Transcriptome profiling of the feeding-to-fasting transition in chicken liver

Table 2 PPRE prediction in Gallus gallus HMGCS2, CPT1A and ACOX1 genomic DNA sequences

Genes	Species	Ensembl ID	PPRE Pattern	Location	Strand	Methods
HMGCS2	RNO	Rodriguez *et al* . 1994[79]	GGGCCAaAGGTCT	Promoter region
	GGA	ENSGALG00000002960	GGGCCAaAGGTCC	-530	+	STAN/PATSER
	HSA	ENSG00000134240	GGGTCAaAGGGCT	-118	+	STAN
	MUS	ENSMUSG00000027875	GGGCCAaAGGGAT	-104	RC	STAN
CPT1A	HSA/MUS/RNO	Napal *et al* ., 2005[80]	AGGGGAaAGGTCA	Intronic region between exon 1 and exon 2
	GGA	ENSGALG00000007077	AGGGAAaAGGGCA	4964	+	STAN
	HSA	ENSG00000110090	AGGGGAaAGGTCA	2426	+	STAN
	MUS	ENSMUSG00000024900	AGGGGAaAGGTTA	2180	RC	STAN
ACOX1	MUS	Tugwood *et al* ., 1992[81]	AGGACAaAGGTCA	Promoter region
	GGA	ENSGALG00000002159	-	-	-
	HSA	ENSG00000161533	-	-	-
	MUS	ENSMUSG00000020777	-	-	-
	RNO	Krey *et al* ., 1995[82]	AGGTAGaAGGTCA	Promoter region
	GGA	ENSGALG00000002159	AGGAAGaAAGTCA	-3931	+	STAN/PATSER
	HSA	ENSG00000161533	-	-	-	STAN
	MUS	ENSMUSG00000020777	AGGTAAaAGGTCA	52	+	STAN

PPRE patterns used for the research is indicated in bold with the reference associated. GGA: Gallus gallus; HSA: Homo sapiens; MUS: Mus musculus. Nucleic acids in red indicate conserved nucleic acids with the PPREs used for the research. Location: genomic location refers to the start of the Ensembl first exon (+1). Strand: "RC" indicates that the sequence is reverse complemented compared to the genomic sequence displayed at that location, otherwise a "+" is indicated. STAN or PASTER indicates that the PPRE has been identified either by STAN or PATSER softwares respectively (see Methods). For the ACOX1 gene, despite previous results indicating PPRE in the Mus musculus promoting DNA sequence [81], we cannot found any PPRE with the STAN procedure in any species. We used another PPRE pattern [82] identified in the Rattus norvegicus DNA sequence. This pattern allowed us to identify potential PPRE in Gallus gallus and Mus musculus sequences. The absence of result in the Homo sapiens sequence was consistent with the literature [78].

ISSN: 1471-2164