Bioinformatic Analysis
Inspection of the UCSC Genome Browser conservation track within the
human NAGS gene (chr17:42,078,702-42,086,453 of the GRCh37/hg19
human genome assembly) revealed an approximately 200 bp-long conserved
region within first intron of the NAGS gene (chr17:
42,082,680-42,082,880); this region is contained in a cis -acting
conserved regulatory element (chr17:42,082,631-42,082,888) of the cCRE
track (Consortium, 2012) of the UCSC Genome Browser. Corresponding
genomic regions from 20 mammalian species (Table S1) were downloaded,
aligned using Clustal Omega (Sievers et al., 2011) and the alignment was
visualized with WebLogo 3 (Crooks, Hon, Chandonia, & Brenner, 2004).
Transcription factors that bind to the conserved element within first
intron of the human NAGS gene were identified by data mining the
ENCODE project database (Ljubica Caldovic (July 20, 2020)) (Caldovic,
2018). The hepatocyte nuclear factor 4α (HNF4α) binding site
(chr17:42,082,640-42,082,899 in the GRCh37/hg19 human genome assembly)
was identified from Transcription Factor ChIP-seq Clusters track of the
UCSC Genome Browser. The retinoic X receptor α (RXR α) and Sp1 binding
sites were identified based on their similarity with the respective
MA0115.1 and MA0079.3 position matrices in the JASPAR database of
transcription binding sites (Fornes et al., 2020).
Genomic regions from 24 mammals (Table S2) that correspond to the -3kb
enhancer (Heibel et al., 2012) of the human NAGS gene
(chr17:42,078,635-42,079,129 of the GRCh37/hg19 human genome assembly)
were downloaded, aligned using Clustal Omega (Sievers et al., 2011) and
the alignment was visualized with WebLogo 3 (Crooks et al., 2004).
Histone modifications of the -3 kb enhancer and transcription factors
that bind to it were identified by data mining the ENCODE project
database (Ljubica Caldovic (July 20, 2020)) (Caldovic, 2018). The
glucocorticoid receptor (GR) binding site (chr17:42,078,920-42,078,938
in the GRCh37/hg19 human genome assembly) was identified from the HMR
Conserved Transcription Factor Binding Sites track of the UCSC Genome
Browser. The HNF4a, RXRα, Sp1 and Yin Yang 1 (YY1) transcription factor
binding sites were identified based on their similarity with the
respective MA0114.1, MA1147.1, MA0079.1 and MA0095.2 position matrices
in the JASPAR database of transcription binding sites (Fornes et al.,
2020).