Transcriptomic Profiling of Escherichia coli Reveals Regulatory Roles of the 3' UTR-Derived sRNA UhpU Under Various Growth Conditions

1.To investigate the biological function and regulatory impact of the 3' UTR-derived small RNA (sRNA) UhpU, we performed comparative transcriptomic analysis of wild-type and ?uhpTU deletion strains during growth in M9CA medium supplemented with Glucose-6-phosphate as the sole carbon source. 2:To investigate the biological function and regulatory impact of the transcriptional repressor MprA, we performed transcriptomic analyses in Escherichia coli with short-term pulse expression of MprA during LB growth. Overall design: 1. To assess the endogenous role of UhpU, RNA was isolated from wild-type and ?uhpTU E. coli strains grown in M9CA +0.1% Glucose-6-phosphate medium to OD600 ~0.4. Stranded RNA-seq libraries were prepared after DNase I treatment to compare transcriptomic differences attributable to the absence of UhpU under standard conditions. 2.The E. coli ygaH'-mprA sequence was cloned and expressed in a ?mprA strain. Cultures were grown in LB medium to OD600 ~1.0. MprA expression was induced with 0.2% L-arabinose for 10 minutes. RNA was extracted and processed as above, with the empty vector serving as a negative control.