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In genetics, complementary DNA (cDNA) is DNA synthesized from a single-stranded RNA template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes. When scientists want to express a specific protein in a cell that does not normally express that protein, they will transfer the cDNA that codes for the protein to the recipient cell. In molecular biology, cDNA is also generated to analyze transcriptomic profiles in bulk tissue, single cells, or single nuclei in assays such as microarrays and RNA-seq.
Reverse transcription polymerase chain reaction (RT-PCR) is a laboratory technique combining reverse transcription of RNA into DNA and amplification of specific DNA targets using polymerase chain reaction (PCR). It is primarily used to measure the amount of a specific RNA. This is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression and quantification of viral RNA in research and clinical settings.
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. Although some housekeeping genes are expressed at relatively constant rates in most non-pathological situations, the expression of other housekeeping genes may vary depending on experimental conditions.
Ectopic is a word used with a prefix, ecto, meaning “out of place.” Ectopic expression is an abnormal gene expression in a cell type, tissue type, or developmental stage in which the gene is not usually expressed. The term ectopic expression is predominantly used in studies using metazoans, especially in Drosophila melanogaster for research purposes.
A real-time polymerase chain reaction is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule during the PCR, not at its end, as in conventional PCR. Real-time PCR can be used quantitatively and semi-quantitatively.
The miR-129 microRNA precursor is a small non-coding RNA molecule that regulates gene expression. This microRNA was first experimentally characterised in mouse and homologues have since been discovered in several other species, such as humans, rats and zebrafish. The mature sequence is excised by the Dicer enzyme from the 5' arm of the hairpin. It was elucidated by Calin et al. that miR-129-1 is located in a fragile site region of the human genome near a specific site, FRA7H in chromosome 7q32, which is a site commonly deleted in many cancers. miR-129-2 is located in 11p11.2.
The miR-199 microRNA precursor is a short non-coding RNA gene involved in gene regulation. miR-199 genes have now been predicted or experimentally confirmed in mouse, human and a further 21 other species. microRNAs are transcribed as ~70 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~22 nucleotide product. The mature products are thought to have regulatory roles through complementarity to mRNA.
The steroidogenic factor 1 (SF-1) protein is a transcription factor involved in sex determination by controlling activity of genes related to the reproductive glands or gonads and adrenal glands. This protein is encoded by the NR5A1 gene, a member of the nuclear receptor subfamily, located on the long arm of chromosome 9 at position 33.3. It was originally identified as a regulator of genes encoding cytochrome P450 steroid hydroxylases, however, further roles in endocrine function have since been discovered.
Estrogen-related receptor gamma (ERR-gamma), also known as NR3B3, is a nuclear receptor that in humans is encoded by the ESRRG gene. It behaves as a constitutive activator of transcription.
Opsin-3 also known as encephalopsin or panopsin is a protein that, in humans, is encoded by the OPN3 gene. Alternative splicing of this gene results in multiple transcript variants encoding different protein isoforms.
Folylpolyglutamate synthase, mitochondrial is an enzyme that in humans is encoded by the FPGS gene.
Mediator of RNA polymerase II transcription subunit 22 is an enzyme that in humans is encoded by the MED22 gene.
Thymocyte nuclear protein 1 is a protein that in humans is encoded by the THYN1 gene.
High mobility group nucleosome-binding domain-containing protein 3 is a protein that in humans is encoded by the HMGN3 gene.
RNA-Seq is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome.
Sine oculis-binding protein homolog (SOBP) also known as Jackson circler protein 1 (JXC1) is a protein that in humans is encoded by the SOBP gene. The first SOBP gene was identified in Drosophila melanogaster in a yeast two-hybrid screen that used the SIX domain of the Sine oculis protein as bait. In most genomes, which harbor SOBP, the gene is present as a single copy.
PRR32 is a protein that in humans is encoded by the CXorf64 gene. It was also found that the homologs of the PRR32 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, and rat. It was also found through ncbi that 82 organisms have orthologs with human gene PRR323.
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst non-coding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells. Another is how gene expression is regulated.
FANTOM is an international research consortium first established in 2000 as part of the RIKEN research institute in Japan. The original meeting gathered international scientists from diverse backgrounds to help annotate the function of mouse cDNA clones generated by the Hayashizaki group. Since the initial FANTOM1 effort, the consortium has released multiple projects that look to understand the mechanisms governing the regulation of mammalian genomes. Their work has generated a large collection of shared data and helped advance biochemical and bioinformatic methodologies in genomics research.
References
- 1 2 3 4 5 Hounkpe, Bidossessi Wilfried; Chenou, Francine; de-Lima, Franciele; De-Paula, Erich Vinicius (2020-07-14). "HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets". Nucleic Acids Research. 49 (D1): D947–D955. doi: 10.1093/nar/gkaa609 . ISSN 0305-1048. PMC 7778946 . PMID 32663312.
- 1 2 Eisenberg E, 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.
- ↑ 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. doi:10.1152/physiolgenomics.2001.7.2.95. PMID 11773595.
- ↑ 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.
- 1 2 3 4 5 6 7 Quiagen. "RT2 Profiler PCR Array (96-Well Format and 384-Well Format". Qiagen Catalog No. 330231 PAHS-00ZA.
- ↑ 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.