To construct a regulatory map of the genome of the human pathogen, Mycobacterium 
tuberculosis, we applied two complementary high-resolution approaches: 
strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to 
monitor the genome-wide dynamics of RNA polymerase (RNAP) and the 
anti-terminator NusA. Although NusA does not bind directly to DNA, but rather to 
RNAP and/or to the nascent transcript, we demonstrate that NusA interacts with 
RNAP ubiquitously throughout the chromosome, and that its profile mirrors RNAP 
distribution in both the exponential and stationary phases of growth. Generally, 
promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease 
in signal strength reflecting transcriptional polarity. Differential binding of 
RNAP and NusA in the two growth conditions correlated with transcriptional 
activity as reflected by RNA abundance. Indeed, a significant association 
between expression levels and the presence of NusA throughout the gene body was 
detected, confirming the peculiar transcription-promoting role of NusA. 
Integration of the data sets pinpointed transcriptional units, mapped promoters 
and uncovered new anti-sense and non-coding transcripts. Highly expressed 
transcriptional units were situated mainly on the leading strand, despite the 
relatively unbiased distribution of genes throughout the genome, thus helping 
the replicative and transcriptional complexes to align.