Ensemble Methods for Identifying RNA Operons and Regulons in the Clock Network of Neurospora Crassa

Abstract

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 <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">clock-controlled genes</i> 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 <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">clock-controlled genes</i> provide linkage between hubs in their joint regulation. There were 71 significant feedforward loops within this clock network, the majority of which involved genes <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">lhp-1</i> 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 <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">lhp-1</i> defining an RNA operon. There appears to be no partitioning of light-regulated genes and circadian genes between the 12 hubs. The regulators <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">lhp-1, has-1</i> , and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rrp-3</i> appear to target putative <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">clock-controlled genes</i> 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 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\chi ^{2} =2.133$ </tex-math></inline-formula> 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.