Transcriptional amplification

Last updated
Transcriptional amplification involves increases in global levels of mRNAs produced from expressed genes and may be either uniform across all expressed genes or variable from gene to gene. Types of transcriptional amplification.svg
Transcriptional amplification involves increases in global levels of mRNAs produced from expressed genes and may be either uniform across all expressed genes or variable from gene to gene.

In genetics, transcriptional amplification is the process in which the total amounts of messenger RNA (mRNA) molecules from expressed genes are increased during disease, development, or in response to stimuli.

Contents

At the subset of genes expressed in a given cell, the transcribing activity of RNA Polymerase II results in mRNA production. Transcriptional amplification is specifically defined as the increase in per-cell abundance of this set of expressed mRNAs. Transcriptional amplification is caused by changes in the amount or activity of transcription-regulating proteins.

Mechanisms of transcriptional amplification

Gene expression is regulated by numerous types of proteins that directly or indirectly influence transcription by RNA Polymerase II. As opposed to transcriptional activators or repressors that selectively activate or repress specific genes, amplifiers of transcription act globally on the set of initially expressed genes.

Several known regulators of transcriptional amplification have been characterized including the oncogene Myc., [1] [2] the Rett syndrome protein MECP2, [3] and the BET bromodomain protein BRD4. [4] In particular, the Myc protein amplifies transcription by binding to promoters and enhancers of active genes where it directly recruits the transcription elongation factor P-TEFb. Furthermore, the BRD4 protein is a regulator of Myc activity.

Identifying and measuring transcriptional amplification

Commonly used gene expression experiments interrogate the expression of one (qPCR) or many (microarray, RNA-Seq) genes. These techniques generally measure relative mRNA levels and employ normalization methods that assume only a small number of genes show altered expression. [5] Instead, single cell or cell count normalized absolute measurements of mRNA abundance are required to reveal transcriptional amplification. [6] Additionally, global measurements of mRNA or total mRNA per cell can also uncover evidence for transcriptional amplification. [7] [8]

Cells in which transcription has been amplified have additional suggestive hallmarks that amplification has occurred. Cells with increased mRNA levels may be larger, consistent with an increased abundance of gene products. This increase in the amount of gene product may result in a decreased doubling time.

Role in disease

Transcriptional amplification has been implicated in cancer, [9] [10] Rett syndrome, [11] heart disease, [12] Down syndrome, [13] and cellular aging. [14] In cancer, Myc driven transcriptional amplification is posited to help tumor cells overcome rate-limiting constraints in growth and proliferation. [15] Drugs that target the transcription or mRNA processing machinery are known to be particularly effective against Myc-driven tumor models, [16] [17] suggesting that dampening of transcriptional amplification can have anti-tumor effects. Similarly, small molecules targeting the BET bromodomain protein BRD4, which is up-regulated during heart failure, can block cardiac hypertrophy in mouse models. [18] [19] In Rett syndrome, which is caused by loss of function of the transcriptional regulator MeCP2, MeCP2 was shown to specifically amplify transcription in neurons and not neuronal precursors. [20] Restoration of MeCP2 reverses disease symptoms associated with Rett syndrome [21] [22]

Related Research Articles

Transcription (biology) Process of copying a segment of DNA into RNA

Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). Averaged over multiple cell types in a given tissue, the quantity of mRNA is more than 10 times the quantity of ncRNA. The general preponderance of mRNA in cells is valid even though less than 2% of the human genome can be transcribed into mRNA, while at least 80% of mammalian genomic DNA can be actively transcribed, with the majority of this 80% considered to be ncRNA.

Enhancer (genetics) DNA sequence that binds activators to increase the likelihood of gene transcription

In genetics, an enhancer is a short region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors. Enhancers are cis-acting. They can be located up to 1 Mbp away from the gene, upstream or downstream from the start site. There are hundreds of thousands of enhancers in the human genome. They are found in both prokaryotes and eukaryotes.

Oct-4 Mammalian protein found in Homo sapiens

Oct-4, also known as POU5F1, is a protein that in humans is encoded by the POU5F1 gene. Oct-4 is a homeodomain transcription factor of the POU family. It is critically involved in the self-renewal of undifferentiated embryonic stem cells. As such, it is frequently used as a marker for undifferentiated cells. Oct-4 expression must be closely regulated; too much or too little will cause differentiation of the cells.

Myc is a family of regulator genes and proto-oncogenes that code for transcription factors. The Myc family consists of three related human genes: c-myc (MYC), l-myc (MYCL), and n-myc (MYCN). c-myc was the first gene to be discovered in this family, due to homology with the viral gene v-myc.

N-Myc

N-myc proto-oncogene protein also known as N-Myc or basic helix-loop-helix protein 37 (bHLHe37), is a protein that in humans is encoded by the MYCN gene.

Induced pluripotent stem cell Pluripotent stem cell generated directly from a somatic cell

Induced pluripotent stem cells are a type of pluripotent stem cell that can be generated directly from a somatic cell. The iPSC technology was pioneered by Shinya Yamanaka’s lab in Kyoto, Japan, who showed in 2006 that the introduction of four specific genes, collectively known as Yamanaka factors, encoding transcription factors could convert somatic cells into pluripotent stem cells. He was awarded the 2012 Nobel Prize along with Sir John Gurdon "for the discovery that mature cells can be reprogrammed to become pluripotent."

Cyclin-dependent kinase 8

Cell division protein kinase 8 is an enzyme that in humans is encoded by the CDK8 gene.

NFYC

Nuclear transcription factor Y subunit gamma is a protein that in humans is encoded by the NFYC gene.

TBX3 Protein-coding gene in the species Homo sapiens

T-box transcription factor TBX3 is a protein that in humans is encoded by the TBX3 gene.

MYCL

L-myc-1 proto-oncogene protein is a protein that in humans is encoded by the MYCL1 gene.

SALL4

Sal-like protein 4(SALL4) is a transcription factor encoded by a member of the Spalt-like (SALL) gene family, SALL4. The SALL genes were identified based on their sequence homology to Spalt, which is a homeotic gene originally cloned in Drosophila melanogaster that is important for terminal trunk structure formation in embryogenesis and imaginal disc development in the larval stages. There are four human SALL proteins with structural homology and playing diverse roles in embryonic development, kidney function, and cancer. The SALL4 gene encodes at least three isoforms, termed A, B, and C, through alternative splicing, with the A and B forms being the most studied. SALL4 can alter gene expression changes through its interaction with many co-factors and epigenetic complexes. It is also known as a key embryonic stem cell (ESC) factor.

BRD4

Bromodomain-containing protein 4 is a protein that in humans is encoded by the BRD4 gene.

Bromodomain-containing protein 3

Bromodomain-containing protein 3 (BRD3) also known as RING3-like protein (RING3L) is a protein that in humans is encoded by the BRD3 gene. This gene was identified based on its homology to the gene encoding the RING3 (BRD2) protein, a serine/threonine kinase. The gene maps to 9q34, a region which contains several major histocompatibility complex (MHC) genes.

GTF2F1

General transcription factor IIF subunit 1 is a protein that in humans is encoded by the GTF2F1 gene.

Alvocidib Chemical compound

Alvocidib is a flavonoid alkaloid CDK9 kinase inhibitor under clinical development by Tolero Pharmaceuticals for the treatment of acute myeloid leukemia. It has been studied also for the treatment of arthritis and atherosclerotic plaque formation. The target of alvocidib is the positive transcription elongation factor P-TEFb. Treatment of cells with alvocidib leads to inhibition of P-TEFb and the loss of mRNA production.

JQ1

JQ1 is a thienotriazolodiazepine and a potent inhibitor of the BET family of bromodomain proteins which include BRD2, BRD3, BRD4, and the testis-specific protein BRDT in mammals. BET inhibitors structurally similar to JQ1 are being tested in clinical trials for a variety of cancers including NUT midline carcinoma. It was developed by the James Bradner laboratory at Brigham and Women's Hospital and named after chemist Jun Qi. The chemical structure was inspired by patent of similar BET inhibitors by Mitsubishi Tanabe Pharma [WO/2009/084693]. Structurally it is related to benzodiazepines. While widely used in laboratory applications, JQ1 is not itself being used in human clinical trials because it has a short half life.

GLIS1

Glis1 is gene encoding a Krüppel-like protein of the same name whose locus is found on Chromosome 1p32.3. The gene is enriched in unfertilised eggs and embryos at the one cell stage and it can be used to promote direct reprogramming of somatic cells to induced pluripotent stem cells, also known as iPS cells. Glis1 is a highly promiscuous transcription factor, regulating the expression of numerous genes, either positively or negatively. In organisms, Glis1 does not appear to have any directly important functions. Mice whose Glis1 gene has been removed have no noticeable change to their phenotype.

BET inhibitors are a class of drugs that reversibly bind the bromodomains of Bromodomain and Extra-Terminal motif (BET) proteins BRD2, BRD3, BRD4, and BRDT, and prevent protein-protein interaction between BET proteins and acetylated histones and transcription factors.

In genetics, a super-enhancer is a region of the mammalian genome comprising multiple enhancers that is collectively bound by an array of transcription factor proteins to drive transcription of genes involved in cell identity. Because super-enhancers are frequently identified near genes important for controlling and defining cell identity, they may thus be used to quickly identify key nodes regulating cell identity.

Richard A. Young

Richard Allen Young is an American geneticist, a Member of Whitehead Institute, and a professor of biology at the Massachusetts Institute of Technology. He is a pioneer in the systems biology of gene control who has developed genomics technologies and concepts key to understanding gene control in human health and disease. He has served as an advisor to the World Health Organization and the National Institutes of Health. He is a member of the National Academy of Sciences and the National Academy of Medicine. Scientific American has recognized him as one of the top 50 leaders in science, technology and business. Young is among the most Highly Cited Researchers in his field.

References

  1. ↑ Lin, CY; Lovén, J; Rahl, PB; Paranal, RM; Burge, CB; Bradner, JE; Lee, TI; Young, RA (28 September 2012). "Transcriptional amplification in tumor cells with elevated c-Myc". Cell. 151 (1): 56–67. doi:10.1016/j.cell.2012.08.026. PMC   3462372 . PMID   23021215.
  2. ↑ Nie, Z; Hu, G; Wei, G; Cui, K; Yamane, A; Resch, W; Wang, R; Green, DR; Tessarollo, L; Casellas, R; Zhao, K; Levens, D (28 September 2012). "c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells". Cell. 151 (1): 68–79. doi:10.1016/j.cell.2012.08.033. PMC   3471363 . PMID   23021216.
  3. ↑ Li, Y; Wang, H; Muffat, J; Cheng, AW; Orlando, DA; Lovén, J; Kwok, SM; Feldman, DA; Bateup, HS; Gao, Q; Hockemeyer, D; Mitalipova, M; Lewis, CA; Vander Heiden, MG; Sur, M; Young, RA; Jaenisch, R (3 October 2013). "Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons". Cell Stem Cell. 13 (4): 446–58. doi:10.1016/j.stem.2013.09.001. PMC   4053296 . PMID   24094325.
  4. ↑ Anand, P; Brown, JD; Lin, CY; Qi, J; Zhang, R; Artero, PC; Alaiti, MA; Bullard, J; Alazem, K; Margulies, KB; Cappola, TP; Lemieux, M; Plutzky, J; Bradner, JE; Haldar, SM (1 August 2013). "BET bromodomains mediate transcriptional pause release in heart failure". Cell. 154 (3): 569–82. doi:10.1016/j.cell.2013.07.013. PMC   4090947 . PMID   23911322.
  5. ↑ Hannah, MA; Redestig, H; Leisse, A; Willmitzer, L (July 2008). "Global mRNA changes in microarray experiments". Nature Biotechnology. 26 (7): 741–2. doi:10.1038/nbt0708-741. PMID   18612292. S2CID   32566304.
  6. ↑ Lovén, J; Orlando, DA; Sigova, AA; Lin, CY; Rahl, PB; Burge, CB; Levens, DL; Lee, TI; Young, RA (26 October 2012). "Revisiting global gene expression analysis". Cell. 151 (3): 476–82. doi:10.1016/j.cell.2012.10.012. PMC   3505597 . PMID   23101621.
  7. ↑ Lin, CY; Lovén, J; Rahl, PB; Paranal, RM; Burge, CB; Bradner, JE; Lee, TI; Young, RA (28 September 2012). "Transcriptional amplification in tumor cells with elevated c-Myc". Cell. 151 (1): 56–67. doi:10.1016/j.cell.2012.08.026. PMC   3462372 . PMID   23021215.
  8. ↑ Kanno, J; Aisaki, K; Igarashi, K; Nakatsu, N; Ono, A; Kodama, Y; Nagao, T (29 March 2006). ""Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays". BMC Genomics. 7: 64. doi:10.1186/1471-2164-7-64. PMC   1448209 . PMID   16571132.
  9. ↑ Lin, CY; Lovén, J; Rahl, PB; Paranal, RM; Burge, CB; Bradner, JE; Lee, TI; Young, RA (28 September 2012). "Transcriptional amplification in tumor cells with elevated c-Myc". Cell. 151 (1): 56–67. doi:10.1016/j.cell.2012.08.026. PMC   3462372 . PMID   23021215.
  10. ↑ Nie, Z; Hu, G; Wei, G; Cui, K; Yamane, A; Resch, W; Wang, R; Green, DR; Tessarollo, L; Casellas, R; Zhao, K; Levens, D (28 September 2012). "c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells". Cell. 151 (1): 68–79. doi:10.1016/j.cell.2012.08.033. PMC   3471363 . PMID   23021216.
  11. ↑ Li, Y; Wang, H; Muffat, J; Cheng, AW; Orlando, DA; Lovén, J; Kwok, SM; Feldman, DA; Bateup, HS; Gao, Q; Hockemeyer, D; Mitalipova, M; Lewis, CA; Vander Heiden, MG; Sur, M; Young, RA; Jaenisch, R (3 October 2013). "Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons". Cell Stem Cell. 13 (4): 446–58. doi:10.1016/j.stem.2013.09.001. PMC   4053296 . PMID   24094325.
  12. ↑ Anand, P; Brown, JD; Lin, CY; Qi, J; Zhang, R; Artero, PC; Alaiti, MA; Bullard, J; Alazem, K; Margulies, KB; Cappola, TP; Lemieux, M; Plutzky, J; Bradner, JE; Haldar, SM (1 August 2013). "BET bromodomains mediate transcriptional pause release in heart failure". Cell. 154 (3): 569–82. doi:10.1016/j.cell.2013.07.013. PMC   4090947 . PMID   23911322.
  13. ↑ Lane, AA; Chapuy, B; Lin, CY; Tivey, T; Li, H; Townsend, EC; van Bodegom, D; Day, TA; Wu, SC; Liu, H; Yoda, A; Alexe, G; Schinzel, AC; Sullivan, TJ; Malinge, S; Taylor, JE; Stegmaier, K; Jaffe, JD; Bustin, M; te Kronnie, G; Izraeli, S; Harris, MH; Stevenson, KE; Neuberg, D; Silverman, LB; Sallan, SE; Bradner, JE; Hahn, WC; Crispino, JD; Pellman, D; Weinstock, DM (June 2014). "Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation". Nature Genetics. 46 (6): 618–23. doi:10.1038/ng.2949. PMC   4040006 . PMID   24747640.
  14. ↑ Hu, Z; Chen, K; Xia, Z; Chavez, M; Pal, S; Seol, JH; Chen, CC; Li, W; Tyler, JK (15 February 2014). "Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging". Genes & Development. 28 (4): 396–408. doi:10.1101/gad.233221.113. PMC   3937517 . PMID   24532716.
  15. ↑ Ruggero, D (1 December 2009). "The role of Myc-induced protein synthesis in cancer". Cancer Research. 69 (23): 8839–43. doi:10.1158/0008-5472.CAN-09-1970. PMC   2880919 . PMID   19934336.
  16. ↑ Christensen, CL; Kwiatkowski, N; Abraham, BJ; Carretero, J; Al-Shahrour, F; Zhang, T; Chipumuro, E; Herter-Sprie, GS; Akbay, EA; Altabef, A; Zhang, J; Shimamura, T; Capelletti, M; Reibel, JB; Cavanaugh, JD; Gao, P; Liu, Y; Michaelsen, SR; Poulsen, HS; Aref, AR; Barbie, DA; Bradner, JE; George, RE; Gray, NS; Young, RA; Wong, KK (8 December 2014). "Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor". Cancer Cell. 26 (6): 909–22. doi:10.1016/j.ccell.2014.10.019. PMC   4261156 . PMID   25490451.
  17. ↑ Hsu, TY; Simon, LM; Neill, NJ; Marcotte, R; Sayad, A; Bland, CS; Echeverria, GV; Sun, T; Kurley, SJ; Tyagi, S; Karlin, KL; Dominguez-Vidaña, R; Hartman, JD; Renwick, A; Scorsone, K; Bernardi, RJ; Skinner, SO; Jain, A; Orellana, M; Lagisetti, C; Golding, I; Jung, SY; Neilson, JR; Zhang, XH; Cooper, TA; Webb, TR; Neel, BG; Shaw, CA; Westbrook, TF (17 September 2015). "The spliceosome is a therapeutic vulnerability in MYC-driven cancer". Nature. 525 (7569): 384–8. doi:10.1038/nature14985. PMC   4831063 . PMID   26331541.
  18. ↑ Anand, P; Brown, JD; Lin, CY; Qi, J; Zhang, R; Artero, PC; Alaiti, MA; Bullard, J; Alazem, K; Margulies, KB; Cappola, TP; Lemieux, M; Plutzky, J; Bradner, JE; Haldar, SM (1 August 2013). "BET bromodomains mediate transcriptional pause release in heart failure". Cell. 154 (3): 569–82. doi:10.1016/j.cell.2013.07.013. PMC   4090947 . PMID   23911322.
  19. ↑ Stratton, MS; Lin, CY; Anand, P; Tatman, PD; Ferguson, BS; Wickers, ST; Ambardekar, AV; Sucharov, CC; Bradner, JE; Haldar, SM; McKinsey, TA (2 August 2016). "Signal-Dependent Recruitment of BRD4 to Cardiomyocyte Super-Enhancers Is Suppressed by a MicroRNA". Cell Reports. 16 (5): 1366–78. doi:10.1016/j.celrep.2016.06.074. PMC   4972677 . PMID   27425608.
  20. ↑ Li, Y; Wang, H; Muffat, J; Cheng, AW; Orlando, DA; Lovén, J; Kwok, SM; Feldman, DA; Bateup, HS; Gao, Q; Hockemeyer, D; Mitalipova, M; Lewis, CA; Vander Heiden, MG; Sur, M; Young, RA; Jaenisch, R (3 October 2013). "Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons". Cell Stem Cell. 13 (4): 446–58. doi:10.1016/j.stem.2013.09.001. PMC   4053296 . PMID   24094325.
  21. ↑ Luikenhuis, S; Giacometti, E; Beard, CF; Jaenisch, R (20 April 2004). "Expression of MeCP2 in postmitotic neurons rescues Rett syndrome in mice". Proceedings of the National Academy of Sciences of the United States of America. 101 (16): 6033–8. doi: 10.1073/pnas.0401626101 . PMC   395918 . PMID   15069197.
  22. ↑ Garg, SK; Lioy, DT; Cheval, H; McGann, JC; Bissonnette, JM; Murtha, MJ; Foust, KD; Kaspar, BK; Bird, A; Mandel, G (21 August 2013). "Systemic delivery of MeCP2 rescues behavioral and cellular deficits in female mouse models of Rett syndrome". The Journal of Neuroscience. 33 (34): 13612–20. doi:10.1523/JNEUROSCI.1854-13.2013. PMC   3755711 . PMID   23966684.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.