Abstract:Optogenetics provides new ways to activate gene transcription; however, no attempts have been made as yet to modulate mammalian transcription factors. We report the light-mediated regulation of the repressor element 1 (RE1)-silencing transcription factor (REST), a master regulator of neural genes. To tune REST activity, we selected two protein domains that impair REST-DNA binding or recruitment of the cofactor mSin3a. Computational modeling guided the fusion of the inhibitory domains to the light-sensitive Ave… Show more
“…Using the WebGestalt toolkit [43] to test for enrichment of transcription factor binding sites (TFBS), we found M30 was highly enriched for NRSF/REST (repressor element 1-silencing transcription factor) targets (BH P = 2.55 × 10 –8 , r = 8.50). REST is a repressor of neuron-specific genes in early fetal development whose activity is downregulated in mature neurons [44] and dysregulated in a large array of brain pathologies including epilepsy [45–48]. The strong enrichment for REST-target genes in M30 is consistent with the tightly regulated developmental trajectory of expression of this module during brain development and supports the hypothesis that M30 genes non-randomly share a common regulation.Fig.…”
BackgroundThe relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy.ResultsWe identified a co-expression network of 320 genes (M30), which is significantly enriched for non-synonymous de novo mutations ascertained from patients with monogenic epilepsy and for common variants associated with polygenic epilepsy. The genes in the M30 network are expressed widely in the human brain under tight developmental control and encode physically interacting proteins involved in synaptic processes. The most highly connected proteins within the M30 network were preferentially disrupted by deleterious de novo mutations for monogenic epilepsy, in line with the centrality-lethality hypothesis. Analysis of M30 expression revealed consistent downregulation in the epileptic brain in heterogeneous forms of epilepsy including human temporal lobe epilepsy, a mouse model of acquired temporal lobe epilepsy, and a mouse model of monogenic Dravet (SCN1A) disease. These results suggest functional disruption of M30 via gene mutation or altered expression as a convergent mechanism regulating susceptibility to epilepsy broadly. Using the large collection of drug-induced gene expression data from Connectivity Map, several drugs were predicted to preferentially restore the downregulation of M30 in epilepsy toward health, most notably valproic acid, whose effect on M30 expression was replicated in neurons.ConclusionsTaken together, our results suggest targeting the expression of M30 as a potential new therapeutic strategy in epilepsy.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1097-7) contains supplementary material, which is available to authorized users.
“…Using the WebGestalt toolkit [43] to test for enrichment of transcription factor binding sites (TFBS), we found M30 was highly enriched for NRSF/REST (repressor element 1-silencing transcription factor) targets (BH P = 2.55 × 10 –8 , r = 8.50). REST is a repressor of neuron-specific genes in early fetal development whose activity is downregulated in mature neurons [44] and dysregulated in a large array of brain pathologies including epilepsy [45–48]. The strong enrichment for REST-target genes in M30 is consistent with the tightly regulated developmental trajectory of expression of this module during brain development and supports the hypothesis that M30 genes non-randomly share a common regulation.Fig.…”
BackgroundThe relationship between monogenic and polygenic forms of epilepsy is poorly understood and the extent to which the genetic and acquired epilepsies share common pathways is unclear. Here, we use an integrated systems-level analysis of brain gene expression data to identify molecular networks disrupted in epilepsy.ResultsWe identified a co-expression network of 320 genes (M30), which is significantly enriched for non-synonymous de novo mutations ascertained from patients with monogenic epilepsy and for common variants associated with polygenic epilepsy. The genes in the M30 network are expressed widely in the human brain under tight developmental control and encode physically interacting proteins involved in synaptic processes. The most highly connected proteins within the M30 network were preferentially disrupted by deleterious de novo mutations for monogenic epilepsy, in line with the centrality-lethality hypothesis. Analysis of M30 expression revealed consistent downregulation in the epileptic brain in heterogeneous forms of epilepsy including human temporal lobe epilepsy, a mouse model of acquired temporal lobe epilepsy, and a mouse model of monogenic Dravet (SCN1A) disease. These results suggest functional disruption of M30 via gene mutation or altered expression as a convergent mechanism regulating susceptibility to epilepsy broadly. Using the large collection of drug-induced gene expression data from Connectivity Map, several drugs were predicted to preferentially restore the downregulation of M30 in epilepsy toward health, most notably valproic acid, whose effect on M30 expression was replicated in neurons.ConclusionsTaken together, our results suggest targeting the expression of M30 as a potential new therapeutic strategy in epilepsy.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1097-7) contains supplementary material, which is available to authorized users.
“…In one relevant application, GAVPO was used to control Brn2 expression in embryonic stem cells, in order to query how timing and dose affect the regulatory network of pluripotency TFs [70]. Alternatively, multiple groups have engineered DNA binding motifs and functional domains such that their association can be controlled optically [39, 61, 64]. When delivered to cells these constructs enable tight temporal control of transcriptional activity, transcriptional repression, or targeted epigenetic modifications [39, 45, 61].…”
Section: Co-occupancy Of Regulatory Dnamentioning
confidence: 99%
“…Alternatively, multiple groups have engineered DNA binding motifs and functional domains such that their association can be controlled optically [39, 61, 64]. When delivered to cells these constructs enable tight temporal control of transcriptional activity, transcriptional repression, or targeted epigenetic modifications [39, 45, 61]. Thus in principle, multiple TFs can be delivered to neurons, with the expression or function of one or more factors regulated by optical stimulation.…”
Recovery from injuries to the central nervous system, including spinal cord injury, is constrained in part by the intrinsically low ability of many CNS neurons to mount an effective regenerative growth response. To improve outcomes, it is essential to understand and ultimately reverse these neuron-intrinsic constraints. Genetic manipulation of key transcription factors (TFs), which act to orchestrate production of multiple regeneration-associated genes, has emerged as a promising strategy. It is likely that no single TF will be sufficient to fully restore neuron-intrinsic growth potential, and that multiple, functionally interacting factors will be needed. An extensive literature, mostly from non-neural cell types, has identified potential mechanisms by which TFs can functionally synergize. Here we examine four potential mechanisms of TF/TF interaction; physical interaction, transcriptional cross-regulation, signaling-based cross regulation, and co-occupancy of regulatory DNA. For each mechanism, we consider how existing knowledge can be used to guide the discovery and effective use of TF combinations in the context of regenerative neuroscience. This mechanistic insight into TF interactions is needed to accelerate the design of effective TF-based interventions to relieve neuron-intrinsic constraints to regeneration and to foster recovery from CNS injury.
“…Blue light triggers the unwinding of the Jα helix between LOV2 and Rac1 [3], exposing the binding surface of Rac1 to downstream effectors. Other proteins, including a calcium channel regulator [38] and transcription factors [39], have also been caged at the C-terminus of Jα helix. Noticeably, the caging efficiency in these systems is largely dependent on the interaction between target protein and the LOV domain [37,39].…”
Section: Regulation Of Protein Accessibility (Steric Caging)mentioning
confidence: 99%
“…Other proteins, including a calcium channel regulator [38] and transcription factors [39], have also been caged at the C-terminus of Jα helix. Noticeably, the caging efficiency in these systems is largely dependent on the interaction between target protein and the LOV domain [37,39]. Therefore, this strategy seems mostly applicable to small peptides, such as kinase inhibitory peptides [40,41] or protein trafficking peptides [42–46].…”
Section: Regulation Of Protein Accessibility (Steric Caging)mentioning
Optogenetic tools offer fast and reversible control of protein activity with subcellular spatial precision. In the past few years, remarkable progress has been made in engineering photoactivatable systems regulating the activity of cellular proteins. In this review, we discuss general strategies in designing and optimizing such optogenetic tools and highlight recent advances in the field, with specific focus on applications regulating protein catalytic activity.
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