Comparison between the Amount of Environmental Change and the Amount of Transcriptome Change

Abstract

Cells must coordinate adjustments in genome expression to accommodate changes in their environment. We hypothesized that the amount of transcriptome change is proportional to the amount of environmental change. To capture the effects of environmental changes on the transcriptome, we compared transcriptome diversities (defined as the Shannon entropy of frequency distribution) of silkworm fat-body tissues cultured with several concentrations of phenobarbital. Although there was no proportional relationship, we did identify a drug concentration “tipping point” between 0.25 and 1.0 mM. Cells cultured in media containing lower drug concentrations than the tipping point showed uniformly high transcriptome diversities, while those cultured at higher drug concentrations than the tipping point showed uniformly low transcriptome diversities. The plasticity of transcriptome diversity was corroborated by cultivations of fat bodies in MGM-450 insect medium without phenobarbital and in 0.25 mM phenobarbital-supplemented MGM-450 insect medium after previous cultivation (cultivation for 80 hours in MGM-450 insect medium without phenobarbital, followed by cultivation for 10 hours in 1.0 mM phenobarbital-supplemented MGM-450 insect medium). Interestingly, the transcriptome diversities of cells cultured in media containing 0.25 mM phenobarbital after previous cultivation (cultivation for 80 hours in MGM-450 insect medium without phenobarbital, followed by cultivation for 10 hours in 1.0 mM phenobarbital-supplemented MGM-450 insect medium) were different from cells cultured in media containing 0.25 mM phenobarbital after previous cultivation (cultivation for 80 hours in MGM-450 insect medium without phenobarbital). This hysteretic phenomenon of transcriptome diversities indicates multi-stability of the genome expression system. Cellular memories were recorded in genome expression networks as in DNA/histone modifications.

Transcriptome Dedifferentiation Observed in Animal Primary Cultures is Essential to Plant Reprogramming

“…This is thought to be re-differentiation to construct new plants and reprogramming can be explained as an integration of dedifferentiation and regeneration. Callus may be regarded as dedifferentiated cells which holding down the redifferentiation process; using callus and plant tissue culture, bi-/multi-stability of transcriptome [8,9] could be demonstrated in plant. If their re-differentiation process is caused by the determination of intercellular division of labor based on cell-tocell communication [10], it will be possible to examine them in a test that separates cultured cells.…”

Synergic Interaction between Permethrin and Bt toxins discovered using RNA-seq

“…RNA samples were readily obtained from cultured tissues in the present study thus avoiding such variable factors; in this way, biologically significant differentially expressed genes were realized. Drug concentration is also an important factor in comparative transcriptomics as has been reported 7,18,19 . Such methods, predicting NCR toxins using comparative transcriptomics, would be useful not only in pest control but also in research fields affected by biological drug resistance, e.g., antibiotics and cancer research.…”

“…Total RNA was extracted using TRIzol LS (Invitrogen) and the RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) following the manufacturers' instructions as previously described 7 . Silkworm fat bodies (30 mg) soaked in 300 µL TRIzol LS were homogenized.…”

“…Silkworm fat bodies (30 mg) soaked in 300 µL TRIzol LS were homogenized. We isolated total RNA from the homoginates as previously described 7 . The integrity of rRNA in each sample was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).…”

Calculating Kolmogorov Complexity from the Transcriptome Data

“…Transcriptome diversity also used for measurement of cellular dedifferentiation [6]. Our Previous study compared transcriptome diversity between cells cultured in vitro in media supplemented with several concentrations of phenobarbital, to investigate how the amount of environmental change (in terms of drug concentration) affects the amount of transcriptome change and multi-stability of the genome expression system was indicated by an observation of hysteretic phenomenon of transcriptome diversities [7].…”