Supplemental Table 1. List of spacer sequences used in this study.

  

	Supplemental	
		Spacer sequences (5' to 3')
	Sp (St) Ctl sgRNA	AACTTTCAGTTTAGCGGTCT
	Sp sgRNA S1	TATGCAATATGTCTTGAATA
	Sp sgRNA S2	CAAGACATATTGCATAAGCT
	Sp sgRNA S3	ATTCGCGGTTTTCGACTTCC
	Sp sgRNA S4	GGGTTCAGTTAGTCACCTGC
	Sp sgRNA S5	TCCCTCTCAAGCCGCCAGCA
	Sp sgRNA S6	TCTGAGACGTGATGGTGGCG
	Sp sgRNA S7	ACCATTCCCGTCATTATTGT
	Sp sgRNA S8	TTGCTGAAAAACTCGGCGGC
	St sgRNA T1	GAGCACTCGTATAGTAGATG
	St sgRNA T2	TTAGAATACTAACAAACTCG
	St sgRNA T3	ATTCTAACATCTACTAGAAT
	St sgRNA T4	GTTTAAGGTCCCGTGACAAG
	St sgRNA T5	CGGTAGTCGCACCGGTGGTT
	St sgRNA T6	CTGAAGGCAGCGATAATCGC
	St sgRNA T7	CTGATTGAACAACTGGAAAG

Table 2 . List of primers used in chromosome conformation capture assays.

 2 

	Primer Name	Primer sequence
	P1	5' TGCTCGTAACGCACTTTCTG 3'
	P2	5' GCAGATACACTTGCTGATGCG 3'
	P3	5' GGACAAACTCAAGGTCATTCGC 3'
	P4	5' ACGTTAGATACCCAGCTTATGC 3'
	P5	5' CCGAAATGGTTGCCGATGTG 3'

Table 3 . List of primers used in qRT-PCR experiments.

 3 

	Target Name	Primer sequence	Primer	Amplicon size
			Efficiency	
	Sp Cas9	5' ATGGAGAGATTCGCAAACGC 3'	94.8%	94bp
		5' TTGCGCACTGTGGCAAAATC 3'		
	St Cas9	5' ACATCCGCAAGTACAGCAAG 3'	93.8%	118bp
		5' ACCACCTTGTTGTTGCTGTC 3'		
	norV	5' TGGCACAAATTCCCGATACG 3'	94.6%	143bp
		5' AATGAGCTGTTTGCCGTTGC 3'		
	norW	5' TGCACCTGTTTCCACAAACC 3'	100.2%	91bp
		5' AGCTTGTCGTATTGCCACTG 3'		
	gyrA	5' TGGAAGTTGACGCCAAAACC 3'	94.9%	124bp
		5' ATGCCTTCCACGCGTTTTTC 3'		
	rho	5' AAATCCGCCGTTTCAACCTC 3'	89.7%	137bp
		5' TTTGTTGCGGGCGTTTTCAG 3'		

Supplementary Figure 3. Loop modelling.

A. Statistical-mechanical model for LacI repression with two operators and DNA looping 1 . 
Shaded boxes indicate species available in the absence or presence of the distal operator. Data are mean ± 95% confidence intervals (n = 9). F loop is calculated as [(LacZ OD--bkgd) -(LacZ OD+ -bkgd)] / (LacZ OD--bkgd) (Supplementary Figures 3A-C), and is expressed as mean ± standard deviation (n = 9). 

Supplementary Figure 5. DNA looping via Sp_St_dCas9 fusion.

A. Schematic representation of the 1.2 kb looping reporter (see also Supplementary Figure 1).