Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

BMC Genomics

Table 2 The nine most abundant cis-antisense candidate sRNAs with predicted sigma 70 promoters

sRNA name	Size (nt)	Mean no. of Reads*^a	Putative target genes*^b		Northern blot band size^*c (nt)		Ref.*^d
			Name	Product	Total	LM
ECS003	116	357.9	ymfL & ymfM	e14 prophage; predicted protein	~70	~70	-
ECS008	75	53.4	yfaS_1	pseudogene; predicted protein	ND	ND	-
ECS0011	71	46.5	IS128	small RNA (unknown function)	~95	~95	[9]
					~100	~100
ECS0012	66	39.6	ybhJ	predicted hydratase	smear	~120	-
ECS0013	67	38.1	rumA	23S ribosomal RNA 5-methyluridine methyltransferase	ND	ND	-
ECS0015	54	25.7	nudC	NADH pyrophosphatase	ND	ND	-
ECS0017	92	22.3	ykgM &ykgO	predicted ribosomal protein	~275	ND	[11]
ECS0018	90	21.6	gltBDF operon	glutamate synthase & periplasmic protein	ND	ND	[9, 13]
ECS0021	57	17.6	ytfP &ytfN	conserved protein	ND	ND	-

Nine cis-antisense candidate sRNAs were extracted from classes A and B (Figure 1B) for northern blot analysis. *^a The average number of deep sequencing reads mapped to each candidate sRNA: total number of reads divided by the length of the candidate sRNA. *^b The names and products of the sense-strand genes (putative target genes) corresponding to each cis- antisense candidate sRNA. *^c Major signal sizes detected by northern blotting (Figure 3). Total, total RNA; LM, low-molecular-weight RNA. Hyphens indicate that no signal was detected in the northern blot analysis. *^d References to predicted sRNAs in previous studies located around each candidate sRNA. The details of the candidate sRNAs are given in Additional File 4.

ISSN: 1471-2164