Scaling Law
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ABSTRACT:
PROVIDER: PRJEB24588 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Combinatorial genetics reveals a scaling law for the effects of mutations on splicing
| PRJNA436581 | ENA
Project description:Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modelling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighbouring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
2019-01-17 | GSE111316 | GEO
Project description:Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law
| PRJNA647333 | ENA
Project description:NPTX2, Homeostatic Scaling, and Schizophrenia
| PRJNA633132 | ENA
Project description:Synaptic scaling is a form of homeostatic plasticity which allows neurons to reduce their action potential firing rate in response to chronic alterations in neural activity. Synaptic scaling requires profound changes in gene expression, but the relative contribution of local and cell-wide mechanisms to synaptic scaling is controversial. Here we performed a comprehensive multi-omics characterization of the somatic and process compartments of primary rat hippocampal neurons during synaptic scaling. Thereby, we uncovered highly compartment-specific and correlated changes in the neuronal transcriptome and proteome. Specifically, we identified highly compartment-specific downregulation of crucial regulators of neuronal excitability and excitatory synapse structure. Motif analysis further suggests an important role for trans-acting post-transcriptional regulators, including RNA-binding proteins and microRNAs, in the local regulation of the corresponding mRNAs. Altogether, our study indicates that compartmentalized gene expression changes are widespread in synaptic scaling and might co-exist with neuron-wide mechanism to allow synaptic computation and homeostasis.
2021-07-06 | GSE155540 | GEO
Project description:To better comprehend how synaptic scaling affects the neuronal transcriptome, we used the whole genome microarray expression profiling in hippocampal cultures treated with AMPARs and synaptic NMDARs antagonists for 9h and 26h, or under control conditions. Gene ontology enrichment analysis showed altered transcripts associated with synaptic signalling and synaptic plasticity classes, including transcripts of several proteins already associated with synaptic scaling mechanisms.
2019-02-13 | GSE111384 | GEO
Project description:Homeostatic scaling adjusts synaptic strength in response to persistent changes in neuronal network activity. This compensatory mechanism requires proteome remodeling accomplished via regulation of protein synthesis as well as degradation, but the global patterns of proteome remodeling and the underlying dynamics of individual proteins remain elusive. Here we used dynamic SILAC labeling in cultured hippocampal cells to identify proteins involved in homeostatic up- or down-scaling and to quantify their changes in synthesis and degradation as well as resulting changes in protein abundance or turnover. Our data demonstrate that a large fraction of the neuronal proteome is remodeled during homeostatic scaling. Most proteins were down-regulated by decreased synthesis or up-regulated by decreased degradation. Comparably fewer proteins showed increased synthesis or degradation rates. More than half of the quantified synaptic proteins were regulated, including pre- as well as postsynaptic proteins with diverse molecular functions.
2020-03-31 | PXD016004 | Pride
Project description:Homeostatic plasticity, a form of synaptic plasticity, maintains the fine balance between overall excitation and inhibition in developing and mature neuronal networks. Although the synaptic mechanisms of homeostatic plasticity are well characterized, the associated transcriptional program remains poorly understood. We show that the Kleefstra syndrome-associated protein, EHMT1, plays a critical and cell-autonomous role in synaptic scaling by responding to attenuated neuronal firing or sensory drive. Chronic activity deprivation increased the amount of neuronal dimethylated H3 at lysine 9 (H3K9me2), the catalytic product of EHMT1 and an epigenetic marker for gene repression. Genetic knockdown and pharmacological blockade of EHMT1 or EHMT2 prevented the increase of H3K9me2 and synaptic scaling up. Furthermore, BDNF repression was preceded by EHMT1/2-mediated H3K9me2 deposition at the Bdnf promoter during synaptic scaling up, both in vivo or in vivo. These findings suggest that changes in chromatin state through H3K9me2 governs a repressive program to achieve synaptic scaling.
2016-06-30 | GSE68960 | GEO
Project description:Homeostatic plasticity, a form of synaptic plasticity, maintains the fine balance between overall excitation and inhibition in developing and mature neuronal networks. Although the synaptic mechanisms of homeostatic plasticity are well characterized, the associated transcriptional program remains poorly understood. We show that the Kleefstra syndrome-associated protein, EHMT1, plays a critical and cell-autonomous role in synaptic scaling by responding to attenuated neuronal firing or sensory drive. Chronic activity deprivation increased the amount of neuronal dimethylated H3 at lysine 9 (H3K9me2), the catalytic product of EHMT1 and an epigenetic marker for gene repression. Genetic knockdown and pharmacological blockade of EHMT1 or EHMT2 prevented the increase of H3K9me2 and synaptic scaling up. Furthermore, BDNF repression was preceded by EHMT1/2-mediated H3K9me2 deposition at the Bdnf promoter during synaptic scaling up, both in vivo or in vivo. These findings suggest that changes in chromatin state through H3K9me2 governs a repressive program to achieve synaptic scaling. 12 samples (4 conditions in biological triplicate), 3 wt, 3 wt tetradotoxin treated, 3 k.d., 3 k.d. tetradotoxin treated
2016-06-30 | E-GEOD-68960 | biostudies-arrayexpress
Project description:We investigated the cis-regulatory divergences in alternative splicing and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid mouse. By obtaining more than 240 million read pairs on average in each sample from 5 organs and ESC as well as published data in liver, we comprehensively analyzed the allelic splicing patterns across tissues in hybrid mice. We find that tissue-dependent regulation causing large splicing differences is highly conserved and likely functional, while splicing divergence mainly affects genes under relaxed selective constraints. Although cis-divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform could tolerate more mutations, which explains the paradoxical sequence conservation pattern in their exonic versus intronic splicing site flanking regions. Finally, we demonstrated that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attributed such buffering effect to trans-regulatory splicing efficiency.
2021-10-07 | GSE154727 | GEO