Discovering Regulators in Post-Transcriptional Control of the Biological Clock of $Neurospora~crassa$ Using Variable Topology Ensemble Methods on GPUs
| Autor: | H.-B. Schüttler, Cristian Caranica, James F. Griffith, Thiab R. Taha, Jonathan Arnold, Ahmad Al-Omari |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
RNA operon General Computer Science biology Operon General Engineering Crassa RNA ribosome biogenesis biology.organism_classification Topology Ribosome Neurospora crassa Clock network 03 medical and health sciences 030104 developmental biology circadian rhythms General Materials Science Variable topology ensemble methods lcsh:Electrical engineering. Electronics. Nuclear engineering Gene Post-transcriptional regulation lcsh:TK1-9971 |
| Zdroj: | IEEE Access, Vol 6, Pp 54582-54594 (2018) |
| ISSN: | 2169-3536 |
| Popis: | In the previous paper, we reconstructed the entire transcriptional network for all 2418 clock-associated genes in the model filamentous fungus, Neurospora crassa ( N. crassa ). Several authors have suggested that there is extensive post-transcriptional control in the genome-wide clock network (IEEE 3: 27, 2015). Here we have successfully reconstructed the entire clock network in N. crassa with a variable topology ensemble method (VTENS), assigning each clock-associated gene to the regulation of one or more of five transcription factors as well as to six RNA operons. The resulting network provides a unifying framework to explore the clock’s linkage to metabolism through post-transcriptional regulation, in which ~850 genes are predicted to fall under the regulatory control of an RNA operon. A unique feature of all of the RNA operons inferred is their functional connection to genes connected to the ribosome. We have been successful in distinguishing several hypotheses about regulatory topologies of the clock network through protein profiling of the regulators. |
| Databáze: | OpenAIRE |
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