Housekeeping gene

This article discusses the general topic of housekeeping genes. For a list of housekeeping genes that should be used as reference standards please see reference genes

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][3] Although some housekeeping genes (such as LDHA,[4] NONO,[4] PGK1,[4] PPIH,[4]) are expressed at relatively constant levels in most non-pathological situations, other housekeeping genes may vary depending on experimental conditions.[5]

In a study involving cardiac stem cells, ACTB and GAPDH were found to be the most consistent (although recent data now suggests otherwise), while β2M, HPRT1, and RPLP1 varied significantly between neonatal and adult cardiac cells.[6] The origin of the term "housekeeping gene" remains obscure. Literature from 1976 used the term to describe specifically tRNA and rRNA.[7] 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.

Commonly used housekeeping genes are LDHA,[4] NONO,[4] PGK1,[4] PPIH,[4]

The following represent genes that should probably not be used for reference purposes: GUSB,[4] RPLP0,[4] and TFRC.[4] GAPDH, HSP90, and β-actin. Although they were once considered as "housekeeping genes," recent data suggests that they are not as reliable as once thought.[8] Although the terms "housekeeping genes" and "reference genes" are used somewhat interchangeably, caution must be used in selecting genes for reference purposes.

Common housekeeping genes in human

The following is a partial list of "housekeeping genes." For a more complete list see list compiled by Eli Eisenberg and Erez Lavanon.[8] Entries that appear without a reference are from this updated list from 2013.

Gene Expression

Transcription Factors

Sterol Regulatory Element Binding Protein
Repressors

RNA Splicing

Small nuclear ribonucleoprotein-associated proteins B and B'

Translation Factors

tRNA Synthetases
RNA Binding Protein

Ribosomal Proteins

RPS19BP1

Mitochondrial Ribosomal Proteins

RNA Polymerase

Protein Processing

Heat Shock Proteins

Histone

Cell Cycle

There is significant overlap in function with regards to some of these proteins. In particular, the Rho-related genes are important in nuclear trafficking (i.e.: mitosis) as well as with mobility along the cytoskeleton in general. These genes of particular interest in cancer research.

Apoptosis

Oncogenes

DNA Repair/Replication

Metabolism

Carbohydrate Metabolism[9]

Citric Acid Cycle

Lipid Metabolism

Amino Acid Metabolism

NADH Dehydrogenase

Cytochrome C Oxidase

(Note that COX1, COX2, and COX3 are mitochondrially encoded)

ATPase

Lysosome

Proteasome

Ribonuclease

Thioreductase

Structural

Cytoskeletal

[1][4] [11]

Organelle Synthesis

A specialized form of cell signaling

Mitochondrion

Surface

Cell Adhesion

Channels and Transporters

Receptors

HLA/Immunoglobulin/Cell recognition

Kinases/Signalling

Growth Factors

Tissue Necrosis Factor

Casein Kinase

Miscellaneous

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

See also

References

  1. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 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.
  2. ↑ kon 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.
  3. ↑ Zhu, J.; et al. (2008). "On the nature of human housekeeping genes.". Trends in Genetics 24 (10): 481–484. doi:10.1016/j.tig.2008.08.004. PMID 18786740.
  4. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Quiagen. "RT2 Profiler PCR Array (96-Well Format and 384-Well Format". Qiagen catalog no. 330231 PAHS-00ZA.
  5. ↑ 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.
  6. ↑ 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.
  7. ↑ Rifkind RA.; Marks, PA; Bank, A; Terada, M; Maniatis, GM; Reuben, R; Fibach, E; et al. (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.
  8. 1 2 Eisenberg E, and Levanon EY (October 2013). "Human housekeeping genes, revisited". TRENDS in Genetics 29 (10): 569–574. doi:10.1016/j.tig.2013.05.010. PMID 23810203.
  9. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 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.
  10. ↑ 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.
  11. 1 2 3 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.
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