Table 1.

An Overview of the Transcription Cycle and Selected Examples of Regulatory Factors

Stage of Transcription	Intermediate1	Examples of Regulation	Reference(s)
Promoter recognition
(i) RNA polymerase (Eσ) binds to DNA	RDNS	6S RNA	[70]
(ii) Promoter binding	RPC	Alternative σ factors, CAP (class I sites)	[9, 19]
(iii) Nucleation	RPN
(iv) Melting of promoter DNA	RPO	CAP (class II sites)	[71]
Transcript Initiation and Clearance
(i) NTP/RNA binding at (i) site	RPO	Growth-rate control (ATP as effector); NTP-sensitive start site selection	[33, 72]
(ii) NTP binding at (i+1) site	RPO	E. coli codBA (sensitive to UTP-binding at the i+1 site for one of two alternate transcripts)	[33]
(iii) Bond formation, PPi release	ITC
(iv) Translocation – repeat cycle; OR Release abortive transcript; start again	ITC
(v) Release core promoter contacts (escape)	ITC / EC	CAP at malT, P22 Arc	[44, 73, 74]
Elongation		NusG, RfaH	[44, 75]
NTP binding at (i+1) site, bond formation, translocation (back-tracking)	EC	GreA, GreB; UTP-sensitive attenuation	[33, 76]
Termination		Rho, Riboswitches	[48, 77]
Pausing of RNAP, Transcript and core release	PTC	RapA; proposed to mediate core release, B. subtilis δ subunit and RNA displacement	[50–52]
Recycling
Binding of σ to core to regenerate holoenzyme	Eσ	Crl (for σS), anti-σ factors	[55, 78]

¹The abbreviations for the various intermediates are RD_NS (RNAP bound to DNA, non-specifically), RP_C, RP_N and RP_O (closed, nucleated, and open complex, respectively), ITC (initial transcribing complex), EC (elongation complex), PTC (post-termination complex), Eσ (holoenzyme).