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Journal articles on the topic 'Housekeeping expression'

Author: Grafiati

Published: 4 June 2021

Last updated: 14 February 2022

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1

Barber, Robert D., Dan W. Harmer, Robert A. Coleman, and Brian J. Clark. "GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues." Physiological Genomics 21, no. 3 (2005): 389–95. http://dx.doi.org/10.1152/physiolgenomics.00025.2005.

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Quantitative gene expression data are often normalized to the expression levels of control or so-called “housekeeping” genes. An inherent assumption in the use of housekeeping genes is that expression of the genes remains constant in the cells or tissues under investigation. Although exceptions to this assumption are well documented, housekeeping genes are of value in fully characterized systems. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is one of the most commonly used housekeeping genes used in comparisons of gene expression data. To investigate the value of GAPDH as a housekeeping gene in human tissues, the expression of GAPDH mRNA was measured in a panel of 72 different pathologically normal human tissue types. Measurements were obtained from 371,088 multiplexed, quantitative real-time RT-PCRs with specific target genes. Significant differences in the expression levels of GAPDH mRNA were observed between tissue types and between donors of the same tissue. A 15-fold difference in GAPDH mRNA copy numbers was observed between the highest and lowest expressing tissue types, skeletal muscle and breast, respectively. No specific effect of either age or gender was observed on GAPDH mRNA expression. These data provide an extensive analysis of GAPDH mRNA expression in human tissues and confirm previous reports of the marked variability of GAPDH expression between tissue types. These data establish comparative levels of expression and can be used to add value to gene expression data in which GAPDH is used as the internal control.

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2

Hanafy, Sherif, and Fakhreddin Jamali. "Adjuvant arthritis influences expression of housekeeping genes." Inflammation Research 60, no. 6 (2011): 521–23. http://dx.doi.org/10.1007/s00011-011-0327-4.

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3

Mondello, Chiara, and Peter N. Goodfellow. "Methylation and expression of a housekeeping gene." Trends in Genetics 1 (January 1985): 124–25. http://dx.doi.org/10.1016/0168-9525(85)90047-2.

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4

Chen, Ren, Mayumi Gyokusen, Yoshihisa Nakazawa, and Koichiro Gyokusen. "Selection of Housekeeping Genes for Transgene Expression Analysis in Eucommia ulmoides Oliver Using Real-Time RT-PCR." Journal of Botany 2010 (March 17, 2010): 1–7. http://dx.doi.org/10.1155/2010/230961.

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In order to select appropriate housekeeping genes for accurate calibration of experimental variations in real-time (RT-) PCR results in transgene expression analysis, particularly with respect to the influence of transgene on stability of endogenous housekeeping gene expression in transgenic plants, we outline a reliable strategy to identify the optimal housekeeping genes from a set of candidates by combining statistical analyses of their (RT-) PCR amplification efficiency, gene expression stability, and transgene influences. We used the strategy to select two genes, ACTα and EF1α, from 10 candidate housekeeping genes, as the optimal housekeeping genes to evaluate transgenic Eucommia ulmoides Oliver root lines overexpressing IPPI or FPPS1 genes, which are involved in isoprenoid biosynthesis.

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5

Rekawiecki, Robert, Magdalena Kowalik, and Jan Kotwica. "Validation of housekeeping genes for studying differential gene expression in the bovine myometrium." Acta Veterinaria Hungarica 61, no. 4 (2013): 505–16. http://dx.doi.org/10.1556/avet.2013.037.

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The aim of this study was to determine the steady-state expression of 13 selected housekeeping genes in the myometrium of cyclic and pregnant cows. Cells taken from bovine myometrium on days 1–5, 6–10, 11–16 and 17–20 of the oestrous cycle and in weeks 3–5, 6–8 and 9–12 of pregnancy were used. Reverse transcribed RNA was amplified in real-time PCR using designed primers. Reaction efficiency was determined with the Linreg programme. The geNorm and NormFinder programmes were used to select the best housekeeping genes. They calculate the expression stability factor for each used housekeeping gene with the smallest value for most stably expressed genes. According to geNorm, the most stable housekeeping genes in the myometrium were C2orf29, TPB and TUBB2B, while the least stably expressed genes were 18S RNA, HPRT1 and GAPDH. NormFinder identified the best genes in the myometrium as C2orf29, MRPL12 and TBP, while the worst genes were 18S RNA, B2M and SF3A1. Differences in stability factors between the two programmes may also indicate that the physiological status of the female, e.g. pregnancy, affects the stability of expression of housekeeping genes. The different expression stability of housekeeping genes did not affect progesterone receptor expression but it could be important if small differences in gene expression were measured between studies.

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6

Cohen-Tannoudji, Michel, Sandrine Vandormael-Pournin, Jean-Michel Drezen, Pascale Mercier, Charles Babinet, and Dominique Morello. "lacZ sequences prevent regulated expression of housekeeping genes." Mechanisms of Development 90, no. 1 (2000): 29–39. http://dx.doi.org/10.1016/s0925-4773(99)00226-9.

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7

He, Bing, Hui Chen, Pibiao Shi, et al. "Systematic Identification and Validation of Housekeeping and Tissue-Specific Genes in Allotetraploid Chenopodium quinoa." Horticulturae 7, no. 8 (2021): 235. http://dx.doi.org/10.3390/horticulturae7080235.

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Quinoa is a gluten-free food crop that contains all the essential amino acids and vitamins. The selection of proper housekeeping and tissue-specific genes is the crucial prerequisite for gene expression analysis using the common approach, real-time quantitative PCR (RT-qPCR). In this study, we identified 40 novel candidate housekeeping genes by the minimum transcript per million (TPM), coefficient of variation (CV) and maximum fold change (MFC) methods and 19 candidate tissue-specific genes by the co-expression network method based on an RNA-seq dataset that included 53 stem, leaf, flower and seed samples, as well as additional shoot and root samples under different stresses. The expression stability of 12 housekeeping and tissue-specific genes, as well as that of another two traditionally used housekeeping genes, was further evaluated using qPCR and ranked using NormFinder, BestKeeper and the comparative delta-Ct method. The results demonstrated that MIF, RGGA, VATE and UBA2B were ranked as the top four most stable candidate housekeeping genes. qPCR analysis also revealed three leaf-specific genes and five root-specific genes, but no stem-specific gene was identified. Gene Ontology (GO) enrichment analysis identified that housekeeping genes were mainly enriched in the small molecule metabolic process, organonitrogen compound metabolic process, NAD binding and ligase activity. In addition, tissue-specific genes are closely associated with the major functions of a specific tissue. Specifically, GO terms “photosynthesis” and “thylakoid” were most significantly overrepresented in candidate leaf-specific genes. The novel housekeeping and tissue-specific genes in our study will enable better normalization and quantification of transcript levels in quinoa.

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8

Meller, M., S. Vadachkoria, D. A. Luthy, and M. A. Williams. "Evaluation of housekeeping genes in placental comparative expression studies." Placenta 26, no. 8-9 (2005): 601–7. http://dx.doi.org/10.1016/j.placenta.2004.09.009.

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9

Chambers, R. C. "Gene expression profiling: good housekeeping and a clean message." Thorax 57, no. 9 (2002): 754–56. http://dx.doi.org/10.1136/thorax.57.9.754.

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10

Roslim, Dewi Indriyani, Liza Aulia Yusfi, Desriani Ritawati Hutagalung, et al. "Isolation of Housekeeping Genes on Durik-durik (Syzygium sp)." Biosaintifika: Journal of Biology & Biology Education 10, no. 2 (2018): 237–44. http://dx.doi.org/10.15294/biosaintifika.v10i2.14234.

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Housekeeping gene is a gene expressed with a fixed level and in abundant amounts under various conditions. After validation, the housekeeping gene can be used as an internal control to normalize gene expression data. This study reports the isolation of several housekeeping genes in Durik-durik plant (Syzygium sp). This plant material in form of fresh leaves from Durik-durik plants are taken from Kajuik Lake, Riau Province. The next stage is total DNA isolation, polymerase chain reaction, electrophoresis, sequencing and data analysis using bioinformatic tools. The isolated housekeeping genes included 18S rRNA, actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Beta-tubulin and Ubiquitin with sizes of 400 bp, 679 bp, 1134 bp, 836 bp, 1167 bp and 2155 bp, respectively. In addition to 18S rRNA, the five housekeeping genes are the first reported from the genus Syzygium and referable to isolate housekeeping genes in other species in this genus. The six housekeeping genes can be used as internal controls on Durik-durik plants after validation.

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11

Vandecasteele, S. J., W. E. Peetermans, R. Merckx, and J. Van Eldere. "Quantification of Expression of Staphylococcus epidermidis Housekeeping Genes with Taqman Quantitative PCR during In Vitro Growth and under Different Conditions." Journal of Bacteriology 183, no. 24 (2001): 7094–101. http://dx.doi.org/10.1128/jb.183.24.7094-7101.2001.

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ABSTRACT The aims of the present study were (i) to develop and test a sensitive and reproducible method for the study of gene expression in staphylococci and (ii) to study the expression of five housekeeping genes which are involved in nucleic acid metabolism (gmk, guanylate kinase; the dihydrofolate reductase [DHFR] gene), glucose metabolism (tpi, triosephosphate isomerase), and protein metabolism (the 16S rRNA gene;hsp-60, heat-shock protein 60) during in vitro exponential and stationary growth. A modified method for instant mRNA isolation was combined with gene quantification via Taqman real-time quantitative PCR. The detection limit of our method was 10 copies of RNA. The average intersample variability was 16%. A 10-fold increase in the expression of the hsp-60 gene was induced by exposure to a 10°C heat shock (37 to 47°C) for 10 min. During in vitro growth, the expression of all five housekeeping genes showed rapid up-regulation after inoculation of the bacteria in brain heart infusion medum and started to decline during the mid-exponential-growth phase. Maximal gene expression was 110- to 300-fold higher than gene expression during stationary phase. This indicates that housekeeping metabolism is a very dynamic process that is extremely capable of adapting to different growth conditions. Expression of the 16S rRNA gene decreases significantly earlier than that of other housekeeping genes. This confirms earlier findings forEscherichia coli that a decline in bacterial ribosomal content (measured by 16S rRNA gene expression) precedes the decline in protein synthesis (measured by mRNA expression).

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12

Halouani, Aymen, Habib Jmii, Hélène Michaux, et al. "Housekeeping Gene Expression in the Fetal and Neonatal Murine Thymus Following Coxsackievirus B4 Infection." Genes 11, no. 3 (2020): 279. http://dx.doi.org/10.3390/genes11030279.

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The thymus fulfills the role of T-cell production and differentiation. Studying transcription factors and genes involved in T-cell differentiation and maturation during the fetal and neonatal periods is very important. Nevertheless, no studies to date have been interested in evaluating the expressions of housekeeping genes as internal controls to assess the varying expressions of different genes inside this tissue during that period or in the context of viral infection. Thus, we evaluated by real-time quantitative polymerase chain reaction (qPCR) the expression of the most common internal control genes in the thymus of Swiss albino mice during the fetal and neonatal period, and following in utero infection with Coxsackievirus B4. The stability of expression of these reference genes in different samples was investigated using the geNorm application. Results demonstrated that the expression stability varied greatly between genes. Oaz1 was found to have the highest stability in different stages of development, as well as following Coxsackievirus B4 infection. The current study clearly demonstrated that Oaz1, with very stable expression levels that outperformed other tested housekeeping genes, could be used as a reference gene in the thymus and thymic epithelial cells during development and following Coxsackievirus B4 infection.

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13

Aihara, Yasuo, Babak S. Jahromi, Reza Yassari, Masataka Takahashi, and R. Loch Macdonald. "Induction of housekeeping gene expression after subarachnoid hemorrhage in dogs." Journal of Neuroscience Methods 172, no. 1 (2008): 1–7. http://dx.doi.org/10.1016/j.jneumeth.2008.03.020.

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14

VERMA, ASHISH S., and BERNARD H. SHAPIRO. "Sex-dependent expression of seven housekeeping genes in rat liver." Journal of Gastroenterology and Hepatology 21, no. 6 (2006): 1004–8. http://dx.doi.org/10.1111/j.1440-1746.2005.03948.x.

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15

Steele, Brandi K., Craig Meyers, and Michelle A. Ozbun. "Variable expression of some “housekeeping” genes during human keratinocyte differentiation." Analytical Biochemistry 307, no. 2 (2002): 341–47. http://dx.doi.org/10.1016/s0003-2697(02)00045-3.

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16

Rees, Yih-Yiing Wu, Jonathan L. "Variation in Epidermal Housekeeping Gene Expression in Different Pathological States." Acta Dermato-Venereologica 80, no. 1 (2000): 2–3. http://dx.doi.org/10.1080/000155500750012397.

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17

Ross, P. J., K. Wang, Z. Beyhan, A. Kocabas, and J. B. Cibelli. "194 HOUSEKEEPING GENE EXPRESSION OF BOVINE FERTILIZED AND CLONED EMBRYOS." Reproduction, Fertility and Development 21, no. 1 (2009): 195. http://dx.doi.org/10.1071/rdv21n1ab194.

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Real-time RT-PCR can accurately quantify mRNA levels in pre-implantation embryos; however, comparisons among different embryonic stages and among embryos produced by different means often rely on a control gene, which is commonly assumed to remain constant across samples. The objective of this study was to compare housekeeping gene expression levels, relative to total mRNA, across different stages of bovine pre-implantation development in embryos generated by IVF and somatic cell nuclear transfer (SCNT). Embryos were produced according to standard protocols (Ross et al. 2006 Biotechniques 41, 741–750). Total RNA was collected from 3 pools of 10 oocyte/embryos at metaphase II (MII), PN, 2-cell, 4-cell, 8-cell, morula, and blastocyst stages and reverse-transcribed using oligo-dT primers. The cDNA was then amplified using PCR (Kocabas et al. 2006 PNAS 103, 14 027–14 032). All amplified cDNA samples were diluted to 1 ng μL–1, as determined by NanoDrop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and corroborated using a Qubit fluorometer (Invitrogen, Carlsbad, CA, USA). For real-time PCR, 2 μL of cDNA was analyzed in duplicates. Absolute quantification was performed as previously described (Iager et al. 2008 Cloning Stem Cells doi:10.1089), using SYBR-green chemistry and standard curves specific for each gene. The number of RNA copies per nanogram of amplified cDNA was compared among samples using ANOVA. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), cyclophilin A, β-actin, ribosomal protein L-15 (RPL-15), and β-glucuronidase (GUS) expression levels were similar in MII oocyte, 1-, 2-, 4-, and 8-cell embryos, while a significant increase at morula and blastocyst stages was observed (P < 0.05). A similar pattern of expression was observed for 18S ribosomal RNA, but with a significant decrease from morula to blastocyst stages (P < 0.05). Histone H2A expression was significantly higher at 1-cell stage, similar from 2-cell to morula stages and lowest at the blastocyst stage. We then compared expression between IVF and SCNT embryos at 2-, 4-, and 8-cell and blastocyst stages. GAPDH, RPL-15, GUS, and β-actin were significantly different among groups in at least 3 of the analyzed stages, which in all cases included blastocysts. 18s-rRNA was different among IVF and SCNT embryos only at the 8-cell stage, while no differences were observed at any stages for histone H2A and cyclophilin A. At the blastocyst stage, the lowest overall variability among IVF and SCNT embryos was observed for 18s-rRNA. In conclusion, none of the evaluated housekeeping genes showed consistent mRNA expression levels across developmental stages of IVF embryos. In addition, SCNT embryos, compared to IVF, had different levels of gene expression for commonly used housekeeping genes, which, if neglected, might result in data misinterpretation. In our conditions, histone H2A had similar expression levels between IVF and SCNT embryos across different stages and showed less variability than cyclophilin A. Finally, for comparisons at the blastocyst stage, 18s-rRNA had the least variability among IVF and SCNT embryos.

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18

Powell, Timothy R., Georgia Powell-Smith, Kate Haddley, et al. "Mood-stabilizers differentially affect housekeeping gene expression in human cells." International Journal of Methods in Psychiatric Research 23, no. 2 (2014): 279–88. http://dx.doi.org/10.1002/mpr.1435.

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19

Bauer, Deborah Elaine, Vahram Haroutunian, Robert E. McCullumsmith, and James H. Meador-Woodruff. "Expression of four housekeeping proteins in elderly patients with schizophrenia." Journal of Neural Transmission 116, no. 4 (2009): 487–91. http://dx.doi.org/10.1007/s00702-008-0143-3.

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20

Yang, Teizhu, Bingning Gu, Guolyu Xu, et al. "Identification of candidate reference genes for qRT-PCR normalization studies of salinity stress and injury in Onchidium reevesii." PeerJ 7 (April 26, 2019): e6834. http://dx.doi.org/10.7717/peerj.6834.

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Real-time quantitative reverse transcription-PCR (qRT-PCR) is an undeniably effective tool for measuring levels of gene expression, but the accuracy and reliability of the statistical data obtained depend mainly on the basal expression of selected housekeeping genes in many samples. To date, there have been few analyses of stable housekeeping genes in Onchidium reevesii under salinity stress and injury. In this study, the gene expression stabilities of seven commonly used housekeeping genes, CYC, RPL28S, ACTB, TUBB, EF1a, Ubiq and 18S RNA, were investigated using BestKeeper, geNorm, NormFinder and RefFinfer. Although the results of the four programs varied to some extent, in general, RPL28S, TUBB, ACTB and EF1a were ranked highly. ACTB and TUBB were found to be the most stable housekeeping genes under salinity stress, and EF1a plus TUBB was the most stable combination under injury stress. When analysing target gene expression in different tissues, RPL28S or EF1a should be selected as the reference gene according to the level of target gene expression. Under extreme environmental stress (salinity) conditions, ACTB (0 ppt, 5 ppt, 15 ppt, 25 ppt) and TUBB (35 ppt) are reasonable reference gene choices when expression stability and abundance are considered. Under conditions of 15 ppt salinity and injury stress, our results showed that the best two-gene combination was TUBB plus EF1a. Therefore, we suggest that RPL28S, ACTB and TUBB are suitable reference genes for evaluating mRNA transcript levels. Based on candidate gene expression analysis, the tolerance of O. reevesii to low salinity (low osmotic pressure) is reduced compared to its tolerance to high salinity (high osmotic pressure). These findings will help researchers obtain accurate results in future quantitative gene expression analyses of O. reevesii under other stress conditions.

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Nascimento, Pábola Santos, Marcelo Tigre Moura, Roberta Lane Oliveira Silva, et al. "Housekeeping genes for RT-qPCR in ovine preimplantation embryos." Zygote 28, no. 5 (2020): 432–39. http://dx.doi.org/10.1017/s0967199420000295.

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SummaryHousekeeping genes (HKG) are paramount for accurate gene expression analysis during preimplantation development. Markedly, quantitative reverse transcription polymerase chain reaction (RT-qPCR) in ovine embryos currently lacks HKGs. Therefore, we tested 11 HKGs for RT-qPCR normalization during ovine parthenogenetic preimplantation development. Seven HKGs reached the qPCR efficiency threshold (97.20–105.96%), with correlation coefficients ranging from −0.922 to −0.998 and slopes from −3.22 to −3.59. GeNorm ranked glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and TATA-binding protein (TBP) as the best HKG pair, while H3 histone, family 3A (H3F3A) was the third HKG. Relative gene expression was measured for zinc finger protein X-linked (ZFX) and developmental pluripotency-associated 3 (DPPA3) transcripts during ovine parthenogenetic preimplantation development. ZFX did not show any transcript abundance fluctuation among oocytes, cleavage-stage embryos, and morulae. DPPA3 transcript abundance was also similar among all developmental stages, therefore suggesting that it may not display a maternal gene expression profile. In silico analysis of ovine DPPA3 mRNA and protein showed high conservation to bovine orthologues. However, DPPA3 orthologues differed in regulatory motifs. In conclusion, GAPDH, TBP and H3F3A are stable HKGs in ovine parthenogenetic embryos and allow accurate RT-qPCR-based gene expression analysis.

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22

Olbrich, Maren, Elke Gerstner, Gerhard Welzl, et al. "Quantification of mRNAs and Housekeeping Gene Selection for Quantitative Real-Time RT-PCR Normalization in European Beech (Fagus sylvatica L.) during Abiotic and Biotic Stress." Zeitschrift für Naturforschung C 63, no. 7-8 (2008): 574–82. http://dx.doi.org/10.1515/znc-2008-7-819.

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Analyses of different plant stressors are often based on gene expression studies. Quantitative real-time RT-PCR (qRT-PCR) is the most sensitive method for the detection of low abundance transcripts. However, a critical point to note is the selection of housekeeping genes as an internal control. Many so-called ‘housekeeping genes’ are often affected by different stress factors and may not be suitable for use as an internal reference. We tested six housekeeping genes of European beech by qRT-PCR using the Sybr Green PCR kit. Specific primers were designed for 18S rRNA, actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH1, GAPDH2), α-tubulin, and ubiquitin-like protein. Beech saplings were treated with increased concentrations of either ozone or CO2. In parallel, the expression of these genes was analyzed upon pathogen infection with Phytophthora citricola. To test the applicability of these genes as internal controls under realistic outdoor conditions, sun and shade leaves of 60-year-old trees were used for comparison. The regulation of all genes was tested using a linear mixed-effect model of the R-system. Results from independent experiments showed that the only gene not affected by any treatment was actin. The expression of the other housekeeping genes varied more or less with the degree of stress applied. These results highlight the importance of undergoing an individual selection of internal control genes for different experimental conditions.

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Sengupta, Aniruddha, Bradley A. Carlson, James A. Weaver, et al. "A functional link between housekeeping selenoproteins and phase II enzymes." Biochemical Journal 413, no. 1 (2008): 151–61. http://dx.doi.org/10.1042/bj20080277.

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Sec (selenocysteine) is biosynthesized on its tRNA and incorporated into selenium-containing proteins (selenoproteins) as the 21st amino acid residue. Selenoprotein synthesis is dependent on Sec tRNA and the expression of this class of proteins can be modulated by altering Sec tRNA expression. The gene encoding Sec tRNA (Trsp) is a single-copy gene and its targeted removal in liver demonstrated that selenoproteins are essential for proper function wherein their absence leads to necrosis and hepatocellular degeneration. In the present study, we found that the complete loss of selenoproteins in liver was compensated for by an enhanced expression of several phase II response genes and their corresponding gene products. The replacement of selenoprotein synthesis in mice carrying mutant Trsp transgenes, wherein housekeeping, but not stress-related selenoproteins are expressed, led to normal expression of phase II response genes. Thus the present study provides evidence for a functional link between housekeeping selenoproteins and phase II enzymes.

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Das, Rajat K., Sarmistha Banerjee, and Bernard H. Shapiro. "Extensive Sex- and/or Hormone-Dependent Expression of Rat Housekeeping Genes." Endocrine Research 38, no. 2 (2012): 105–11. http://dx.doi.org/10.3109/07435800.2012.723294.

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Finnegan, Maria C. M., John R. Goepel, Barry W. Hancock, and Malcolm H. Goyns. "Investigation of the Expression of Housekeeping Genes in Non-Hodgkin's Lymphoma." Leukemia & Lymphoma 10, no. 4-5 (1993): 387–93. http://dx.doi.org/10.3109/10428199309148565.

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Shaw, Grace T. W., Edward S. C. Shih, Chun-Houh Chen, and Ming-Jing Hwang. "Preservation of Ranking Order in the Expression of Human Housekeeping Genes." PLoS ONE 6, no. 12 (2011): e29314. http://dx.doi.org/10.1371/journal.pone.0029314.

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Greer, Samantha, Rice Honeywell, Mulu Geletu, Rozanne Arulanandam, and Leda Raptis. "Housekeeping genes; expression levels may change with density of cultured cells." Journal of Immunological Methods 355, no. 1-2 (2010): 76–79. http://dx.doi.org/10.1016/j.jim.2010.02.006.

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Schroder, Amy L., Katherine E. Pelch, and Susan C. Nagel. "Estrogen modulates expression of putative housekeeping genes in the mouse uterus." Endocrine 35, no. 2 (2009): 211–19. http://dx.doi.org/10.1007/s12020-009-9154-6.

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Sengupta, Aniruddha, Bradley A. Carlson, Victoria J. Hoffmann, Vadim N. Gladyshev, and Dolph L. Hatfield. "Loss of housekeeping selenoprotein expression in mouse liver modulates lipoprotein metabolism." Biochemical and Biophysical Research Communications 365, no. 3 (2008): 446–52. http://dx.doi.org/10.1016/j.bbrc.2007.10.189.

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Selvakesavan, Rajendran K., and Gregory Franklin. "Nanoparticles Affect the Expression Stability of Housekeeping Genes in Plant Cells." Nanotechnology, Science and Applications Volume 13 (August 2020): 77–88. http://dx.doi.org/10.2147/nsa.s265641.

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Mahoney, Douglas J., Kate Carey, Ming-Hua Fu, et al. "Real-time RT-PCR analysis of housekeeping genes in human skeletal muscle following acute exercise." Physiological Genomics 18, no. 2 (2004): 226–31. http://dx.doi.org/10.1152/physiolgenomics.00067.2004.

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Studies examining gene expression with RT-PCR typically normalize their mRNA data to a constitutively expressed housekeeping gene. The validity of a particular housekeeping gene must be determined for each experimental intervention. We examined the expression of various housekeeping genes following an acute bout of endurance (END) or resistance (RES) exercise. Twenty-four healthy subjects performed either a interval-type cycle ergometry workout to exhaustion (∼75 min; END) or 300 single-leg eccentric contractions (RES). Muscle biopsies were taken before exercise and 3 h and 48 h following exercise. Real-time RT-PCR was performed on β-actin, cyclophilin (CYC), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and β2-microglobulin (β2M). In a second study, 10 healthy subjects performed 90 min of cycle ergometry at ∼65% of V̇o2 max, and we examined a fifth housekeeping gene, 28S rRNA, and reexamined β2M, from muscle biopsy samples taken immediately postexercise. We showed that CYC increased 48 h following both END and RES exercise (3- and 5-fold, respectively; P < 0.01), and 28S rRNA increased immediately following END exercise (2-fold; P = 0.02). β-Actin trended toward an increase following END exercise (1.85-fold collapsed across time; P = 0.13), and GAPDH trended toward a small yet robust increase at 3 h following RES exercise (1.4-fold; P = 0.067). In contrast, β2M was not altered at any time point postexercise. We conclude that β2M and β-actin are the most stably expressed housekeeping genes in skeletal muscle following RES exercise, whereas β2M and GAPDH are the most stably expressed following END exercise.

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Wen, Yan, Ziliang Zou, Hongshun Li, Zhonghuai Xiang, and Ningjia He. "Analysis of codon usage patterns inMorus notabilisbased on genome and transcriptome data." Genome 60, no. 6 (2017): 473–84. http://dx.doi.org/10.1139/gen-2016-0129.

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Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other species within the order Rosales. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level. Translational selection optimal codons were identified and highly expressed genes of M. notabilis tended to use the optimal codons. Genes with higher expression levels have shorter coding region and lower amino acid complexity. Housekeeping genes showed stronger translational selection, which, notably, was not caused by the large differences between the expression level of housekeeping genes and other genes.

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Sato, Hiroki, Misako Yoneda, Reiko Honma, Fusako Ikeda, Shinya Watanabe, and Chieko Kai. "Measles Virus Infection Inactivates Cellular Protein Phosphatase 5 with Consequent Suppression of Sp1 and c-Myc Activities." Journal of Virology 89, no. 19 (2015): 9709–18. http://dx.doi.org/10.1128/jvi.00825-15.

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ABSTRACTMeasles virus (MeV) causes several unique syndromes, including transient immunosuppression. To clarify the cellular responses to MeV infection, we previously analyzed a MeV-infected epithelial cell line and a lymphoid cell line by microarray and showed that the expression of numerous genes was up- or downregulated in the epithelial cells. In particular, there was a characteristic comprehensive downregulation of housekeeping genes during late stage infection. To identify the mechanism underlying this phenomenon, we examined the phosphorylation status of transcription factors and kinase/phosphatase activities in epithelial cells after infection. MeV infection inactivated cellular protein phosphatase 5 (PP5) that consequently inactivated DNA-dependent protein kinase, which reduced Sp1 phosphorylation levels, and c-Myc degradation, both of which downregulated the expression of many housekeeping genes. In addition, intracellular accumulation of viral nucleocapsid inactivated PP5 and subsequent downstream responses. These findings demonstrate a novel strategy of MeV during infection, which causes the collapse of host cellular functions.IMPORTANCEMeasles virus (MeV) is one of the most important pathogens in humans. We previously showed that MeV infection induces the comprehensive downregulation of housekeeping genes in epithelial cells. By examining this phenomenon, we clarified the molecular mechanism underlying the constitutive expression of housekeeping genes in cells, which is maintained by cellular protein phosphatase 5 (PP5) and DNA-dependent protein kinase. We also demonstrated that MeV targets PP5 for downregulation in epithelial cells. This is the first report to show how MeV infection triggers a reduction in overall cellular functions of infected host cells. Our findings will help uncover unique pathogenicities caused by MeV.

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Moura, Ana Carolina de, Virgínia Meneghini Lazzari, Grasiela Agnes, Silvana Almeida, Márcia Giovenardi, and Ana Beatriz Gorini da Veiga. "Transcriptional expression study in the central nervous system of rats: what gene should be used as internal control?" Einstein (São Paulo) 12, no. 3 (2014): 336–41. http://dx.doi.org/10.1590/s1679-45082014ao3042.

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Objective A growing number of published articles report the expression of specific genes with different behavior patterns in rats. The levels of messenger ribonucleic acid transcripts are usually analyzed by reverse transcription followed by polymerase chain reaction and quantified after normalization with an internal control or reference gene (housekeeping gene). Nevertheless, housekeeping genes exhibit different expression in the central nervous system, depending on the physiological conditions and the area of the brain to be studied. The choice of a good internal control gene is essential for obtaining reliable results. This study evaluated the expression of three housekeeping genes (beta-actin, cyclophilin A, and ubiquitin C) in different areas of the central nervous system in rats (olfactory bulb, hippocampus, striatum, and prefrontal cortex). Methods Wistar rats (virgin females, n=6) during the diestrum period were used. Total ribonucleic acid was extracted from each region of the brain; the complementary deoxyribonucleic acid was synthesized by reverse transcription and amplified by real-time quantitative polymerase chain reaction using SYBR™ Green and primers specific for each one of the reference genes. The stability of the expression was determined using NormFinder. Results Beta-actin was the most stable gene in the hippocampus and striatum, while cyclophilin A and ubiquitin C showed greater stability in the prefrontal cortex and the olfactory bulb, respectively. Conclusion Based on our study, further studies of gene expression using rats as animal models should take into consideration these results when choosing a reliable internal control gene.

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Chang, Yu-Chun, Yan Ding, Lingsheng Dong, Lang-Jing Zhu, Roderick V. Jensen, and Li-Li Hsiao. "Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer." PeerJ 6 (May 9, 2018): e4719. http://dx.doi.org/10.7717/peerj.4719.

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Background Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from another. Current focus on identifying “specific disease markers” is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers. Methods Microarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t-test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training samples and then validated using an independent test set. Gene Ontology was examined by PANTHER. Results This study showed that the differential expression patterns of 242, 245, and 99 HKGs were able to distinguish normal lung from AD, SCLC, and SQCLC, respectively. From these, 70 HKGs were common across the three lung cancer subtypes. These HKGs have low expression variation compared to current lung cancer markers (e.g., EGFR, KRAS) and were involved in the most common biological processes (e.g., metabolism, stress response). In addition, the expression pattern of 106 HKGs alone was a significant classifier of AD versus SQCLC. We further highlighted that a panel of 13 HKGs was an independent predictor of overall survival and cumulative risk in AD patients. Discussion Here we report HKG expression patterns may be an effective tool for evaluation of lung cancer states. For example, the differential expression pattern of 70 HKGs alone can separate normal lung tissue from various lung cancers while a panel of 106 HKGs was a capable class predictor of subtypes of non-small cell carcinomas. We also reported that HKGs have significantly lower variance compared to traditional cancer markers across samples, highlighting the robustness of a panel of genes over any one specific biomarker. Using RNA-seq data, we showed that the expression pattern of 13 HKGs is a significant, independent predictor of overall survival for AD patients. This reinforces the predictive power of a HKG panel across different gene expression measurement platforms. Thus, we propose the expression patterns of HKGs alone may be sufficient for the diagnosis and prognosis of individuals with lung cancer.

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Grundler, Florian, and Julia Hofmann. "Identification of reference genes for qRT-PCR studies of gene expression in giant cells and syncytia induced in Arabidopsis thaliana by Meloidogyne incognita and Heterodera schachtii." Nematology 9, no. 3 (2007): 317–23. http://dx.doi.org/10.1163/156854107781352034.

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AbstractSedentary plant-parasitic nematodes, such as cyst and root-knot nematodes, induce feeding structures in the host root that undergo extensive changes in the gene expression. This phenomenon has previously been studied by gene chip analysis and qRT-PCR. Housekeeping genes are often used routinely as internal references for relative qRT-PCR analyses. However, due to the strong influence of nematode infection on host cell metabolism and physiology, expression of housekeeping genes may be altered considerably, thus limiting reliability of qRT-PCR analyses. Therefore, in the present work we tested UBQ10, ACT2, EF1a, UBP22 and 18S rRNA as potential candidates for relative qRT-PCR studies of gene expression in nematode infection sites in roots of Arabidopsis thaliana. Among the tested candidates only UBP22 and 18S rRNA were stably expressed and, therefore, are reliable reference genes for studying cyst and root-knot nematode infections.

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Murphy, R. M., K. K. O. Watt, D. Cameron-Smith, C. J. Gibbons, and R. J. Snow. "Effects of creatine supplementation on housekeeping genes in human skeletal muscle using real-time RT-PCR." Physiological Genomics 12, no. 2 (2003): 163–74. http://dx.doi.org/10.1152/physiolgenomics.00060.2002.

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The present study examined the validity and reliability of measuring the expression of various genes in human skeletal muscle using quantitative real-time RT-PCR on a GeneAmp 5700 sequence detection system with SYBR Green 1 chemistry. In addition, the validity of using some of these genes as endogenous controls (i.e., housekeeping genes) when human skeletal muscle was exposed to elevated total creatine levels and exercise was also examined. For all except 28S, linear relationships between the logarithm of the starting RNA concentrations and the cycle threshold (CT) values were established for β-actin, β2-microglobulin (β2M), cyclophilin (CYC), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). We found a linear response between CT values and the logarithm of a given amount of starting cDNA for all the genes tested. The overall intra-assay coefficient of variance for these genes was 1.3% and 21% for raw CT values and the linear value of 2−CT, respectively. Interassay variability was 2.3% for raw CT values and 34% for the linear value of 2−CT. We also examined the expression of various housekeeping genes in human skeletal muscle at days 0, 1, and 5 following oral supplementation with either creatine or a placebo employing a double-blind crossover study design. Treatments were separated by a 5-wk washout period. Immediately following each muscle sampling, subjects performed two 30-s all-out bouts on a cycle ergometer. Creatine supplementation increased ( P < 0.05) muscle total creatine content above placebo levels; however, there were no changes ( P > 0.05) in CT values across the supplementation periods for any of the genes. Nevertheless, 95% confidence intervals showed that GAPDH was variable, whereas β-actin, β2M, and CYC were the least varying genes. Normalization of the data to these housekeeping genes revealed variable behavior for β2M with more stable expressions for both β-actin and CYC. We conclude that, using real-time RT-PCR, β-actin or CYC may be used as housekeeping genes to study gene expression in human muscle in experiments employing short-term creatine supplementation combined with high-intensity exercise.

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Julian, Guilherme Silva, Renato Watanabe de Oliveira, Sergio Tufik, and Jair Ribeiro Chagas. "Analysis of the stability of housekeeping gene expression in the left cardiac ventricle of rats submitted to chronic intermittent hypoxia." Jornal Brasileiro de Pneumologia 42, no. 3 (2016): 211–14. http://dx.doi.org/10.1590/s1806-37562015000000133.

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ABSTRACT Obstructive sleep apnea (OSA) has been associated with oxidative stress and various cardiovascular consequences, such as increased cardiovascular disease risk. Quantitative real-time PCR is frequently employed to assess changes in gene expression in experimental models. In this study, we analyzed the effects of chronic intermittent hypoxia (an experimental model of OSA) on housekeeping gene expression in the left cardiac ventricle of rats. Analyses via four different approaches-use of the geNorm, BestKeeper, and NormFinder algorithms; and 2−ΔCt (threshold cycle) data analysis-produced similar results: all genes were found to be suitable for use, glyceraldehyde-3-phosphate dehydrogenase and 18S being classified as the most and the least stable, respectively. The use of more than one housekeeping gene is strongly advised.

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Ramírez-Tejero, Jorge A., Jaime Jiménez-Ruiz, María de la O. Leyva-Pérez, Juan Bautista Barroso, and Francisco Luque. "Gene Expression Pattern in Olive Tree Organs (Olea europaea L.)." Genes 11, no. 5 (2020): 544. http://dx.doi.org/10.3390/genes11050544.

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The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of different tissues/organs from adult olive tree cv. “Picual” under field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue, 32,030 of which were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each plant part was studied. The flower was clearly the organ with the most exclusively expressed genes, 3529, many of which were involved in reproduction. Many of these organ-specific genes are generally involved in regulatory activities and have a nuclear protein localization, except for leaves, where there are also many genes with a plastid localization. This was also observed in stems to a lesser extent. Moreover, pathogen defense and immunity pathways were highly represented in roots. These data show a complex pattern of gene expression in different organs, and provide relevant data about housekeeping and organ-specific genes in cultivated olive.

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Alieva, Anelya Kh, Elena V. Filatova, Margarita M. Rudenok, Petr A. Slominsky, and Maria I. Shadrina. "Housekeeping Genes for Parkinson’s Disease in Humans and Mice." Cells 10, no. 9 (2021): 2252. http://dx.doi.org/10.3390/cells10092252.

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A critical aspect of real-time PCR is the presence of housekeeping genes (HKGs) as an internal control for the normalization of expression data for genes of interest. It is necessary to select correct HKGs in the investigation of various pathologies. Thereby, we analyzed the stability of expression of the HKGs in Parkinson’s disease (PD). The work was carried out in the peripheral blood of patients with PD and in the brain tissues and peripheral blood of mice with MPTP-induced PD. As a result, Aars was the most stably expressed HKG in the mouse brain as a whole. However, different genes were more stably expressed in different parts of the brain. Polr2f was the most stably expressed in the cortex, Psmd6 was the most stably expressed in the cerebellum, and Psmd7 was the most stably expressed in the striatum and substantia nigra. HKGs were different in similar tissues of the studied organisms. Polr2f was the most stably expressed HKG in the peripheral blood of mice, whereas PSMD6 was the most stably expressed gene in humans. Thus, there is no universal HKG both for different brain tissues of one organism and for similar tissues of different organisms. Furthermore, the identified most stably expressed HKGs can be considered as such only under conditions in PD.

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Kim, Hye Jeong, Jong In Na, Byung Woo Min, et al. "Evaluation of Protein Expression in Housekeeping Genes across Multiple Tissues in Rats." Korean Journal of Pathology 48, no. 3 (2014): 193. http://dx.doi.org/10.4132/koreanjpathol.2014.48.3.193.

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Faheem, Mehwish, and Saba Khaliq. "Validation of Housekeeping Genes for Gene Expression Profiling in Fish: A Necessity." Critical Reviews in Eukaryotic Gene Expression 29, no. 6 (2019): 565–79. http://dx.doi.org/10.1615/critreveukaryotgeneexpr.2019028964.

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Ghareeb, Hassan, Zoltán Bozsó, Peter G. Ott, and Kerstin Wydra. "Silicon and Ralstonia solanacearum modulate expression stability of housekeeping genes in tomato." Physiological and Molecular Plant Pathology 75, no. 4 (2011): 176–79. http://dx.doi.org/10.1016/j.pmpp.2011.02.003.

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Alqarni, Budoor, Brendan Colley, Janosch Klebensberger, Diane McDougald, and Scott A. Rice. "Expression stability of 13 housekeeping genes during carbon starvation of Pseudomonas aeruginosa." Journal of Microbiological Methods 127 (August 2016): 182–87. http://dx.doi.org/10.1016/j.mimet.2016.06.008.

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Gautier, Claudie, Majid Mehtali, and Richard Lathe. "A ubiquitous mammalian expression vector, pHMG, based on a housekeeping gene promoter." Nucleic Acids Research 17, no. 20 (1989): 8389. http://dx.doi.org/10.1093/nar/17.20.8389.

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Albert, Henrik A., Thomas Martin, and Samuel S. M. Sun. "Structure and expression of a sugarcane gene encoding a housekeeping phosphoenolpyruvate carboxylase." Plant Molecular Biology 20, no. 4 (1992): 663–71. http://dx.doi.org/10.1007/bf00046451.

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Nakao, Reiko, Saori Yamamoto, Yuki Yasumoto, Koji Kadota, and Katsutaka Oishi. "Impact of denervation-induced muscle atrophy on housekeeping gene expression in mice." Muscle & Nerve 51, no. 2 (2014): 276–81. http://dx.doi.org/10.1002/mus.24310.

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Casadei, Raffaella, Maria Chiara Pelleri, Lorenza Vitale, et al. "Identification of housekeeping genes suitable for gene expression analysis in the zebrafish." Gene Expression Patterns 11, no. 3-4 (2011): 271–76. http://dx.doi.org/10.1016/j.gep.2011.01.003.

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E., Calvo, Rubiano C., Vargas A., and Wasserman M. "Expression of housekeeping genes during the asexual cell cycle of Plasmodium falciparum." Parasitology Research 88, no. 3 (2002): 267–71. http://dx.doi.org/10.1007/s00436-001-0526-y.

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Dheda, Keertan, Jim F. Huggett, Stephen A. Bustin, Margaret A. Johnson, Graham Rook, and Alimuddin Zumla. "Validation of housekeeping genes for normalizing RNA expression in real-time PCR." BioTechniques 37, no. 1 (2004): 112–19. http://dx.doi.org/10.2144/04371rr03.

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