Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

Table 1 Novel ncRNAs validated in this study

Name	Beginning	End	length(nt)	5'-start	Promoter	Adjacent genes	Strand	Conservation	Prediction
CRISPR locus
Cr 1-1	149430	147916	60	149408	Cons (53 nt)	PAB0095/PABt02	→←←	All^§	H/R
Cr 4-4	1760062	1761854	60	1760285	Cons (53 nt)	PAB1170/PaBt46	←→→		H/R
Cr 4-12			60	1760832
Conserved unique locus
sRk11	197248	197534	50	197484	TATA	PAB2227/PAB2402	←←←	All	H/R
sRk28	527697	527833	70/ 100	527798	-	PAB1992/PAB1991	←←←	All except Tsi	H/R
sRk33*	636804	636904	100	636804	Cons	PAB1916/PAB0465	←→→	All	H/R
sRk61	1348633	1348700	60/95	1348615	-	PAB1455/PAB0921	←→→	Pho	R
Conserved repetitive locus
sRk48	985849	986002	130	985805	Cons	PAB0686/PAB0686.1n	→→→	Pho, Pfu, Tko, Tsi	H/R
sRk49	1067535	1067886	150/220	1067923	TATA (60 nt)	PAB0740/PAB0741	→←→	Pho	R
sRk52	1104008	1104286	130/190	1104056	Cons	PABt30/PAB0766	←→→	Pho, Pfu, Tko, Tsi	H/R
Specific repetitive locus
sRkB	809887	810256	216/343	810048	Cons	PAB1794/PAB0571	←→→		H
sRkC	1612986	1613347	145/220	1613195	Cons	PAB1080.4n/PAB1080.5n	←←←		H

The positions indicate the beginning and the end of each predicted region. The RNA lengths are based on Northern blot analysis. The 5' ends of ncRNAs were determined by primer extension experiments (Additional file 3, Figure S2). Promotors were predicted based on search of entire (Cons: BRE/TATA) or partial (TATA) motif consensus located 15 to 30 nt (otherwise pointed out in parenthesis) upstream of the 5' transcription start. Conservation among the 7 annotated thermococcal genomes: P. abyssi, P. horikoshii (Pho), P. furiosus (Pfu), T. kodokarensis (Tko), T. sibiricus(Tsi), T. gammatolerans and T. onnurineus. Prediction tools are denoted for each region: bias composition (H) and comparative analysis (R). ^§ CRISPR 1 and 4 direct repeats are conserved. * sRk33 is annotated as SscA in P. furiosus [22].

ISSN: 1471-2164