Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS

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.

[1]  A. Visel,et al.  Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development , 2013, Cell.

[2]  H. Okuno,et al.  Synaptic activity-responsive element in the Arc/Arg3.1 promoter essential for synapse-to-nucleus signaling in activated neurons , 2009, Proceedings of the National Academy of Sciences.

[3]  Steven W. Flavell,et al.  Activity-Dependent Regulation of MEF2 Transcription Factors Suppresses Excitatory Synapse Number , 2006, Science.

[4]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[5]  Edward M. Callaway,et al.  Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types , 2009, Frontiers in neural circuits.

[6]  Andreas R. Pfenning,et al.  Core and region-enriched networks of behaviorally regulated genes and the singing genome , 2014, Science.

[7]  T. Derrien,et al.  Long Noncoding RNAs with Enhancer-like Function in Human Cells , 2010, Cell.

[8]  L. Grøntved,et al.  eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. , 2013, Molecular cell.

[9]  J. Ragoussis,et al.  A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers , 2010, PLoS biology.

[10]  Christopher S. Poultney,et al.  Synaptic, transcriptional, and chromatin genes disrupted in autism , 2014, Nature.

[11]  D. Tuan,et al.  Transcription of the hypersensitive site HS2 enhancer in erythroid cells. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[12]  R. Maehr,et al.  Functional annotation of native enhancers with a Cas9 -histone demethylase fusion , 2015, Nature Methods.

[13]  Tae-Kyung Kim,et al.  Enhancer RNA facilitates NELF release from immediate early genes. , 2014, Molecular cell.

[14]  P. Kantoff,et al.  Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation , 2014, Proceedings of the National Academy of Sciences.

[15]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[16]  M. Rosenfeld,et al.  LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation , 2015, Neuron.

[17]  S. Dudek,et al.  Splitting Hares and Tortoises: A classification of neuronal immediate early gene transcription based on poised RNA polymerase II , 2013, Neuroscience.

[18]  W. Denk,et al.  Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Christopher M. Vockley,et al.  Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum , 2015, Nature Neuroscience.

[20]  Takashi Kawashima,et al.  A new era for functional labeling of neurons: activity-dependent promoters have come of age , 2014, Front. Neural Circuits.

[21]  Christopher B. Burge,et al.  Promoter directionality is controlled by U1 snRNP and polyadenylation signals , 2013, Nature.

[22]  C. Spencer,et al.  Biological Insights From 108 Schizophrenia-Associated Genetic Loci , 2014, Nature.

[23]  Vijay K. Tiwari,et al.  DNA-binding factors shape the mouse methylome at distal regulatory regions , 2011, Nature.

[24]  Barak A. Cohen,et al.  Complex effects of nucleotide variants in a mammalian cis-regulatory element , 2012, Proceedings of the National Academy of Sciences.

[25]  M. Hemberg,et al.  Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers. , 2015, Cold Spring Harbor perspectives in biology.

[26]  Bing Ren,et al.  CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells , 2014, PloS one.

[27]  M. Creyghton,et al.  Large-scale identification of coregulated enhancer networks in the adult human brain. , 2014, Cell reports.

[28]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[29]  Terrence J. Sejnowski,et al.  Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain , 2015, Neuron.

[30]  Nadav Ahituv,et al.  Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression , 2014, Cell.

[31]  Alan M. Moses,et al.  In vivo enhancer analysis of human conserved non-coding sequences , 2006, Nature.

[32]  Stephan J Sanders,et al.  The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment , 2015, Nature Communications.

[33]  Axel Visel,et al.  Genomic Perspectives of Transcriptional Regulation in Forebrain Development , 2015, Neuron.

[34]  C. Gieger,et al.  Restless Legs Syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon , 2014, Genome research.

[35]  J. Banerji,et al.  A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes , 1983, Cell.

[36]  L. Steinmetz,et al.  Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality , 2013, Nature Structural &Molecular Biology.

[37]  Thomas Vierbuchen,et al.  Genome-wide identification and characterization of functional neuronal activity–dependent enhancers , 2014, Nature Neuroscience.

[38]  S. Akbarian,et al.  Isolation of neuronal chromatin from brain tissue , 2008, BMC Neuroscience.

[39]  P. Chambon,et al.  The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. , 1981, Nucleic acids research.

[40]  Thomas J. Ha,et al.  Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells , 2015, Science.

[41]  Hongkui Zeng,et al.  Transcriptional Regulation of Enhancers Active in Protodomains of the Developing Cerebral Cortex , 2014, Neuron.

[42]  Carolyn A. Morrison,et al.  Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity , 2013, Nature Neuroscience.

[43]  Skirmantas Kriaucionis,et al.  MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. , 2012, Cell.

[44]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[45]  Gail Mandel,et al.  Defining the CREB Regulon A Genome-Wide Analysis of Transcription Factor Regulatory Regions , 2004, Cell.

[46]  A. Stark,et al.  Transcriptional enhancers: from properties to genome-wide predictions , 2014, Nature Reviews Genetics.

[47]  André L. Martins,et al.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers , 2014, Nature Genetics.

[48]  Larry N. Singh,et al.  U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation , 2010, Nature.

[49]  K. Obata,et al.  Preferential labeling of inhibitory and excitatory cortical neurons by endogenous tropism of adeno-associated virus and lentivirus vectors , 2009, Neuroscience.

[50]  N. Wray,et al.  Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders , 2015, Neuron.

[51]  N. Heintz,et al.  MeCP2 binds to 5hmc enriched within active genes and accessible chromatin in the nervous system , 2012, Cell.

[52]  Shane J. Neph,et al.  A comparative encyclopedia of DNA elements in the mouse genome , 2014, Nature.

[53]  Laura J. Scott,et al.  Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways , 2015, Nature Neuroscience.

[54]  J. Stender,et al.  Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. , 2013, Molecular cell.

[55]  B. L,et al.  The accessible chromatin landscape of the human genome , 2016 .

[56]  S. Tonegawa,et al.  A tissue-specific transcription enhancer element is located in the major intron of a rearranged immunoglobulin heavy chain gene , 1983, Cell.

[57]  H. Ashe,et al.  Intergenic transcription and transinduction of the human beta-globin locus. , 1997, Genes & development.

[58]  S. Lomvardas,et al.  An Epigenetic Trap Stabilizes Singular Olfactory Receptor Expression , 2013, Cell.

[59]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[60]  J. Pike,et al.  Selective Distal Enhancer Control of the Mmp13 Gene Identified through Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Genomic Deletions* , 2015, The Journal of Biological Chemistry.

[61]  Axel Visel,et al.  Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers , 2014, PLoS genetics.

[62]  Allon M. Klein,et al.  Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.

[63]  Kenichi Ohki,et al.  Functional labeling of neurons and their projections using the synthetic activity–dependent promoter E-SARE , 2013, Nature Methods.

[64]  C. Glass,et al.  Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation , 2013, Nature.

[65]  A. Sandelin,et al.  A Unified Architecture of Transcriptional Regulatory Elements , 2015, bioRxiv.

[66]  M. Nóbrega,et al.  Scanning Human Gene Deserts for Long-Range Enhancers , 2003, Science.

[67]  Matthew D. Schultz,et al.  Global Epigenomic Reconfiguration During Mammalian Brain Development , 2013, Science.

[68]  M. Greenberg,et al.  Stimulation of neuronal acetylcholine receptors induces rapid gene transcription. , 1986, Science.

[69]  David C Fargo,et al.  Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin. , 2015, Molecular cell.

[70]  Z. Weng,et al.  Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex , 2010, Proceedings of the National Academy of Sciences.

[71]  Evan Z. Macosko,et al.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets , 2015, Cell.

[72]  Howard Y. Chang,et al.  Single-cell chromatin accessibility reveals principles of regulatory variation , 2015, Nature.

[73]  Christopher M. Vockley,et al.  Epigenome editing by a CRISPR/Cas9-based acetyltransferase activates genes from promoters and enhancers , 2015, Nature Biotechnology.

[74]  Gabriel Kreiman,et al.  Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites , 2012, Nucleic acids research.

[75]  Alan R. Mardinly,et al.  Npas4 Regulates Excitatory-Inhibitory Balance within Neural Circuits through Cell-Type-Specific Gene Programs , 2014, Cell.

[76]  Athar N. Malik,et al.  MEF2D Drives Photoreceptor Development through a Genome-wide Competition for Tissue-Specific Enhancers , 2015, Neuron.

[77]  C. Gerfen,et al.  GENSAT BAC Cre-Recombinase Driver Lines to Study the Functional Organization of Cerebral Cortical and Basal Ganglia Circuits , 2013, Neuron.

[78]  B. Bradley,et al.  Allele-specific FKBP5 DNA demethylation mediates gene–childhood trauma interactions , 2012, Nature Neuroscience.

[79]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[80]  S. Lomvardas,et al.  Co-Opting the Unfolded Protein Response to Elicit Olfactory Receptor Feedback , 2013, Cell.