular braincase configuration. In addition to changes at the cortical level, we hypothesize that the anatomical shift that led to globularity also entailed significant changes at the subcortical level. We claim that the functional consequences of such changes must also be taken into account to gain a fuller understanding of our linguistic capacity. Here we focus on the thalamus, which we argue is central to language and human cognition, as it modulates fronto-parietal activity. With this new neurobiological perspective in place, we examine its possible molecular basis. We construct a candidate gene set whose members are involved in the development and connectivity of the thalamus, in the evolution of the human head, and are known to give rise to language-associated cognitive disorders. We submit that the new gene candidate set opens up new windows into our understanding of the genetic basis of our linguistic capacity. Thus, our hypothesis aims at generating new testing grounds concerning core aspects of language ontogeny and phylogeny.
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Affiliation(s)
- Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA) Barcelona, Spain ; Department of Linguistics, Universitat de Barcelona Barcelona, Spain
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39
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Wolf ZT, Leslie EJ, Arzi B, Jayashankar K, Karmi N, Jia Z, Rowland DJ, Young A, Safra N, Sliskovic S, Murray JC, Wade CM, Bannasch DL. A LINE-1 insertion in DLX6 is responsible for cleft palate and mandibular abnormalities in a canine model of Pierre Robin sequence. PLoS Genet 2014; 10:e1004257. [PMID: 24699068 PMCID: PMC3974639 DOI: 10.1371/journal.pgen.1004257] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/04/2014] [Indexed: 02/05/2023] Open
Abstract
Cleft palate (CP) is one of the most commonly occurring craniofacial birth defects in humans. In order to study cleft palate in a naturally occurring model system, we utilized the Nova Scotia Duck Tolling Retriever (NSDTR) dog breed. Micro-computed tomography analysis of CP NSDTR craniofacial structures revealed that these dogs exhibit defects similar to those observed in a recognizable subgroup of humans with CP: Pierre Robin Sequence (PRS). We refer to this phenotype in NSDTRs as CP1. Individuals with PRS have a triad of birth defects: shortened mandible, posteriorly placed tongue, and cleft palate. A genome-wide association study in 14 CP NSDTRs and 72 unaffected NSDTRs identified a significantly associated region on canine chromosome 14 (24.2 Mb–29.3 Mb; praw = 4.64×10−15). Sequencing of two regional candidate homeobox genes in NSDTRs, distal-less homeobox 5 (DLX5) and distal-less homeobox 6 (DLX6), identified a 2.1 kb LINE-1 insertion within DLX6 in CP1 NSDTRs. The LINE-1 insertion is predicted to insert a premature stop codon within the homeodomain of DLX6. This prompted the sequencing of DLX5 and DLX6 in a human cohort with CP, where a missense mutation within the highly conserved DLX5 homeobox of a patient with PRS was identified. This suggests the involvement of DLX5 in the development of PRS. These results demonstrate the power of the canine animal model as a genetically tractable approach to understanding naturally occurring craniofacial birth defects in humans. Cleft palate is one of the most commonly occurring birth defects in children, and yet its cause is not completely understood. In order to better understand cleft palate we have turned to man's best friend, the domestic dog. Common breeding practices have made the dog a unique animal model to help understand the genetic basis of naturally occurring birth defects. A genome-wide association study of Nova Scotia Duck Tolling Retrievers with naturally occurring cleft palate led to the investigation of two homeobox genes, DLX5 and DLX6. Dogs with this mutation also have a shortened lower jaw, which resembles those who have Pierre Robin Sequence (PRS). Investigation into people with PRS identifies a mutation within a highly conserved and functional region of DLX5 that may contribute to the development of PRS. This exemplifies how the dog will help us better understand common birth defects.
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Affiliation(s)
- Zena T Wolf
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Elizabeth J Leslie
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Boaz Arzi
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Kartika Jayashankar
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Nili Karmi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Zhonglin Jia
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China; Department of Cleft Lip and Palate Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Douglas J Rowland
- Center for Molecular and Genomic Imaging, University of California, Davis, Davis, California, United States of America
| | - Amy Young
- Department of Animal Science, University of California, Davis, Davis, California, United States of America
| | - Noa Safra
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Saundra Sliskovic
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, Iowa, United States of America
| | - Claire M Wade
- Faculty of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Danika L Bannasch
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, United States of America
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40
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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Makunin IV, Shloma VV, Stephen SJ, Pheasant M, Belyakin SN. Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One 2013; 8:e82362. [PMID: 24349264 PMCID: PMC3862641 DOI: 10.1371/journal.pone.0082362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 10/24/2013] [Indexed: 11/18/2022] Open
Abstract
Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.
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Affiliation(s)
- Igor V. Makunin
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
- * E-mail:
| | - Viktor V. Shloma
- Institute of Molecular and Cellular Biology SD RAS, Novosibirsk, Russia
| | - Stuart J. Stephen
- Computational Biology Group, CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Michael Pheasant
- Research Computing Centre, The University of Queensland, Brisbane, Queensland, Australia
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A DNA-centric protein interaction map of ultraconserved elements reveals contribution of transcription factor binding hubs to conservation. Cell Rep 2013; 5:531-45. [PMID: 24139795 DOI: 10.1016/j.celrep.2013.09.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/06/2013] [Accepted: 09/11/2013] [Indexed: 12/19/2022] Open
Abstract
Ultraconserved elements (UCEs) have been the subject of great interest because of their extreme sequence identity and their seemingly cryptic and largely uncharacterized functions. Although in vivo studies of UCE sequences have demonstrated regulatory activity, protein interactors at UCEs have not been systematically identified. Here, we combined high-throughput affinity purification, high-resolution mass spectrometry, and SILAC quantification to map intrinsic protein interactions for 193 UCE sequences. The interactome contains over 400 proteins, including transcription factors with known developmental roles. We demonstrate based on our data that UCEs consist of strongly conserved overlapping binding sites. We also generated a fine-resolution interactome of a UCE, confirming the hub-like nature of the element. The intrinsic interactions mapped here are reflected in open chromatin, as indicated by comparison with existing ChIP data. Our study argues for a strong contribution of protein-DNA interactions to UCE conservation and provides a basis for further functional characterization of UCEs.
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43
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Berghoff EG, Clark MF, Chen S, Cajigas I, Leib DE, Kohtz JD. Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes. Development 2013; 140:4407-16. [PMID: 24089468 DOI: 10.1242/dev.099390] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Several lines of evidence suggest that long non-coding RNA (lncRNA)-dependent mechanisms regulate transcription and CpG DNA methylation. Whereas CpG island methylation has been studied in detail, the significance of enhancer DNA methylation and its relationship with lncRNAs is relatively unexplored. Previous experiments proposed that the ultraconserved lncRNA Evf2 represses transcription through Dlx6 antisense (Dlx6as) transcription and methyl-CpG binding protein (MECP2) recruitment to the Dlx5/6 ultraconserved DNA regulatory enhancer (Dlx5/6ei) in embryonic day 13.5 medial ganglionic eminence (E13.5 MGE). Here, genetic epistasis experiments show that MECP2 transcriptional repression of Evf2 and Dlx5, but not Dlx6, occurs through antagonism of DLX1/2 in E13.5 MGE. Analysis of E13.5 MGE from mice lacking Evf2 and of partially rescued Evf2 transgenic mice shows that Evf2 prevents site-specific CpG DNA methylation of Dlx5/6ei in trans, without altering Dlx5/6 expression. Dlx1/2 loss increases CpG DNA methylation, whereas Mecp2 loss does not affect Dlx5/6ei methylation. Based on these studies, we propose a model in which Evf2 inhibits enhancer DNA methylation, effectively modulating competition between the DLX1/2 activator and MECP2 repressor. Evf2 antisense transcription and Evf2-dependent balanced recruitment of activator and repressor proteins enables differential transcriptional control of adjacent genes with shared DNA regulatory elements.
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Affiliation(s)
- Emily G Berghoff
- Developmental Biology and Department of Pediatrics, Lurie Children's Research Center, and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
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Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JLR. A high-resolution enhancer atlas of the developing telencephalon. Cell 2013; 152:895-908. [PMID: 23375746 DOI: 10.1016/j.cell.2012.12.041] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 10/31/2012] [Accepted: 12/20/2012] [Indexed: 11/25/2022]
Abstract
The mammalian telencephalon plays critical roles in cognition, motor function, and emotion. Though many of the genes required for its development have been identified, the distant-acting regulatory sequences orchestrating their in vivo expression are mostly unknown. Here, we describe a digital atlas of in vivo enhancers active in subregions of the developing telencephalon. We identified more than 4,600 candidate embryonic forebrain enhancers and studied the in vivo activity of 329 of these sequences in transgenic mouse embryos. We generated serial sets of histological brain sections for 145 reproducible forebrain enhancers, resulting in a publicly accessible web-based data collection comprising more than 32,000 sections. We also used epigenomic analysis of human and mouse cortex tissue to directly compare the genome-wide enhancer architecture in these species. These data provide a primary resource for investigating gene regulatory mechanisms of telencephalon development and enable studies of the role of distant-acting enhancers in neurodevelopmental disorders.
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Affiliation(s)
- Axel Visel
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Abstract
Three genes GTF2IRD1, GTF2I, and GTF2IRD2, which encode members of the GTF2I (or TFII-I) family of so-called general transcription factors, were discovered and studied during the last two decades. Chromosome location and similarity of exon-intron structures suggest that the family evolved by duplications. The initial duplication of ancestral proto-GTF2IRD1 gene likely occurred in early vertebrates prior to origin of cartilaginous fish and led to formation of GTF2I (>450 MYA), which was later lost in bony fish but successfully evolved in the land vertebrates. The second duplication event, which created GTF2IRD2, occurred prior to major radiation events of eutherian mammalian evolution (>100 MYA). During recent steps of primate evolution there was another duplication which led to formation of GTF2IRD2B (<4 MYA). Two latest duplications were coupled with inversions. Genes belonging to the family have several highly conservative repeats which are implicated in DNA binding. Phylogenetic analysis of the repeats revealed a pattern of intragenic duplications, deletions and substitutions which led to diversification of the genes and proteins. Distribution of statistically rare atypical substitutions (p ≤ 0.01) sheds some light on structural differentiation of repeats and hence evolution of the genes. The atypical substitutions are often located on secondary structures joining α-helices and affect 3D arrangement of the protein globule. Such substitutions are commonly traced at the early stages of evolution in Tetrapoda, Amniota, and Mammalia.
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Ryu T, Seridi L, Ravasi T. The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol 2012; 12:236. [PMID: 23217155 PMCID: PMC3556307 DOI: 10.1186/1471-2148-12-236] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 11/09/2012] [Indexed: 11/10/2022] Open
Abstract
Background Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors.
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Affiliation(s)
- Taewoo Ryu
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Birnbaum RY, Everman DB, Murphy KK, Gurrieri F, Schwartz CE, Ahituv N. Functional characterization of tissue-specific enhancers in the DLX5/6 locus. Hum Mol Genet 2012; 21:4930-8. [PMID: 22914741 DOI: 10.1093/hmg/dds336] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Disruption of distaless homeobox 5 and 6 (Dlx5/6) in mice results in brain, craniofacial, genital, ear and limb defects. In humans, chromosomal aberrations in the DLX5/6 region, some of which do not encompass DLX5/6, are associated with split hand/foot malformation 1 (SHFM1) as well as intellectual disability, craniofacial anomalies and hearing loss, suggesting that the disruption of DLX5/6 regulatory elements could lead to these abnormalities. Here, we characterized enhancers in the DLX5/6 locus whose tissue-specific expression and genomic location along with previously characterized enhancers correlate with phenotypes observed in individuals with chromosomal abnormalities. By analyzing chromosomal aberrations at 7q21, we refined the minimal SHFM1 critical region and used comparative genomics to select 26 evolutionary conserved non-coding sequences in this critical region for zebrafish enhancer assays. Eight of these sequences were shown to function as brain, olfactory bulb, branchial arch, otic vesicle and fin enhancers, recapitulating dlx5a/6a expression. Using a mouse enhancer assay, several of these zebrafish enhancers showed comparable expression patterns in the branchial arch, otic vesicle, forebrain and/or limb at embryonic day 11.5. Examination of the coordinates of various chromosomal rearrangements in conjunction with the genomic location of these tissue-specific enhancers showed a correlation with the observed clinical abnormalities. Our findings suggest that chromosomal abnormalities that disrupt the function of these tissue-specific enhancers could be the cause of SHFM1 and its associated phenotypes. In addition, they highlight specific enhancers in which mutations could lead to non-syndromic hearing loss, craniofacial defects or limb malformations.
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Affiliation(s)
- Ramon Y Birnbaum
- Department of Bioengineering and Therapeutic Sciences and 2Institute for Human Genetics, University of California-San Francisco, CA, USA
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Conceptualizing neurodevelopmental disorders through a mechanistic understanding of fragile X syndrome and Williams syndrome. Curr Opin Neurol 2012; 25:112-24. [PMID: 22395002 DOI: 10.1097/wco.0b013e328351823c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW The overarching goal of this review is to compare and contrast the cognitive-behavioral features of fragile X syndrome (FraX) and Williams syndrome and to review the putative neural and molecular underpinnings of these features. Information is presented in a framework that provides guiding principles for conceptualizing gene-brain-behavior associations in neurodevelopmental disorders. RECENT FINDINGS Abnormalities, in particular cognitive-behavioral domains with similarities in underlying neurodevelopmental correlates, occur in both FraX and Williams syndrome including aberrant frontostriatal pathways leading to executive function deficits, and magnocellular/dorsal visual stream, superior parietal lobe, inferior parietal lobe, and postcentral gyrus abnormalities contributing to deficits in visuospatial function. Compelling cognitive-behavioral and neurodevelopmental contrasts also exist in these two disorders, for example, aberrant amygdala and fusiform cortex structure and function occurring in the context of contrasting social behavioral phenotypes, and temporal cortical and cerebellar abnormalities potentially underlying differences in language function. Abnormal dendritic development is a shared neurodevelopmental morphologic feature between FraX and Williams syndrome. Commonalities in molecular machinery and processes across FraX and Williams syndrome occur as well - microRNAs involved in translational regulation of major synaptic proteins; scaffolding proteins in excitatory synapses; and proteins involved in axonal development. SUMMARY Although the genetic variations leading to FraX and Williams syndrome are different, important similarities and contrasts in the phenotype, neurocircuitry, molecular machinery, and cellular processes in these two disorders allow for a unique approach to conceptualizing gene-brain-behavior links occurring in neurodevelopmental disorders.
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Halgren C, Bache I, Bak M, Myatt MW, Anderson CM, Brøndum-Nielsen K, Tommerup N. Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity. Eur J Hum Genet 2012; 20:1315-9. [PMID: 22617346 PMCID: PMC3499750 DOI: 10.1038/ejhg.2012.92] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Only 20 patients with deletions of 18q12.2 have been reported in the literature and the associated phenotype includes borderline intellectual disability, behavioral problems, seizures, obesity, and eye manifestations. Here, we report a male patient with a de novo translocation involving chromosomes 12 and 18, with borderline IQ, developmental and behavioral disorders, myopia, obesity, and febrile seizures in childhood. We characterized the rearrangement with Affymetrix SNP 6.0 Array analysis and next-generation mate pair sequencing and found truncation of CELF4 at 18q12.2. This second report of a patient with a neurodevelopmental phenotype and a translocation involving CELF4 supports that CELF4 is responsible for the phenotype associated with deletion of 18q12.2. Our study illustrates the utility of high-resolution genome-wide techniques in identifying neurodevelopmental and neurobehavioral genes, and it adds to the growing evidence, including a transgenic mouse model, that CELF4 is important for human brain development.
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Affiliation(s)
- Christina Halgren
- Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research, University of Copenhagen, Faculty of Health Sciences, Copenhagen, Denmark.
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Jarinova O, Ekker M. Regulatory variations in the era of next-generation sequencing: Implications for clinical molecular diagnostics. Hum Mutat 2012; 33:1021-30. [DOI: 10.1002/humu.22083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/06/2012] [Indexed: 01/05/2023]
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