LCHN

KIAA1147 is located on the 7th chromosome in humans from bases 141652381-141702188 on the negative strand.{{Cite web|url=https://useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000257093;r=7:141656728-141702153|title=Gene: KIAA1147 (ENSG00000257093) - Summary - Homo sapiens - Ensembl genome browser 91|website=useast.ensembl.org|language=en-gb|access-date=2018-02-04}} Additional names for KIAA1147 include PRO25611,{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene/57189|title=KIAA1147 KIAA1147 [Homo sapiens (human)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2018-02-04}} AI841796 in the mouse{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene/243780|title=E330009J07Rik RIKEN cDNA E330009J07 gene [Mus musculus (house mouse)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2018-02-04}} and RGD1563986 in the rat.{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene/312270|title=RGD1563986 similar to RIKEN cDNA E330009J07 gene [Rattus norvegicus (Norway rat)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2018-02-04}} Only one mRNA transcript of KIAA1147 has been reported in NCBI, and is composed of 9 exons.

File:LCHN Diagram.png

File:LCHN and DENND1b.pngHuman LCHN is a cytoplasmic protein composed of 455 amino acids predicted to be 51.4 kD before modifications with isoelectric point of 5.06.{{Cite web|url=https://www.ebi.ac.uk/Tools/seqstats/saps/|title=SAPS < Sequence Statistics < EMBL-EBI|last=EMBL-EBI|website=www.ebi.ac.uk|language=en|access-date=2018-05-01}} The majority of its 455 amino acids make up the tripartite DENN domains which are commonly found in proteins that act as Rab-GEFs and regulate vesicular trafficking. LCHN has several predicted phosphorylation sites{{Cite web|url=http://www.cbs.dtu.dk/services/NetPhos/|title=NetPhos 3.1 Server|website=www.cbs.dtu.dk|language=en|access-date=2018-05-01}} and contains many motifs for kinase binding.{{Cite web|url=http://elm.eu.org|title=ELM - Search the ELM resource|website=elm.eu.org|language=en|access-date=2018-05-01}} The uDENN and cDENN domains of LCHN are predicted to be primarily coil, while the dDENN domain is predicted to be a combination of alpha helix and beta sheet.{{Cite web|url=https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html|title=NPS@ : SOPMA secondary structure prediction|last=UCBL|first=Institut de Biologie et Chimie des Proteines - UMR5086 - CNRS -|website=npsa-prabi.ibcp.fr|access-date=2018-05-01}}{{Cite web|url=https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html|title=NPS@ : GOR4 secondary structure prediction|last=UCBL|first=Institut de Biologie et Chimie des Proteines - UMR5086 - CNRS -|website=npsa-prabi.ibcp.fr|access-date=2018-05-01}}{{Cite web|url=http://www.biogem.org/tool/chou-fasman/index.php|title=CFSSP: Chou & Fasman Secondary Structure Prediction Server|last=Kumar|first=Prof. T. Ashok|website=www.biogem.org|access-date=2018-05-01}} The cDENN domain is the most highly conserved domain within DENN family proteins, and is also primarily coil in protein DENND1B,{{Cite journal|url=https://www.rcsb.org/structure/3TW8|title=GEF domain of DENND 1B in complex with Rab GTPase Rab35|last1=Wu|first1=X.D.|last2=Kummel|first2=D.|date=2011-11-16|website=www.rcsb.org|language=en|doi=10.2210/pdb3tw8/pdb|access-date=2018-05-01|last3=Reinisch|first3=K.M.|url-access=subscription}} which has been crystallized and confirmed to interact with the guanine nucleotide exchange domain of Rab-35. LCHN also contains a Stability of Polarity Axis (SPA) region. that may allow it to play a role in cell division.{{Cite web|url=https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=312210|title=NCBI CDD Conserved Protein Domain SPA|website=www.ncbi.nlm.nih.gov|language=en|access-date=2018-05-03}}

File:LCHN Subcellular Localization.png

The Human Protein Atlas reports high levels of KIAA1147 transcription in several brain regions including cerebral cortex, cerebellum, and retina, as well as non-brain regions including spleen, thymus, stomach, prostate, lung, and ascending colon.{{Cite web|url=https://www.proteinatlas.org/ENSG00000257093-KIAA1147/tissue|title=Tissue expression of KIAA1147 - Summary - The Human Protein Atlas|website=www.proteinatlas.org|access-date=2018-05-03}} Immunohistochemistry has shown LCHN to be localized to the cytoplasmic face of the Golgi apparatus in cell culture,{{Cite web|url=https://www.proteinatlas.org/ENSG00000257093-KIAA1147/cell|title=Cell atlas - KIAA1147 - The Human Protein Atlas|website=www.proteinatlas.org|access-date=2018-05-03}} and the brain in mouse fetal development.{{Cite web|url=https://gp3.mpg.de/results/kiaa1147|title=Genepaint - Home of High Resolution Gene Expression Data|website=gp3.mpg.de|access-date=2018-05-03}} In the adult mouse and human brain, LCHN is expressed relatively ubiquitously.{{Cite web|url=http://mouse.brain-map.org/gene/show/89126|title=Gene Detail :: Allen Brain Atlas: Mouse Brain|website=mouse.brain-map.org|access-date=2018-05-03}}{{Cite web|url=http://www.brainspan.org/lcm/search?exact_match=true&search_term=KIAA1147&search_type=gene&donors=14751,12690,12840,12566|title=Prenatal LMD Microarray :: BrainSpan: Atlas of the Developing Human Brain|website=www.brainspan.org|access-date=2018-05-03}} Expression of LCHN has been shown to increase in response to chronic alcoholism,{{Cite web|url=https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4879https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4879|title=GEO DataSet Browser|last=geo|website=www.ncbi.nlm.nih.gov|access-date=2018-05-03}} immature and mature dendritic response to hypoxia, and ischemic stroke.

There are binding sites for two main groups of transcription factors in the predicted promoter of KIAA1147. The first group consists of elements related to the cell cycle and neuronal development and includes AP-2, NRF1, BRAC, E2F, NEUR, and NRSF.{{Cite web|url=https://www.genomatix.de/online_help/help_eldorado/annotation_analysis_help.html|title=ElDorado: Annotation & Analysis|website=www.genomatix.de|access-date=2018-05-05}} The second consists of elements related to brain insult, including HIFF (hypoxia inducible factor), CREB (cAMP responsive factor linked to ER stress response), GREF (glucocorticoid responsible factor), HEAT (heat shock responsive factor), and HDBP (Huntington's disease regulatory binding protein). In patients with FTD-ALS, there has been reported abnormal upstream CpG methylation of KIAA1147

Yeast two-hybrid assays have shown LCHN to physically interact with SETBP1,{{cite journal | vauthors = Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M | title = A proteome-scale map of the human interactome network | journal = Cell | volume = 159 | issue = 5 | pages = 1212–1226 | date = November 2014 | pmid = 25416956 | pmc = 4266588 | doi = 10.1016/j.cell.2014.10.050 }} a protein that contains 3 nuclear localization signals.{{cite web|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=SETBP1|title=SETBP1 Gene - GeneCards {{!}} SETBP Protein {{!}} SETBP Antibody|last=Database|first=GeneCards Human Gene|website=www.genecards.org|access-date=2018-05-03}} Despite the lack of a predicted nuclear localization signal in its own sequence, this interaction suggests that LCHN may be able to enter and have functional importance in the nucleus.

In affinity chromatography studies, LCHN has been reported to have a physical association with TGOLN2,{{cite journal | vauthors = Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP | title = The BioPlex Network: A Systematic Exploration of the Human Interactome | journal = Cell | volume = 162 | issue = 2 | pages = 425–440 | date = July 2015 | pmid = 26186194 | pmc = 4617211 | doi = 10.1016/j.cell.2015.06.043 }}{{cite journal | vauthors = Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW | title = Architecture of the human interactome defines protein communities and disease networks | journal = Nature | volume = 545 | issue = 7655 | pages = 505–509 | date = May 2017 | pmid = 28514442 | pmc = 5531611 | doi = 10.1038/nature22366 | bibcode = 2017Natur.545..505H }} a surface protein of the Golgi apparatus.{{Cite web|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=TGOLN2|title=TGOLN2 Gene - GeneCards {{!}} TGON2 Protein {{!}} TGON2 Antibody|last=Database|first=GeneCards Human Gene|website=www.genecards.org|access-date=2018-05-03}} This likely explains immunohistochemical finding of strong LCHN localization near the Golgi apparatus despite being a predicted cytoplasmic protein.

Affinity chromatography studies have also reported a physical association between LCHN and kallikreins KLK5 and KLK11, serine proteases.{{cite journal | vauthors = Kalinska M, Meyer-Hoffert U, Kantyka T, Potempa J | title = Kallikreins - The melting pot of activity and function | journal = Biochimie | volume = 122 | pages = 270–82 | date = March 2016 | pmid = 26408415 | pmc = 4747678 | doi = 10.1016/j.biochi.2015.09.023 }} It is possible that cleavage by these proteases may be relevant to LCHN's function.

LCHN has been reported to be capable of a physical association with EFNB3, an ephrin receptor ligand with reported importance in neuronal development.{{Cite web|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=EFNB3|title=EFNB3 Gene - GeneCards {{!}} EFNB3 Protein {{!}} EFNB3 Antibody|last=Database|first=GeneCards Human Gene|website=www.genecards.org|access-date=2018-05-03}} This, coupled with the high expression of LCHN in the developing central nervous system, suggests that binding of LCHN to EFNB3 may modulate neuronal development.

File:LCHN brain development.png

LCHN expression has been reported to be unregulated following ischemic stroke, chronic alcoholism, and cell culture responses of immature and mature dendrites to prolonged hypoxia. Additionally, decreased expression as a result of CpG methylation has been implicated to be pathogenic in patients with FTD-ALS. Within the predicted promoter of KIAA1147, there are predicted binding sites for hypoxia response elements that would accompany ischemic stroke, heat shock proteins, factors related to the glucocorticoid mediated stress response, and cAMP responsive factors related to the ER stress response.{{Cite journal|last1=Xu|first1=Chunyan|last2=Bailly-Maitre|first2=Beatrice|last3=Reed|first3=John C.|date=2005-10-01|title=Endoplasmic reticulum stress: cell life and death decisions|journal=Journal of Clinical Investigation|volume=115|issue=10|pages=2656–2664|doi=10.1172/JCI26373|issn=0021-9738|pmc=1236697|pmid=16200199}} Due to the reported evidence of LCHN upregulation following ischemic stroke, which often results in neuronal damage or death,{{Cite journal|last1=Taoufik|first1=Era|last2=Probert|first2=Lesley|date=2008|title=Ischemic neuronal damage|journal=Current Pharmaceutical Design|volume=14|issue=33|pages=3565–3573|issn=1873-4286|pmid=19075733|doi=10.2174/138161208786848748}} as well presence of several binding sites for factors induced by rapid trauma to the brain, it is likely that KIAA1147 plays a role in the brain’s response to sudden stress and injury.

The presence of the SPA domain within LCHN suggests that it may play a role in cell division. LCHN has been shown to physically associate with EFNB3, a protein with reported importance in neuronal development. A second reported association with SETBP1 may open up the possibility for LCHN to play a role in cell cycle regulation from within the nucleus. The predicted KIAA1147 promoter contains binding sites for cell-division related factors and factors known to have specific expression during neuronal development. RNA in situ hybridization has shown KIAA1147 to be located at high levels in the developing brain. Together, these data suggest that LCHN plays a role in regulating cellular division during development of the brain.

LCHN has been shown to be upregulated following a number of insults to the brain including the response to chronic alcoholism, immature and mature dendritic response to hypoxia, and ischemic stroke. Recent studies have implicated abnormal CpG methylation of LCHN in FTD-ALS. No disease causing SNPs in LCHN have been reported with high frequency.{{Cite web|url=https://www.ncbi.nlm.nih.gov/snp|title=Home - SNP - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2018-05-05}}

File:Animalian LCHN Orthologs.png

File:Non-Animalian LCHN Orthologs.png

There are no reported paralogs of LCHN in humans. LCHN homologs exist in animals dating back to the earliest sponges, with a notable lack of reported expression in Drosophila and C. elegans. There are also a number of LCHN homologs in protists including choanoflagellates, amoeba, and algae, as well as other unicellular eukaryotes including fungi.

{{clear}}

{{Reflist}}

Category:Genes on human chromosome 7