Cholesin is a protein which in humans is encoded by the gene CHLSN. It functions as a hormone that regulates the synthesis of cholesterol, and the way it does it is distinctive in that it can be involved in either increasing or decreasing synthesis, rather than a simple one-way effect. This function appears to be occur through binding to its receptor GPR146.
It is most highly produced in the upper digestive system and respiratory system, in addition to the (hormone producing) endocrine system. Additionally, this gene is predicted to be a microRNA (miRNA) protein coding host gene, meaning that it may contain miRNA genes in its introns and/or exons.
Gene
Location CHLSN is located on the short arm of chromosome 7 (7p22.3), and spans 160,361 bps on the minus (-) strand and contains a total of 13 exons.
Gene Neighborhood Genes within the neighborhood of CHLSN are the following: LOC105375120, GPR146, LOC114004405, LOC107986755, ZFAND2A, LOC102723758, LOC106799841, COX19, ADAP1, CYP2W1, MIR339, GPER1, and LOC101927021.
Other animals Cholesin is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi.
mRNA
Alternative Splicing CHLSN has a total of 7 experimentally curated mRNA transcripts. The longest and most complete of these transcripts (transcript 4) being 2138bp, producing a 194 amino acid-long (aa) protein, and consisting of 5 exons. Of these transcripts, four of them encode for the same 194aa protein (isoform a), only differing in their 5' and 3' untranslated regions (UTRs). The three other transcripts encode isoform b, c, and d, respectively. The table below is representative of these transcripts.
CHLSN Experimentally Determined
NCBI Reference Sequences (RefSeq) mRNA Transcripts Name NCBI Accession # Transcript Length # of Exons Protein Length IsoformTranscript Variant 1NM_032350.51311bp5194aaaTranscript Variant 2NM_001134395.11301bp5194aaaTranscript Variant 3NM_001134396.11282bp5194aaaTranscript Variant 4NM_001318252.22138bp5194aaaTranscript Variant 7NM_001350968.11081bp6193aabTranscript Variant 8NM_001350969.11500bp5180aacTranscript Variant 9NM_001350970.11448bp360aad Alternatively, when the primary genomic assembly, GRCh38.p13, is used for annotation (NCBI: NC_000007.14), there are 10 computationally predicted mRNA transcripts. The most complete and supported of these transcripts (transcript variant X6) is 1896bp, producing a 225aa-long protein. In total, there are 6 different isoforms predicted for CHLSN. Of these transcripts, 5 of them encode for the same isoform (X3). The remaining transcripts encode isoforms X2, X4, X5, X6, and X7 as represented below. CHLSN Computationally Determined
NCBI Reference Sequences (RefSeq) mRNA Transcripts Name NCBI Accession # Transcript Length Protein Length IsoformTranscript Variant X2XM_017012719.11447bp375aaX2Transcript Variant X3XM_011515582.31192bp225aaX3Transcript Variant X4XM_024446977.11057bp193aaX4Transcript Variant X5XM_011515581.31240bp225aaX3Transcript Variant X6XM_011515584.21896bp225aaX3Transcript Variant X7XM_017012720.21199bp225aaX3Transcript Variant X8XM_011515583.21215bp225aaX3Transcript Variant X9XM_017012721.22121bp211aaX5Transcript Variant X10XM_024446978.12207bp180aaX6Transcript Variant X11XM_024446979.1933bp93aaX7
5' and 3' UTR Based on the experimentally determined CHLSN mRNA transcript variant 4, the 5' UTR of CHLSN is 934 nucleotides (nt) long, while the 3' UTR is 619nt. The coding sequence (CDS) of this transcript spans nt 935..1519 for a total length of 584nt and is encoded in reading frame 2.
Protein
General Properties The CHLSN Isoform a's 194aa protein sequence from NCBI is as follows: >NP_001127867.1 cholesin isoform a [Homo sapiens] MAKQKRKVPEVTEKKNKKLKKASAEGPLLGPEAAPSGEGAGSKGEAVLRPGLDAEPELSPEEQRVLERKL 70 KKERKKEERQRLREAGLVAQHPPARRSGAELALDYLCRWAQKHKNWRFQKTRQTWLLLHMYDSDKVPDEH 140 FSTLLAYLEGLQGRARELTVQKAEALMRELDEEGSDPPLPGRAQRIRQVLQLLS 194 The underlined region within the sequence is indicative of a domain known as DUF2373 ("domain of unknown function 2373"), found in isoforms a, b, and c.
Cholesin has a predicted molecular weight (Mw) of 22 kDa, making cholesin smaller than the average protein (52 kDa). The isoelectric point (theoretical pI) for this isoform is 9.7, meaning that cholesin is slightly basic. As for charge runs and patterns within isoform a, there is a significant mixed charge (*) run (-++0++-+++--+) from aa67 to aa79 and an acidic (-) run from aa171 – aa173. It is likely that this mixed charge run encodes the protein-protein interaction (PPI) site of cholesin.
Characterization of the protein has shown binding to GPR146. Based on a proposed role in regulation of serum cholesterol levels in response to dietary cholesterol intake, the protein has been called cholesin.
Domains and Motifs DUF2373 is a domain of unknown function found in the cholesin. This is a highly conserved c-terminal region found from fungi to humans. As for motifs, a bipartite nuclear localization signal (NLS) was predicted from aa6 to aa21, meaning that cholesin is likely localized in the nucleus. Interestingly, a nuclear export signal (NES) is also found within cholesin at the following amino acids: 150, and 153 - 155, suggesting that cholesin has function both inside and outside the nucleus.
Structure
Secondary Structure The majority of cholesin (isoform a) secondary structure is made up of alpha helices, with the remainder being small portions of random coils, beta turns, or extended strands.
Tertiary Structure The tertiary structure of cholesin consists primarily of alpha helices as determined I-TASSER.
Quaternary Structure The interaction network (quaternary structure) involving the cholesin has significantly more (p < 1.0e-16) interactions than a randomly selected set of proteins.
+Functional Enrichments within the CHLSN NetworkBiological ProcessesrRNA processingmaturation of 5.8S, LSU, and SSU rRNAMolecular Functionscatalytic activity, acting on RNAATP-dependent RNA helicase activityCellular ComponentsnucleoluspreribosomesReactome Pathwaysmajor pathway of rRNA processing in the nucleolus and cytosolrRNA modification in the nucleus and cytosolProtein Domains and Motifshelicase conserved C-terminal domainDEAD/DEAH box helicase The closest predicted functional partners of cholesin are the following proteins: DDX24, DDX52, PES1, EBNA1BP2, RSLD1, NOP14, FTSJ3, KRR1, LYAR, and PWP1. These proteins are predicted to co-express rather than bind directly to cholesin and each other.
Regulation
Gene Regulation
Promoter CHLSN has 6 predicted promoter regions. The promoter with the greatest number of transcripts and CAGE tags overall is promoter set 6 (GXP_6755694) on ElDorado by Genomatix. This promoter region is on the minus (-) strand and has a start position of 1,137,965 and an end position of 1,139,325, making this promoter 1,361bp long. It has 16 coding transcripts and the transcript with the greatest identity to C7orf50 transcript 4 is transcript GXT_27788039 with 98746 CAGE tags. Promoter ID Start Position End Position Length # of Coding Transcripts Greatest # of CAGE Tags in TranscriptsGXP_9000582101306310131631101bp0N/AGXP_6755691102823910300701832bp4169233GXP_6053282105520610563061101bp1449GXP_3207505112728811283881101bp1545GXP_9000584113054111316411101bp0N/AGXP_6755694113796511393251361bp16100,070 The CpG island associated with this promoter has 75 CpGs (22% of island), and is 676bp long. The C count plus G count is 471, the percentage C or G is 70% within this island, and the ratio of observed to expected CpG is 0.91.
Transcription Factor Binding Sites As determined by MatInspector at Genomatix, the following transcription factor (TFs) families are most highly predicted to bind to CHLSN in the promoter region. Transcription FactorDetailed Family InformationNR2FNuclear receptor subfamily 2 factorsPEROPeroxisome proliferator-activated receptorHOMFHomeodomain transcription factorsPRDMPR (PRDI-BF1-RIZ1 homologous) domain transcription factorVTBPVertebrate TATA binding protein factorHZIPHomeodomain-leucine zipper transcription factorsZTREZinc transcriptional regulatory elementXBBFX-box binding factorsSP1FGC-Box factors SP1/GCCAATCCAAT binding factorsZF57KRAB domain zinc finger protein 57CTCFCTCF and BORIS gene family, transcriptional regulators with highly conserved zinc finger domainsMYODMyoblast determining factorsKLFSKrueppel like transcription factors
Expression Pattern CHLSN shows ubiquitous expression in the kidneys, brain, fat, prostate, spleen and 22 other tissues and low tissue and immune cell specificity . This expression is very high, 4 times above the average gene; therefore, there is a higher abundance of CHLSN mRNA than the average gene within a cell. There does not appear to be a definitive cell type in which this gene is not expressed.
Transcription Regulation
Splice Enhancers The mRNA of CHLSN is predicted to have exonic splicing enhancers, in which SR proteins can bind, at bp positions 45 (SRSF1 (IgM-BRCA1)), 246 (SRSF6), 703 (SRSF5), 1301 (SRSF1), and 1308 (SRSF2)
miRNA Targeting There are many poorly conserved miRNA binding sites predicted within the 3'UTR of CHLSN mRNA. The notable miRNA families that are predicted to bind to CHLSN mRNA and regulate/repress transcription are the following: miR-138-5p, miR-18-5p, miR-129-3p, miR-124-3p.1, miR-10-5p, and miR-338-3p.
Protein Regulation
Subcellular Localization Cholesin is predicted to localize intercellularly in both the nucleus and cytoplasm, but primarily within the nucleoplasm and nucleoli.
Post-Translational Modification Cholesin is predicted to be mucin-type GalNAc o-glycosylated at the following amino acid sites: 12, 23, 36, 42, 59, and 97. Additionally, this protein is predicted to be SUMOylated at aa71 with the SUMO protein binding from aa189 through aa193. Cholesin is also predicted to be kinase-specific phosphorylated at the following amino acids: 12, 23, 36, 42, 59, 97, 124, 133, 159, and 175. Interestingly, many of these sites overlap with the o-glycosylation sites. Of these phosphorylation sites, the majority are serines (53%) with the remainder being either tyrosines or threonines. The most associated kinases with these sites are the following kinase groups: AGC, CAMK, TKL, and STE. Finally, this protein is predicted to have 8 glycations of the ε amino groups of lysines at the following sites: aa3, 5, 14, 15, 17, 21, 76, and 120.
Homology
Paralogs No paralogs of cholesin have been detected in the human genome; however, there is slight evidence (58% similarity) of a paralogous DUF2373 domain in the protein of KIDINS220.
Orthologs Below is a table of a variety of orthologs of the human CHLSN. The table includes closely, moderately, and distantly related orthologs. CHLSN is highly evolutionary conserved from mammals to fungi. When these ortholog sequences are compared, the most conserved portions are those of DUF2373. CHLSN has evolved moderately and evenly over time with a divergence rate greater than Hemoglobin but less than Cytochrome C.