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In previous work we reconstructed the entire transcriptional network for all 2,418 clock-associated genes in the model filamentous fungus, 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 5 transcription factors as well as to 6 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.