101
|
A transducible nuclear/nucleolar protein, mLLP, regulates neuronal morphogenesis and synaptic transmission. Sci Rep 2016; 6:22892. [PMID: 26961175 PMCID: PMC4790632 DOI: 10.1038/srep22892] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/23/2016] [Indexed: 12/03/2022] Open
Abstract
Cell-permeable proteins are emerging as unconventional regulators of signal transduction and providing a potential for therapeutic applications. However, only a few of them are identified and studied in detail. We identify a novel cell-permeable protein, mouse LLP homolog (mLLP), and uncover its roles in regulating neural development. We found that mLLP is strongly expressed in developing nervous system and that mLLP knockdown or overexpression during maturation of cultured neurons affected the neuronal growth and synaptic transmission. Interestingly, extracellular addition of mLLP protein enhanced dendritic arborization, demonstrating the non-cell-autonomous effect of mLLP. Moreover, mLLP interacts with CCCTC-binding factor (CTCF) as well as transcriptional machineries and modulates gene expression involved in neuronal growth. Together, these results illustrate the characteristics and roles of previously unknown cell-permeable protein mLLP in modulating neural development.
Collapse
|
102
|
Berto S, Perdomo-Sabogal A, Gerighausen D, Qin J, Nowick K. A Consensus Network of Gene Regulatory Factors in the Human Frontal Lobe. Front Genet 2016; 7:31. [PMID: 27014338 PMCID: PMC4782181 DOI: 10.3389/fgene.2016.00031] [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] [Received: 10/30/2015] [Accepted: 02/18/2016] [Indexed: 01/29/2023] Open
Abstract
Cognitive abilities, such as memory, learning, language, problem solving, and planning, involve the frontal lobe and other brain areas. Not much is known yet about the molecular basis of cognitive abilities, but it seems clear that cognitive abilities are determined by the interplay of many genes. One approach for analyzing the genetic networks involved in cognitive functions is to study the coexpression networks of genes with known importance for proper cognitive functions, such as genes that have been associated with cognitive disorders like intellectual disability (ID) or autism spectrum disorders (ASD). Because many of these genes are gene regulatory factors (GRFs) we aimed to provide insights into the gene regulatory networks active in the human frontal lobe. Using genome wide human frontal lobe expression data from 10 independent data sets, we first derived 10 individual coexpression networks for all GRFs including their potential target genes. We observed a high level of variability among these 10 independently derived networks, pointing out that relying on results from a single study can only provide limited biological insights. To instead focus on the most confident information from these 10 networks we developed a method for integrating such independently derived networks into a consensus network. This consensus network revealed robust GRF interactions that are conserved across the frontal lobes of different healthy human individuals. Within this network, we detected a strong central module that is enriched for 166 GRFs known to be involved in brain development and/or cognitive disorders. Interestingly, several hubs of the consensus network encode for GRFs that have not yet been associated with brain functions. Their central role in the network suggests them as excellent new candidates for playing an essential role in the regulatory network of the human frontal lobe, which should be investigated in future studies.
Collapse
Affiliation(s)
- Stefano Berto
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany; Paul-Flechsig Institute for Brain Research, University of LeipzigLeipzig, Germany; Department of Neuroscience, University of Texas Southwestern Medical CenterDallas, TX, USA
| | - Alvaro Perdomo-Sabogal
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany
| | - Daniel Gerighausen
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig Leipzig, Germany
| | - Jing Qin
- Department of Mathematics and Computer Sciences, University of Southern DenmarkOdense, Denmark; Institute for Theoretical Chemistry, University of ViennaVienna, Austria
| | - Katja Nowick
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University LeipzigLeipzig, Germany; Paul-Flechsig Institute for Brain Research, University of LeipzigLeipzig, Germany
| |
Collapse
|
103
|
Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS. J Neurosci 2016; 35:13819-26. [PMID: 26468181 DOI: 10.1523/jneurosci.2622-15.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Sprinkled throughout the genome are a million regulatory sequences called transcriptional enhancers that activate gene promoters in the right cells, at the right time. Enhancers endow the brain with its incredible diversity of cell types and also translate neural activity into gene induction. Thanks to rapid advances in genomic technologies, it is now possible to identify thousands of enhancers rapidly, test their transcriptional function en masse, and address their neurobiological functions via genome editing. Enhancers also promise to be a great technological opportunity for neuroscience, offering the potential for cell-type-specific genetic labeling and manipulation without the need for transgenesis. The objective of this review and the accompanying 2015 SfN mini-symposium is to highlight the use of new and emerging genomic technologies to probe enhancer function in the nervous system. SIGNIFICANCE STATEMENT Transcriptional enhancers turn on genes in the right cells, at the right time. Enhancers are also the genomic sequences that encode the incredible diversity of cell types in the brain and enable the brain to turn genes on in response to new experiences. New technology enables enhancers to be found and manipulated. The study of enhancers promises to inform our understanding of brain development and function. The application of enhancer technology holds promise in accelerating basic neuroscience research and enabling gene therapies to be targeted to specific cell types in the brain.
Collapse
|
104
|
Silver DL. Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex. Bioessays 2015; 38:162-71. [PMID: 26642006 DOI: 10.1002/bies.201500108] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cerebral cortex controls our most distinguishing higher cognitive functions. Human-specific gene expression differences are abundant in the cerebral cortex, yet we have only begun to understand how these variations impact brain function. This review discusses the current evidence linking non-coding regulatory DNA changes, including enhancers, with neocortical evolution. Functional interrogation using animal models reveals converging roles for our genome in key aspects of cortical development including progenitor cell cycle and neuronal signaling. New technologies, including iPS cells and organoids, offer potential alternatives to modeling evolutionary modifications in a relevant species context. Several diseases rooted in the cerebral cortex uniquely manifest in humans compared to other primates, thus highlighting the importance of understanding human brain differences. Future studies of regulatory loci, including those implicated in disease, will collectively help elucidate key cellular and genetic mechanisms underlying our distinguishing cognitive traits.
Collapse
Affiliation(s)
- Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA.,Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.,Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.,Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
105
|
O'Shea KS, McInnis MG. Neurodevelopmental origins of bipolar disorder: iPSC models. Mol Cell Neurosci 2015; 73:63-83. [PMID: 26608002 DOI: 10.1016/j.mcn.2015.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/14/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Bipolar disorder (BP) is a chronic neuropsychiatric condition characterized by pathological fluctuations in mood from mania to depression. Adoption, twin and family studies have consistently identified a significant hereditary component to BP, yet there is no clear genetic event or consistent neuropathology. BP has been suggested to have a developmental origin, although this hypothesis has been difficult to test since there are no viable neurons or glial cells to analyze, and research has relied largely on postmortem brain, behavioral and imaging studies, or has examined proxy tissues including saliva, olfactory epithelium and blood cells. Neurodevelopmental factors, particularly pathways related to nervous system development, cell migration, extracellular matrix, H3K4 methylation, and calcium signaling have been identified in large gene expression and GWAS studies as altered in BP. Recent advances in stem cell biology, particularly the ability to reprogram adult somatic tissues to a pluripotent state, now make it possible to interrogate these pathways in viable cell models. A number of induced pluripotent stem cell (iPSC) lines from BP patient and healthy control (C) individuals have been derived in several laboratories, and their ability to form cortical neurons examined. Early studies suggest differences in activity, calcium signaling, blocks to neuronal differentiation, and changes in neuronal, and possibly glial, lineage specification. Initial observations suggest that differentiation of BP patient-derived neurons to dorsal telencephalic derivatives may be impaired, possibly due to alterations in WNT, Hedgehog or Nodal pathway signaling. These investigations strongly support a developmental contribution to BP and identify novel pathways, mechanisms and opportunities for improved treatments.
Collapse
Affiliation(s)
- K Sue O'Shea
- Department of Cell and Developmental Biology, University of Michigan, 3051 BSRB, 109 Zina Pitcher PL, Ann Arbor, MI 48109-2200, United States; Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States.
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States
| |
Collapse
|
106
|
Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nat Neurosci 2015; 18:1707-12. [PMID: 26605881 PMCID: PMC4675669 DOI: 10.1038/nn.4156] [Citation(s) in RCA: 281] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regulatory regions of the genome. Understanding precisely how these variants contribute to disease will require a deeper appreciation for the mechanisms of gene regulation in the developing and adult human brain. The PsychENCODE project aims to produce a public resource of multidimensional genomic data using tissue- and cell type–specific samples from approximately 1,000 phenotypically well-characterized, high-quality healthy and disease-affected human post-mortem brains, as well as functionally characterize disease-associated regulatory elements and variants in model systems. We are beginning with a focus on autism spectrum disorder, bipolar disorder and schizophrenia, and expect that this knowledge will apply to a wide variety of psychiatric disorders. This paper outlines the motivation and design of PsychENCODE.
Collapse
|
107
|
Shen SQ, Myers CA, Hughes AEO, Byrne LC, Flannery JG, Corbo JC. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res 2015; 26:238-55. [PMID: 26576614 PMCID: PMC4728376 DOI: 10.1101/gr.193789.115] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 11/12/2015] [Indexed: 01/23/2023]
Abstract
Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell–derived organoids.
Collapse
Affiliation(s)
- Susan Q Shen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Connie A Myers
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Leah C Byrne
- Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA
| | - John G Flannery
- Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| |
Collapse
|
108
|
Bayam E, Sahin GS, Guzelsoy G, Guner G, Kabakcioglu A, Ince-Dunn G. Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation. BMC Genomics 2015; 16:681. [PMID: 26341353 PMCID: PMC4560887 DOI: 10.1186/s12864-015-1882-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/26/2015] [Indexed: 12/03/2022] Open
Abstract
Background Cellular differentiation programs are controlled, to a large extent, by the combinatorial functioning of specific transcription factors. Cortical projection neurons constitute the major excitatory neuron population within the cortex and mediate long distance communication between the cortex and other brain regions. Our understanding of effector transcription factors and their downstream transcriptional programs that direct the differentiation process of cortical projection neurons is far from complete. Results In this study, we carried out a ChIP-Seq (chromatin-immunoprecipitation and sequencing) analysis of NEUROD2, an effector transcription factor expressed in lineages of cortical projection neurons during the peak of cortical excitatory neurogenesis. Our results suggest that during cortical development NEUROD2 targets key genes that are required for Reelin signaling, a major pathway that regulates the migration of neurons from germinal zones to their final layers of residence within the cortex. We also find that NEUROD2 binds to a large set of genes with functions in layer-specific differentiation and in axonal pathfinding of cortical projection neurons. Conclusions Our analysis of in vivo NEUROD2 target genes offers mechanistic insight into signaling pathways that regulate neuronal migration and axon guidance and identifies genes that are likely to be required for proper cortical development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1882-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Efil Bayam
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Gulcan Semra Sahin
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey. .,Present Address: Neuroscience Department, Washington State University, Pullman, WA, 99164, USA.
| | - Gizem Guzelsoy
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Gokhan Guner
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Alkan Kabakcioglu
- Physics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| | - Gulayse Ince-Dunn
- Molecular Biology and Genetics Department, Koç University, Rumeli Feneri Yolu, Istanbul, 34450, Turkey.
| |
Collapse
|
109
|
Ypsilanti AR, Rubenstein JLR. Transcriptional and epigenetic mechanisms of early cortical development: An examination of how Pax6 coordinates cortical development. J Comp Neurol 2015; 524:609-29. [PMID: 26304102 DOI: 10.1002/cne.23866] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 12/26/2022]
Abstract
The development of the cortex is an elaborate process that integrates a plethora of finely tuned molecular processes ranging from carefully regulated gradients of transcription factors, dynamic changes in the chromatin landscape, or formation of protein complexes to elicit and regulate transcription. Combined with cellular processes such as cell type specification, proliferation, differentiation, and migration, all of these developmental processes result in the establishment of an adult mammalian cortex with its typical lamination and regional patterning. By examining in-depth the role of one transcription factor, Pax6, on the regulation of cortical development, its integration in the regulation of chromatin state, and its regulation by cis-regulatory elements, we aim to demonstrate the importance of integrating each level of regulation in our understanding of cortical development.
Collapse
Affiliation(s)
- Athéna R Ypsilanti
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, California
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, California
| |
Collapse
|
110
|
Parikshak NN, Gandal MJ, Geschwind DH. Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders. Nat Rev Genet 2015; 16:441-58. [PMID: 26149713 PMCID: PMC4699316 DOI: 10.1038/nrg3934] [Citation(s) in RCA: 287] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic and genomic approaches have implicated hundreds of genetic loci in neurodevelopmental disorders and neurodegeneration, but mechanistic understanding continues to lag behind the pace of gene discovery. Understanding the role of specific genetic variants in the brain involves dissecting a functional hierarchy that encompasses molecular pathways, diverse cell types, neural circuits and, ultimately, cognition and behaviour. With a focus on transcriptomics, this Review discusses how high-throughput molecular, integrative and network approaches inform disease biology by placing human genetics in a molecular systems and neurobiological context. We provide a framework for interpreting network biology studies and leveraging big genomics data sets in neurobiology.
Collapse
Affiliation(s)
- Neelroop N Parikshak
- 1] Program in Neurobehavioral Genetics, Semel Institute, and Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [2] Interdepartmental Program in Neuroscience, University of California, Los Angeles, California 90095, USA
| | - Michael J Gandal
- 1] Program in Neurobehavioral Genetics, Semel Institute, and Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [2] Center for Autism Treatment and Research, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Daniel H Geschwind
- 1] Program in Neurobehavioral Genetics, Semel Institute, and Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [2] Interdepartmental Program in Neuroscience, University of California, Los Angeles, California 90095, USA. [3] Center for Autism Treatment and Research, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA. [4] Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| |
Collapse
|