Species-specific alternative splicing leads to unique expression of sno-lncRNAs

BMC Genomics

Table 1 Summary of sno-lncRNAs identified from human, rhesus and mouse ESCs

Species	Cell line	Location	Expression level (RPKM)	snoRNA caps	Parent gene	Validated by NB	Notes
Human	ESC (H9)	chr15:25310171-25313030	142	SNORD116-6, SORD116-7	SNURF-SNRPN	Yes	sno-IncRNA1
		chr15:25324203-25325381	829	SNORD116-13, SNORD116-14	SNURF-SNRPN	Yes	sno-IncRNA2
		chr15:25330530-25331766	2319	SNORD116-18, SNORD116-19	SNURF-SNRPN	Yes	sno-IncRNA3
		chr15:25332807-25334043	1012	SNORD116-20, SNORD116-21	SNURF-SNRPN	Yes	sno-IncRNA4
		chr15:25344644-25346814	113	SNORD116-26, SNORD116-27	SNURF-SNRPN	Yes	sno-IncRNA5
		chr7:45143947-45144641	186	SNORA5A, SNORA5C	TBRG4	Yes	sno-Inc5AC
		chr17:16342822-16343420	106	SNORD49B, SNORD49A	C17orf76-AS1	Yes	Additional file 1
		chr11:93463680-93464265	18	SNORA25, SNORA32	TAF1D	Yes	Additional file 2
	ENCODE Cell Lines	chr1:173833312-173833583	29	SNORD81, SNORD47	GAS5	N/A	N/A
		chr9:136216948-136217382	14	SNORD36B, Snord36A	RPL7A	N/A	N/A
		chr11:93466393-93466763	8	SNORD5, SNORA18*	TAD1D	N/A	N/A
Rhesus	ESC	chr1:204218457-204219170	14	SNORD78, SNORD77	GAS5	N/A	N/A
		chr1:204219672-204220510	18	SNORD75, SNORD74	GAS5	N/A	N/A
		chr7:2838589-2840464	83	SNORD116, SNORD116	SNURF-SNRPN	N/A	human sno-IncRNA3 homologue
		chr7:2850511-2851734	34	SNORD116, SNORD116	SNURF-SNRPN	N/A	human sno-IncRNA4 homologue
		chr7:164873802-164874792	29	SNORD114, SNORD114	N/A	N/A	N/A
		chr10:15174906-15176653	13	SNORD12B, SNORD12C	ZFAS1	N/A	N/A
		chr19:55523975-55524331	12	SNORD33, SNORD34	RPL13A	N/A	RPL13A region sno-IncRNA homologue
Mouse	ESC (R1)	chr7:52381972-52382315	146	SNORD33, SNORD34	RPL13A	Yes	RPL13A region sno-IncRNA

19 sno-lncRNAs identified in this study were listed with their species source, cell line source, genomic locations, expression level (RPKM), snoRNA ends, parent genes, validation and other notes. It includes eight sno-lncRNAs in human ESCs, three in ENCODE human cell lines, seven in rhesus ESCs and one in mouse ESCs. Expression levels of sno-lncRNAs were evaluated using RPKM in relevant cell lines (the ENCODE GM12878 cell line was used). Due to the poor annotation, host genes and snoRNA ends in rhesus were predicted from human and/or mouse homologous sequences. *one sno-lncRNA that contains a box C/D snoRNA at one end and a box H/ACA snoRNA at the other end was highlighted with asterisk.

ISSN: 1471-2164