in vivo remains to be demonstrated, high-density binding of Fis may occur in vivo through concerted action of both specific and non-specific binding. The in-tandem occurrence of specific sites might initiate a nucleation reaction similar to that of H-NS, and then non-specific binding would lead to the formation of localized high-density Fis arrays. The bridging between these localized regions can create large DNA loops. Fis is exclusively present in the growth phase and not in the stationary phase. Thus, any role in chromosomal condensation by Fis must be specific to growing cells. Nucleoid-associated RNAs (naRNAs) Early studies examining the effect of RNase A treatment on isolated nucleoids indicated that RNA participated in the stabilization of the nucleoid in the condensed state. Moreover, treatment with RNase A disrupted the DNA fibers into thinner fibers, as observed by an atomic force microscopy of the nucleoid using the “on-substrate lysis procedure”. These findings demonstrated the participation of RNA in the nucleoid structure, but the identity of the RNA molecule(s) remained unknown until recently. Most of the studies on HU focused on its DNA binding. However, HU also binds to dsRNA and RNA-DNA hybrids with a lower affinity similar to that with a linear dsDNA. Moreover, HU preferentially binds to RNA containing secondary structures and an RNA-DNA hybrid in which the RNA contains a nick or overhang. The binding affinities of HU with these RNA substrates are similar to those with which it binds to distorted DNA. An immunoprecipitation of HU-bound RNA coupled to reverse transcription and microarray (RIP-Chip) study as well as an analysis of RNA from purified intact nucleoids identified nucleoid-associated RNA molecules that interact with HU. Several of them are non-coding RNAs, and one such RNA named naRNA4 (nucleoid-associated RNA 4), is encoded in a repetitive extragenic palindrome (REP325). In a strain lacking REP325, the nucleoid is decondensed as it is in a strain lacking HU. naRNA4 most likely participate in DNA condensation by connecting DNA segments in the presence of HU. Recent studies provide insights into the molecular mechanism of how naRNA4 establishes DNA-DNA connections. The RNA targets regions of DNA containing cruciform structures and forms an RNA-DNA complex that is critical for establishing DNA-DNA connections. Surprisingly, although HU helps in the formation of the complex, it is not present in the final complex, indicating its potential role as a catalyst (chaperone). The nature of the RNA-DNA complex remains puzzling