| Autor: |
Ahmad M. Al-Omari, James Griffith, Ashley Scruse, Robert W. Robinson, Heinz-Bernd Schuttler, Jonathan Arnold |
| Jazyk: |
angličtina |
| Rok vydání: |
2022 |
| Předmět: |
|
| Zdroj: |
IEEE Access, Vol 10, Pp 32510-32524 (2022) |
| Druh dokumentu: |
article |
| ISSN: |
2169-3536 |
| DOI: |
10.1109/ACCESS.2022.3160481 |
| Popis: |
With both light entrainment data (L/D) and free running data in the dark (D/D), Variable Topology Ensemble Methods (VTENS) were used to reconstruct the entire genome-scale clock network involving 3380 genes and their products under the hypothesis that clock-controlled genes are both transcriptionally regulated and post-transcriptionally regulated through RNA operons. The clock network has 12 hubs with target genes surrounding twelve regulators, and 694 putative clock-controlled genes provide linkage between hubs in their joint regulation. There were 71 significant feedforward loops within this clock network, the majority of which involved genes lhp-1 and NCU06108 targeting genes connected with the ribosome and ribosome biogenesis. All 12 regulators target amino acid biosynthesis. The largest hub (768 genes) surrounded the post-transcriptional regulator lhp-1 defining an RNA operon. There appears to be no partitioning of light-regulated genes and circadian genes between the 12 hubs. The regulators lhp-1, has-1, and rrp-3 appear to target putative clock-controlled genes in ribosome biogenesis. The combined hypothesis of 6 RNA operons and 5 transcriptional regulons was successful in describing the dynamics of the clock network with 3380 genes and their products with a $\chi ^{2} =2.133$ per data point for 60,759 mRNA time points. With little known about allosteric regulation of metabolism, the clock network provided a major link between gene regulation and metabolism. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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