Housekeeping gene
From Wikipedia, the free encyclopedia
In molecular biology, Housekeeping genes are typically constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal and patho-physiological conditions.[1][2] Although some housekeeping genes (such as GAPDH, HSP90, and β-actin) are expressed at relatively constant levels in most non-pathological situations, other housekeeping genes may vary depending on experimental conditions.[3]
In a study involving cardiac stem cells, ACTB and GAPDH were found to be the most consistent, while β2M, HPRT1, and RPLP1 varied significantly between neonatal and adult cardiac cells.[4] The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA.[5] Interpreting gene expression data can be problematic, with most human genes registering 5-10 copies per cell (possibly representing error). Housekeeping genes are expressed in at least 25 copies per cell and sometimes number in the thousands.
Common housekeeping genes in human
Gene Expression
Transcription Factors
Sterol Regulatory Element Binding Protein
- ATF4[1][6] Activating transcription factor 4
- BTF3[1][6]
- E2F4[1]
- ERH (gene)[1][6] Enhancer of rudimentary homolog of drosophila (which in turn is the first enzymatic step in pyrimidine synthesis. Regulated by MITF)
- HMGB1[1][6] High mobility group box binds DNA
- ILF2[1]
- IER2[1] formerly ETR101 Immediate Early Protein
- JUND[1][6]
- LTBP4[1]
- LMO1[1] Rhombotin 1
- MYC[1][6] also considered an oncogene when mutated regulates transcription of 15% of all genes
- PAX8[1]
- PHF1[1][6] Plant homology domain
- PTTG1IP[1]
- SREBF1[1] Sterol Regulatory Element Binding Protein Smith Magenis
- TBP[7] aka TATA-binding protein or GTF2D or TFIID
- TCEB2[1][6] Elongin
- TCOF1[1] interacts with UBF to translate rRNA
Repressors
- ANF91, HPF7, HTF10 [1] Kruppel Associated Box domain
- ID3 (gene)[1] inhibits DNA binding
- PUF60[1][6]
- NFKBIA[1][6] Suppresses NF-kappa
- RING1[1]
RNA Splicing
Small nuclear ribonucleoprotein-associated proteins B and B'
- ADAR[1]
- BAT1[6]
- FBL[1] Fibrillarin
- HNRPD[1][6]
- HNRPK[1][6]
- PTBP1[1]
- PABPN1[1]
- SFRS3[6]
- SFRS9[1]
- SFNRPA[1]
- SNRPB[1][6]
- SNRPD[6]
- SNRPD2[1][6]
- SNRPG[1]
Translation Factors
- EIF1[1][6] aka SUI1
- EIF3C[1] formerly EIF3S8
- EIF3D[1] formerly EIF3S4
- EIF3F[1] formerly EIF3S5
- EIF3I[1] formerly EIF3S2
- EIF3G[1] formerly EIF3S7
- EIF4A2[1]
- EIF4G2[1]
- TUFM[1] Tu translational elongation factor mitochondrial
tRNA Synthetases
RNA Binding Protein
Ribosomal Proteins
- RPL3[1]
- RPL5[1][6]
- RPL8[1]
- RPL9[6]
- RPL10[1][6]
- RPL11[1]
- RPL12[6]
- RPL13[1][6]
- RPL13A[1][6] Introns contain genes for small nucleolar RNAs U32, U33, U34, and U35
- RPL14[1][6]
- RPL15[1]
- RPL17[1]
- RPL18[1]
- RPL19[1]
- RPL25[6]
- RPL27[1]
- RPL29[1]
- RPL30[6]
- RPL32[1]
- RPL34[1]
- RPL35[1][6]
- RPL36[1]
- RPL37[1][6]
- RPL38[1]
- RPL40[6] transcribed with ubiquitin (see FAU (gene))
- RPLP1[1]
- RPLP2[1]
- RPS2[1]
- RPS5[6]
- RPS9[1]
- RPS10[1]
- RPS11[1]
- RPS12[1]
- RPS13[1][6]
- RPS14[1][6]
- RPS15[1]
- RPS16[1][6]
- RPS18[1]
- RPS19[1][6]
- RPS20[6]
- RPS23[6]
- RPS24[1]
- RPS25[1][6]
- RPS26[6]
- RPS27[6] transcribed with ubiquitin (see FAU (gene))
- RPS28[6]
- RPS30[1] transcribed with ubiquitin as the FAU (gene)
- RPN1[1][6] Ribophorin anchors the ribosome to rough endoplasmic reticulum
RNA Polymerase
Protein Processing
- Cyclophilin A[7] Serine-threonine phosphatase inhibitor involved in protein folding
- CANX[1][6] Folding of glycoproteins within endoplasmic reticulum
- CAPNS1[1][6] Calpain protease
- NACA[1][6] Nascent polypeptide associated complex alpha polypeptide
- PFDN1[1] Prefoldin 1
- PFDN5[1] Prefoldin 5
- SNX3[1] Sorting nexin
- SNX17[6]
- SNX27[6]
- SSR2[1] Protein translocation in ER
- SUMO2[1][6] Protein targeting
Heat Shock Proteins
Histone
- CDH4[1] Nucleosome remodeling
- HIST1H2BC[1]
- H2AFY[1] Histone 2 Subfamily
- H2AFZ[1][6] essential for embryogenesis
- H3F3A[1][6] H3 Histone Family
Cell Cycle
- ARHGAP1[1]
- ARHGDIA[1][6]
- CENPB[1] Centromere protein B
- CTBP1[1][6]
- cyclophilin
- CCND3[1]
- GAS1[1][6] Blocks entry into S phase
- PPP2CB[1] Negative regulator of growth and cell division
- PPP2R1A[6] Negative regulator of growth and cell division
- RAD9[1]
- KIAA0174[1][6] or IST1 homolog (locates to central dividing line of dividing cells)
Apoptosis
Oncogenes
DNA Repair/Replication
Metabolism
Carbohydrate Metabolism
- PRKCSH[1][6] Glucosidase 2, subunit beta (activated by PKC)
- B4GALT2[1]
- GUSB[7] Beta Glucuronidase Sly syndrome
- Chitinase[1]
- Phosphogluconate dehydrogenase[1]
- GSK3A[1]
- hexokinase rate limiting step? no reference
- H6PD[1][6]
- Glucose-6-phosphate isomerase[1]
- Phosphofructokinase 1[6]
- Aldolase A[6]
- Aldolase C[1]
- Triosephosphate isomerase[6]
- GAPDH[1][6][7]
- Phosphoglycerate kinase[1][6][7]
- Phosphoglycerate mutase[6]
- Enolase[6]
- PKM2[1][6] Pyruvate kinase, muscle
- Lactate dehydrogenase[1]
- LDHB[1] Lactate dehydrogenase
- TALDO1[1][6] Transaldolase in pentose shunt
- Transketolase[1]
- TSTA3[1] Mannose metabolism
Citric Acid Cycle
Lipid Metabolism
- GM2A[1] not highly expressed constitutively
- HADHA[1] Trifunctional protein subunit alpha
- HADHB[1][6] Trifunctional protein subunit beta
Amino Acid Metabolism
- COMT[1] Catechol-O-methyl transferase
- GGTLA1[1] Gamma glutamyl transferase-like 1
- PHGDH[1][6] Phosphoglycerate dehydrogenase (first and rate-limiting step of serine biosynthesis)
- ODC1[1]
- TPMT[1]
Nucleotide Synthesis
NADH Dehydrogenase
Cytochrome C Oxidase
(Note that COX1, COX2, and COX3 are mitochondrially encoded)
- COX4I1[1]
- COX5A[1]
- COX5B[1][6]
- COX6A1[1]
- COX6B1[1][6]
- COX7A2L[1]
- COX7C[1]
- COX8[1]
- CYC1[1]
- UQCRC1[1]
- UQCRH[1]
- UQCRQ[1][6] see Cytochrome C1
ATPase
Mitochondrial
Lysosomal
Lysosome
- CTSD[1][6] can degrade insulin in hepatocytes
- Cystatin B[1] May protect cell from leaking lysosomes
- LAMP1[1][6]
- Mannose 6-phosphate receptor[1][6]
- SGSH[1][6] Mutations can cause Sanfilippo syndrome
Proteosome
- PSMB1[1]
- PSMB2[1]
- PSMB4[1]
- PSMB6[6]
- PSMA7[1]
- PSMB7[1]
- PSMD8[1]
- PSMD11[1]
- PSME2[1]
- UBA1[1]
- Ubiquitin B[1]
- UBE2I[6]
- UBE2D2[1]
- UBE2M[1]
- USP11[1]
Ribonuclease
Oxidase/Reductase
Structural
Cytoskeletal
- Actinin alpha 4[7]
- ACTG1[1] gamma actin
- ADD1[1]
- ANXA6[1]
- ARPC4[1][6] Actin-related protein 2/3 complex
- Beta-actin[7]
- CAPZB[1][6]
- COL6A1[1]
- DNCL1[1] Cytoplasmic Dynein
- EZR[1][6] Ezrin (anchors actin to plasma membrane)
- KIFC3[1][6] kinesin
- Moesin[1]
- MYH9[1] Myosin chain 9
- RHOA[1][6] also implicated in regulation of cell cycle
- SEPT1[1] homologus to CDC10 in S. cerevesiae
- SEPT2[1]
- SLC9A3R2[1] Links SLC9A3 to cytoskeleton
- TAGLN[1]
- TAGLN2[6]
- TMSB10[1][6] Thymosin beta 10
- TUBB[1][6] Tubulin, beta polypeptide
- TUBB4[1]
- WDR1[1][6] actin dissassembly?
Organelle Synthesis
A specialized form of cell signaling
- BLOC1S1[1][6]
- AP2M1[1]
- ANXA2[1]
- ANXA6[1]
- ANXA7[6]
- AP1B1[1][6] Coated vessicles
- CLTA[1] Clathrin A (vessicles)
- CLTB[1][6] Clathrin B (vessicles)
- GP2 (gene)[1][6] enzymatic secretory granules (hugely upregulated in pancreas)
- KDELR1[1][6] Lys-Asp-Glu-Leu tag that targets to endoplasmic reticulum
Mitochondrion
Surface
Cell Adhesion
Channels and Transporters
- ABCG2[1] formerly BCRP1 xenobiotic transporter (not expressed in great amounts in most tissues)
- CALM1[1][6] Calmodulin grasps calcium ions
- CALM2[1] Calmodulin grasps calcium ions
- HPCAL1[1] also grasps calcium; upregulated in retina
- GRIK5[1]
- MFSD10 aka TETRAN or tetracycline transporter-like protein[1]
- TFRC[7] Transferrin receptor
- FOLR1[7] Folate receptor
- SLC25A11[1] mitochondrial oxoglutarate/malate carrier
Receptors
- ACVRL1[1] TGF Beta receptor family Rendu-Osler-Weber syndrome
- CD23A[1] FCER2 low affinity IgE receptor (lectin)
- GRM4[1] Metabotropic glutamate receptor
- JAG1[1] NOTCH2 Receptor associated with Alagille syndrome
- MC2R[1] Melanocortin receptor type 2 (similar to ACTH receptor)
- SSTR5[1] Somatostatin receptor tends to inhibit other hormones
HLA/Immunoglobulin/Cell recognition
- BAT1[1]
- BSG[1] Basigin Immunoglobulin Superfamily, extracelluar metalloproteinase
- B2M[7] Beta-2 microglobulin[1][6]
- HLA-C[1]
- HLA-G[1]
- MIF[1][6] macrophage migration inhibitory factor
- TAPBP[1]
Kinases/Signalling
- ADRBK1[1] can downregulate response to epinephrine
- AGPAT1[1][6] acyl 3 phosphoglycerol acyl transferase
- ARF1[1][6]
- ARF3[1]
- ARF4[1]
- ARF5[1][6]
- ARL2[1][6] RAS Superfamily
- CSF1[1] Colony stimulating factor not highly expressed constitutively at 5-12
- CSK C-src tyrosine kinase[1]
- DCT[1][6] dopachrome tautomerase
- EFNA3[1]
- FKBP1A[1][6]
- GDI1[1] GDP Dissociation inhibitor (Rab family)
- GNAS1[1] ubiquitously expressed, but differentially imprinted
- GNAI2[1][6]
- HAX1[1][6] associated with tyrosine kinases
- ILK[1] Integrin linked kinase
- MAPKAPK2[1]
- MAP2K2[1][6]
- MAP3K11[1]
- PITPNM[1] Phosphatidylinositol transfer protein
- RAC1[1][6] Ro GTPase involved with many signaling pathways
- RAP1B[1][6] GTPase involved with cell adhesion
- RAGA[1][6] Ras-related GTP Binding
- STK19[1]
- STK24[1] Serine/Threonine Kinase
- STK25[6]
- YWHAB[1][6] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide
- YWHAH[1][6] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, h polypeptide
- YWHAQ[1][6] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide
- YWHAZ[1][6] Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide
Growth Factors
- AIF1[1]
- HDGF[1] Hepatoma derived growth factor (translocates to nucleus)
- HGS[1]
- LTBP4[1]
- VEGFB[1]
- ZFP36L1[1]
Tissue Necrosis Factor
- CD40[1] formerly TNFRSF5
Casein Kinase
Miscellaneous
- ALAS1 Aminolevulinic Acid Synthase type 1 (type 2 is erythroid and associated with porphyria)
- ARHGEF2[1] Rho guanine nucleotide exchange factor
- ARMET[1][6] Mesencephalic astrocyte-derived neurotrophic factor
- AES[1][6] amino terminal enhancer of split
- BECN1[1] involved in autophagy and partners with PI3K
- BUD31[1] formerly Maternal G10 transcript
- Creatine kinase[1] CKB (ATP reservoir)
- Cytidine deaminase[1] questionable: not present in very high levels at all
- CPNE1[1]
- ENSA (gene)[1]
- FTH1[1] Heavy chain of Ferritin
- GDI2[1] rab/ras vessicular trafficking
- GUK1[1][6] Guanylate kinase transfers phosphate from ATP to GMP
- HPRT[1][7] Hypoxanthine-guanine phosphoribosyltransferase
- IFITM1[1] Induced by interferon, transmembrane protein
- JTB (gene)[1][6] Jumping translocation breakpoint
- MMPL2[1]
- NME2[1][6] (formerly NM23B) Nucleoside diphosphate kinase
- NONO[1]
- P4HB[1][6]
- PRDX1[1] peroxiredoxin (reduces peroxides)
- PTMA[1] Prothymosin
- RPA2[1] Binds DNA during replication to keep it straightened out
- SULT1A3[1] Sulfate conjugation (note: SULT1C is cited in earlier literature as being ubiquitous [6] but this may be an example of different tags being used to refer to a common area of 2 closely related genes. If the tag is too short, then it may not be specific enough to truly specify one member of a gene family from another)
- SYNGR2[1][6] Synaptogyrin (may participate in vessicle translocation)
- Tetratricopeptide, TTC1[1] small glutamine rich
tetratricopeptide
Open_reading_frame
Sperm/Testis
Although this page is devoted to genes that should be ubiquitously expressed, this section is for genes whose current name reflects their relative upregulation in testes
- SPAG7[1]
- SRM[1][6] Spermidine synthase
- TEGT[1][6] Bax-1 inhibitor
- DAZAP2[1][6] Deleted in azoospermia
- MEA1[1][6] Male enhanced antigen
See also
- Inducible gene
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 1.29 1.30 1.31 1.32 1.33 1.34 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45 1.46 1.47 1.48 1.49 1.50 1.51 1.52 1.53 1.54 1.55 1.56 1.57 1.58 1.59 1.60 1.61 1.62 1.63 1.64 1.65 1.66 1.67 1.68 1.69 1.70 1.71 1.72 1.73 1.74 1.75 1.76 1.77 1.78 1.79 1.80 1.81 1.82 1.83 1.84 1.85 1.86 1.87 1.88 1.89 1.90 1.91 1.92 1.93 1.94 1.95 1.96 1.97 1.98 1.99 1.100 1.101 1.102 1.103 1.104 1.105 1.106 1.107 1.108 1.109 1.110 1.111 1.112 1.113 1.114 1.115 1.116 1.117 1.118 1.119 1.120 1.121 1.122 1.123 1.124 1.125 1.126 1.127 1.128 1.129 1.130 1.131 1.132 1.133 1.134 1.135 1.136 1.137 1.138 1.139 1.140 1.141 1.142 1.143 1.144 1.145 1.146 1.147 1.148 1.149 1.150 1.151 1.152 1.153 1.154 1.155 1.156 1.157 1.158 1.159 1.160 1.161 1.162 1.163 1.164 1.165 1.166 1.167 1.168 1.169 1.170 1.171 1.172 1.173 1.174 1.175 1.176 1.177 1.178 1.179 1.180 1.181 1.182 1.183 1.184 1.185 1.186 1.187 1.188 1.189 1.190 1.191 1.192 1.193 1.194 1.195 1.196 1.197 1.198 1.199 1.200 1.201 1.202 1.203 1.204 1.205 1.206 1.207 1.208 1.209 1.210 1.211 1.212 1.213 1.214 1.215 1.216 1.217 1.218 1.219 1.220 1.221 1.222 1.223 1.224 1.225 1.226 1.227 1.228 1.229 1.230 1.231 1.232 1.233 1.234 1.235 1.236 1.237 1.238 1.239 1.240 1.241 1.242 1.243 1.244 1.245 1.246 1.247 1.248 1.249 1.250 1.251 1.252 1.253 1.254 1.255 1.256 1.257 1.258 1.259 1.260 1.261 1.262 1.263 1.264 1.265 1.266 1.267 1.268 1.269 1.270 1.271 1.272 1.273 1.274 1.275 1.276 1.277 1.278 1.279 1.280 1.281 1.282 1.283 1.284 1.285 1.286 1.287 1.288 1.289 1.290 1.291 1.292 1.293 1.294 1.295 1.296 1.297 1.298 1.299 1.300 1.301 1.302 1.303 1.304 1.305 1.306 1.307 1.308 1.309 1.310 1.311 1.312 1.313 1.314 1.315 1.316 1.317 1.318 1.319 1.320 1.321 1.322 1.323 1.324 1.325 1.326 1.327 1.328 1.329 1.330 1.331 1.332 1.333 1.334 1.335 Eisenberg E, and Levanon EY (July 2003). "Human housekeeping genes are compact". TRENDS in Genetics 19 (7): 362–365. doi:10.1016/S0168-9525(03)00140-9. PMID 12850439.
- ↑ Butte, AJ., et al.. (2001). "Further defining housekeeping, or "maintenance," genes focus on 'a compendium of gene expression in normal human tissues'.". Physiol.Genomics 7 (2): 95–96. PMID 11773595.
- ↑ Greer S, Honeywell R, Geletu M, Arulanandam R, Raptis L (Feb 19, 2010). "Housekeeping genes; expression levels may change with density of cultured cells.". J Immunol Methods 355 (1–2): 76–9. doi:10.1016/j.jim.2010.02.006. PMID 20171969.
- ↑ Tan SC, Carr CA, Yeoh KK, Schofield CJ, Davies KE, Clarke K. (Nov 2011). "Identification of valid housekeeping genes for quantitative RT-PCR analysis of cardiosphere-derived cells preconditioned under hypoxia or with prolyl-4-hydroxylase inhibitors.". Mol Biol Rep 39 (4): 4857–67. doi:10.1007/s11033-011-1281-5. PMC 3294216. PMID 22065248.
- ↑ Rifkind RA., et al..; Marks, PA; Bank, A; Terada, M; Maniatis, GM; Reuben, R; Fibach, E (Nov–Dec 1976). "Erythroid differentiation and the cell cycle: some implications from murine foetal and erythroleukemic cells". Ann Immunol (Paris) 127 (6): 887–93. PMID 1070288.
- ↑ 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 6.19 6.20 6.21 6.22 6.23 6.24 6.25 6.26 6.27 6.28 6.29 6.30 6.31 6.32 6.33 6.34 6.35 6.36 6.37 6.38 6.39 6.40 6.41 6.42 6.43 6.44 6.45 6.46 6.47 6.48 6.49 6.50 6.51 6.52 6.53 6.54 6.55 6.56 6.57 6.58 6.59 6.60 6.61 6.62 6.63 6.64 6.65 6.66 6.67 6.68 6.69 6.70 6.71 6.72 6.73 6.74 6.75 6.76 6.77 6.78 6.79 6.80 6.81 6.82 6.83 6.84 6.85 6.86 6.87 6.88 6.89 6.90 6.91 6.92 6.93 6.94 6.95 6.96 6.97 6.98 6.99 6.100 6.101 6.102 6.103 6.104 6.105 6.106 6.107 6.108 6.109 6.110 6.111 6.112 6.113 6.114 6.115 6.116 6.117 6.118 6.119 6.120 6.121 6.122 6.123 6.124 6.125 6.126 6.127 6.128 6.129 6.130 6.131 6.132 6.133 6.134 6.135 6.136 6.137 6.138 6.139 Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Zhang W, Zhang X, Zhou W, Haluska FG, Jen J, Sukumar S, Landes GM, Riggins GJ, Vogelstein B, Kinzler KW. (Dec 1999). "Analyses of Human Transcriptomes". Nat Genet 23 (4): 387–388. doi:10.1038/70487. PMID 10581018.
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 7.10 7.11 Caradec J, Sirab N, Keumeugni C, et al.. (2010). "'Desperate house genes': the dramatic example of hypoxia". British Journal of Cancer 102 (6): 1037–43. doi:10.1038/sj.bjc.6605573. PMC 2844028. PMID 20179706.
- ↑ Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, et al. (Dec 21, 2001). "A compendium of gene expression in normal human tissues". Physiol Genomics 7 (2): 97–104. doi:10.1152/physiolgenomics.00040.2001. PMID 11773596.
- http://www.sagenet.org/transciptome/index.html (dead link, dec 2012)
- http://www.tau.ac.il/~elieis/Housekeeping_genes.html
- http://www.tau.ac.il/~elieis/HKG/
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