It is possible to find multiple RNA polymerase pausing sites along a gene sequence. Remarkably, it was clear from gene expression profiles that dynamical behavior of a TSSaRNA may be distinct from that of its cognate gene. In some cases, the cognate gene level does not change, but expression of the TSSaRNA has distinct dynamics, with up to 16 fold up-regulation or down-regulation to different degrees. We also observed instances when both TSSaRNA and cognate gene were differentially regulated, albeit with different patterns. Imposing stringent criteria, we identified at least 10 TSSaRNA differentially expressed relative to their cognate genes. Such differential expression patterns would not be expected if transcription of a TSSaRNA and the full-length transcript of its cognate gene were not regulated by environmental signals, nor could it arise as an experimental artifact of tiling array hybridization and processing. Using pausing sites that can vary their retention time along the growth curve, the RNA polymerase pausing model explains our experimental observation that TSSaRNA can have distinct dynamical behavior relative to their cognate gene. LY2109761 700874-71-1 Although counterintuitive, it is possible to generate dynamical profiles such as the ones where TSSaRNA levels remains constant and its cognate gene varies and vice versa, only exploring the two parameters of the model: elapsed time spent paused and time between successive transcripts initiation events. Therefore, our transcriptome analysis indicates that there is probably RNA polymerase pausing rhythm regulation in response to environmental perturbations. Future experimental work would reveal how this rhythm may be tuned and what are the implication of this regulation. In this study we analyzed the transcriptome of 11 archaea: Halobacterium salinarum NRC-1, Pyrococcus furiosus DSM 3638, Methanococcus maripaludis S2, Sulfolobus solfataricus P2, Nanoarchaeum equitans Kin4-M, Methanopyrus kandleri AV19, Sulfolobus acidocaldarius MW001, Haloferax volcanii DS2, Methanolobus psycrophilus R15, Methanosarcina mazei Go¨1 and Pyrococcus abyssi. Only S. acidocaldarius data did not present sufficient coverage to clearly show at least one TSSaRNAs signature. Therefore, our observations were made for 10 organisms. Archaeal transcriptomes for which dynamical information was available were highlighted in this work: Halobacterium salinarum NRC-1, Pyrococcus furiosus DSM 3638, Methanococcus maripaludis S2 and Sulfolobus solfataricus P2. Original accession numbers for these datasets are: GSE13150, GSE18630, GSE38821, GSE26782, GSE44979, SRP028191, SRX188664. Datasets not available in public databases were obtained directly from publications. A brief description for each dataset used is provided in the Table S3. The expression signal for putative TSSaRNAs locations is a distinct signature characterized by a sharp rise in signal that plateaus over a relatively small distance and then decays precipitously.