Transcription factory

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A generic transcription factory during transcription, highlighting the possibility of transcribing more than one gene at a time. The diagram includes 8 RNA polymerases however the number can vary depending on cell type. The image also includes transcription factors and a porous, protein core. Basic diagram of a transcription factory during transcription.png
A generic transcription factory during transcription, highlighting the possibility of transcribing more than one gene at a time. The diagram includes 8 RNA polymerases however the number can vary depending on cell type. The image also includes transcription factors and a porous, protein core.

Transcription factories, in genetics describe the discrete sites where transcription occurs in the cell nucleus, and are an example of a biomolecular condensate. They were first discovered in 1993 and have been found to have structures analogous to replication factories, sites where replication also occurs in discrete sites. The factories contain an RNA polymerase (active or inactive) and the necessary transcription factors (activators and repressors) for transcription. [1] Transcription factories containing RNA polymerase II are the most studied but factories can exist for RNA polymerase I and III; the nucleolus being seen as the prototype for transcription factories. It is possible to view them under both light and electron microscopy. [2] The discovery of transcription factories has challenged the original view of how RNA polymerase interacts with the DNA polymer and it is thought that the presence of factories has important effects on gene regulation and nuclear structure.

Contents

Discovery

The first use of the term ‘transcription factory’ was used in 1993 by Jackson and his colleagues who noticed that transcription occurred at discrete sites in the nucleus. [3] This contradicted the original view that transcription occurred at an even distribution throughout the nucleus.

Structure

The structure of a transcription factory appears to be determined by cell type, transcriptional activity of the cell and also the method of technique used to visualise the structure. The generalised view of a transcription factory would feature between 4 – 30 RNA polymerase molecules [1] and it is thought that the more transcriptionally active a cell is, the more polymerases that will be present in a factory in order to meet the demands of transcription. The core of the factory is porous and protein rich, with the hyperphosphorylated, elongating form polymerases on the perimeter. The type of proteins present include: ribonucleoproteins, co-activators, transcription factors, RNA helicase and splicing and processing enzymes. [4] A factory only contains one type of RNA polymerase and the diameter of the factory varies depending on the RNA polymerase featured; RNA polymerase I factories are roughly 500 nm in width whereas RNA polymerase II and III factories a magnitude smaller at 50 nm. [5] It has been experimentally shown that the transcription factory is immobilised to a structure and it is postulated that this immobilisation is because of a tethering to the nuclear matrix; this is because it has been shown it is tied to a structure that is unaffected by restriction enzymes. Proteins that have been thought to be involved in the tethering includes spectrin, actin and lamins. [4]

Function

The structure of a transcriptional factory directly relates to its function. Transcription is made more efficient because of the clustered nature of the transcription factory. All the necessary proteins: RNA polymerase, transcription factors and other co-regulators are present in the transcription factory that allows for faster RNA polymerisation when the DNA template reaches the factory, it also allows for a number of genes to be transcribed at the same time. [6]

Genomic location

The amount of transcription factories found per nucleus appears to be determined by cell type, species and the type of measurement. Cultured mouse embryonic fibroblasts have been found to have roughly 1500 factories through immunofluorescence detection of RNAP II however cells taken from different tissues of the same mouse group had between 100 and 300 factories. [7] Measurements of the number of transcription factories in HeLa cells give a varied result. For example, using the traditional fluorescence microscopy approach 300 – 500 factories were found but using both confocal and electron microscopy roughly 2100 were detected. [1]

Factory specialisation

In addition to the specialisation factories have for the type of RNA polymerase they contain, there is a further level of specialisation present. There are some factories that only transcribe a certain set of related genes, this further strengthens the concept that the main function of a transcription factory is for transcriptional efficiency. [7]

Assembly and maintenance

There is much debate to whether transcription factories assemble because of the transcriptional demands of the genome or if they are stable structures that are conserved over time. Experimentally, it appears that they remain fixed over a short period of time; newly made mRNA were pulse labelled over 15 minutes and it showed no new transcription factories appearing. [1] This is also supported by inhibition experiments. In these studies heat shock was used to turn off transcription which resulted in no change in the number of polymerases detected. [8] Upon further analysis of western blot data it was suggested that there was in fact a slight decrease over time of transcription factories. Therefore, it could be claimed that polymerase molecules are released gently over time from the factory when there is a lack of transcription which would eventually lead to the complete loss of the transcription factory. [9]

There is also several pieces of evidence that promotes the idea of transcription factories assembling de novo due to transcriptional demands. GFP polymerase fluorescence experiments have shown that the inducement of transcription in Drosophila polytene nuclei leads to the formation of a factory which contradicts the notion of a stable and secure structure. [10]

Mechanism

The hypothesis that it is the transcription factory that remains immobilised during transcription as opposed to the DNA template. It shows how a section of the gene being transcribed (brown) gets pulled and shuttled through the RNA polymerase during the process. Immobilised transcription factory during transcription.png
The hypothesis that it is the transcription factory that remains immobilised during transcription as opposed to the DNA template. It shows how a section of the gene being transcribed (brown) gets pulled and shuttled through the RNA polymerase during the process.

It was previously thought that it was the relatively small RNA polymerase that moves along the comparatively larger DNA template during transcription. However, increasing evidence supports the notion that due to the tethering of a transcription factory to the nuclear matrix, it is in fact the large DNA template that is moved to accommodate RNA polymerisation. In vitro studies for example have shown that RNA polymerases attached to a surface are capable of both rotating the DNA template and threading it through the polymerase to start transcription; which indicates the capabilities of RNA polymerase to be a molecular motor. [6] Chromosome Conformation Capture (3C) also supports the idea of the DNA template diffusing towards a stationary RNA polymerase. [11]

There remains a doubt to this mechanism of transcription. Firstly, it is unknown how a stationary polymerase is capable of transcribing genes on the (+)-strand and (-)-strand at the same genomic locus at the same time. This is in addition to a lack of conclusive evidence on how the polymerase remains immobilised (how it is tethered) and what structure it is tethered to. [12]

Effect on genomic and nuclear structure

The attraction of related genes to RNAP and the required transcription factors causes the formation of a chromatin loop, thereby affecting the genome structure A transcription factory causing the formation of a chromatin loop.png
The attraction of related genes to RNAP and the required transcription factors causes the formation of a chromatin loop, thereby affecting the genome structure

There are several consequences the formation of a transcription factory has on nuclear and genomic structures. It has been proposed that the factories are responsible for nuclear organisation; they have been suggested to promote chromatin loop formation by two potential mechanisms:

The first mechanism suggests that loops form because 2 genes on the same chromosome require the same transcription machinery that would be found in a specific transcription factory. This requirement will attract the gene loci to the factory thus creating a loop. [13]

Transcription factories are also suggested to be responsible for gene clustering, this is because related genes would require the same transcriptional machinery and if a factory satisfies these needs the genes would be attracted to the factory [14] . While the clustering of genes can be beneficial for transcriptional efficiency, there could be negative consequences to this. Gene translocation events occur when genes are in close proximity to one another; which will occur more often when a transcriptional factory is present. Gene translocation events, like point mutations, generally are detrimental to the organism and so therefore could lead to the possibility of disease. However, on the other hand recent research has suggested that there is no correlation between inter-gene interactions and translocation frequencies. [15]

See also

Related Research Articles

<span class="mw-page-title-main">Cell nucleus</span> Eukaryotic membrane-bounded organelle containing DNA

The cell nucleus is a membrane-bound organelle found in eukaryotic cells. Eukaryotic cells usually have a single nucleus, but a few cell types, such as mammalian red blood cells, have no nuclei, and a few others including osteoclasts have many. The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cellular cytoplasm; and the nuclear matrix, a network within the nucleus that adds mechanical support.

<span class="mw-page-title-main">Nuclear pore</span> Openings in nuclear envelope of eukaryotic cells

A nuclear pore is a channel as part of the nuclear pore complex (NPC), a large protein complex found in the nuclear envelope in eukaryotic cells, enveloping the cell nucleus containing DNA, which facilitates the selective membrane transport of various molecules across the membrane.

<span class="mw-page-title-main">Nucleolus</span> Largest structure in the nucleus of eukaryotic cells

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis, which is the synthesis of ribosomes. The nucleolus also participates in the formation of signal recognition particles and plays a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA, and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

<span class="mw-page-title-main">Gene expression</span> Conversion of a genes sequence into a mature gene product or products

Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, and ultimately affect a phenotype. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication.

<span class="mw-page-title-main">Transcription (biology)</span> 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). mRNA comprises only 1–3% of total RNA samples. 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.

<span class="mw-page-title-main">RNA polymerase</span> Enzyme that synthesizes RNA from DNA

In molecular biology, RNA polymerase, or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.

<span class="mw-page-title-main">Nucleoplasm</span> Protoplasm that permeates a cells nucleus

The nucleoplasm, also known as karyoplasm, is the type of protoplasm that makes up the cell nucleus, the most prominent organelle of the eukaryotic cell. It is enclosed by the nuclear envelope, also known as the nuclear membrane. The nucleoplasm resembles the cytoplasm of a eukaryotic cell in that it is a gel-like substance found within a membrane, although the nucleoplasm only fills out the space in the nucleus and has its own unique functions. The nucleoplasm suspends structures within the nucleus that are not membrane-bound and is responsible for maintaining the shape of the nucleus. The structures suspended in the nucleoplasm include chromosomes, various proteins, nuclear bodies, the nucleolus, nucleoporins, nucleotides, and nuclear speckles.

In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in multicellular eukaryotes, as studied in evolutionary developmental biology.

Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. In many bacteria, the poly(A) tail promotes degradation of the mRNA. It, therefore, forms part of the larger process of gene expression.

<span class="mw-page-title-main">Primary transcript</span> RNA produced by transcription

A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.

<span class="mw-page-title-main">RNA polymerase II</span> Protein complex that transcribes DNA

RNA polymerase II is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.

<span class="mw-page-title-main">Eukaryotic transcription</span> Transcription is heterocatalytic function of DNA

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes comes in three variations, each translating a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.

<span class="mw-page-title-main">POLR2A</span> Protein-coding gene in the species Homo sapiens

DNA-directed RNA polymerase II subunit RPB1, also known as RPB1, is an enzyme that is encoded by the POLR2A gene in humans.

<span class="mw-page-title-main">RNA-binding protein FUS</span> Human protein and coding gene

RNA-binding protein FUS/TLS, also known as heterogeneous nuclear ribonucleoprotein P2 is a protein that in humans is encoded by the FUS gene.

<span class="mw-page-title-main">ERCC8 (gene)</span> Protein-coding gene in humans

DNA excision repair protein ERCC-8 is a protein that in humans is encoded by the ERCC8 gene.

<span class="mw-page-title-main">PTRF</span> Protein-coding gene in the species Homo sapiens

Polymerase I and transcript release factor, also known as Cavin1, Cavin-1 or PTRF, is a protein which in humans is encoded by the PTRF gene.

<span class="mw-page-title-main">POLRMT</span> Protein-coding gene in the species Homo sapiens

DNA-directed RNA polymerase, mitochondrial is an enzyme that in humans is encoded by the POLRMT gene.

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.

<span class="mw-page-title-main">Scaffold/matrix attachment region</span>

The term S/MAR, otherwise called SAR, or MAR, are sequences in the DNA of eukaryotic chromosomes where the nuclear matrix attaches. As architectural DNA components that organize the genome of eukaryotes into functional units within the cell nucleus, S/MARs mediate structural organization of the chromatin within the nucleus. These elements constitute anchor points of the DNA for the chromatin scaffold and serve to organize the chromatin into structural domains. Studies on individual genes led to the conclusion that the dynamic and complex organization of the chromatin mediated by S/MAR elements plays an important role in the regulation of gene expression.

<span class="mw-page-title-main">Nuclear organization</span> Spatial distribution of chromatin within a cell nucleus

Nuclear organization refers to the spatial distribution of chromatin within a cell nucleus. There are many different levels and scales of nuclear organisation. Chromatin is a higher order structure of DNA.

References

  1. 1 2 3 4 Iborra F (1996). "Active RNA polymerases are localised within discrete transcription "factories" in human nuclei". J Cell Sci . 109 (6): 1427–1436. doi: 10.1242/jcs.109.6.1427 . PMID   8799830.
  2. ↑ Schermelleh L (2010). "A guide to super-resolution fluorescence microscopy". J. Cell Biol. 190 (2): 165–175. doi:10.1083/jcb.201002018. PMC   2918923 . PMID   20643879.
  3. ↑ Jackson DA (1993). "Visualization of focal sites of transcription within human nuclei". EMBO J . 12 (3): 1059–1065. doi:10.1002/j.1460-2075.1993.tb05747.x. PMC   413307 . PMID   8458323.
  4. 1 2 Melnik S (2011). "The proteomes of transcription factories containing RNA polymerases I, II or III". Nat. Methods . 8 (11): 963–968. doi:10.1038/nmeth.1705. PMC   3324775 . PMID   21946667.
  5. ↑ Eskiw CH (2011). "Ultrastructural study of transcription factories in mouse erythroblasts". J Cell Sci . 124 (21): 3676–3683. doi:10.1242/jcs.087981. PMC   3215576 . PMID   22045738.
  6. 1 2 Papantonis A (2011). "Fixing the model for transcription: the DNA moves, not the polymerase". Transcription . 2 (1): 41–44. doi:10.4161/trns.2.1.14275. PMC   3023647 . PMID   21326910.
  7. 1 2 Osborne C (2004). "Active genes dynamically colocalize to shared sites of ongoing transcription". Nat. Genet. 36 (10): 1065–1071. doi: 10.1038/ng1423 . PMID   15361872.
  8. ↑ Lindquist S (1986). "The heat-shock response". Annu. Rev. Biochem. 55: 1151–1191. doi:10.1146/annurev.bi.55.070186.005443. PMID   2427013.
  9. ↑ Mitchell J (2008). "Transcription factories are nuclear sub compartments that remain in the absence of transcription". Genes Dev . 22 (1): 20–25. doi:10.1101/gad.454008. PMC   2151011 . PMID   18172162.
  10. ↑ Becker M (2002). "Dynamic behaviour of transcription factors on a natural promoter in living cells". EMBO Rep . 3 (12): 1188–1194. doi:10.1093/embo-reports/kvf244. PMC   1308318 . PMID   12446572.
  11. ↑ Gavrilov A (2010). "Mapping of the nuclear matrix-bound chromatin hubs by a new M3C experimental procedure". Nucleic Acids Res . 38 (22): 8051–8060. doi:10.1093/nar/gkq712. PMC   3001081 . PMID   20705651.
  12. ↑ Pederson T (2000). "Half a century of "the nuclear matrix"". Mol. Biol. Cell . 11 (3): 799–805. doi:10.1091/mbc.11.3.799. PMC   14811 . PMID   10712500.
  13. ↑ Schoenfelder S (2010). "Preferential associations between co-regulated genes reveal a transcriptional interactive in erythroid cells". Nat. Genet. 42 (1): 53–61. doi:10.1038/ng.496. PMC   3237402 . PMID   20010836.
  14. ↑ Cook PR (2010). "A model for all genomes: the role of transcription factories". J. Mol. Biol. 395 (1): 1–10. doi:10.1016/j.jmb.2009.10.031. PMID   19852969.
  15. ↑ Cowell I (2012). "Model for MLL translocations in therapy-related leukaemia involving topoisomerase IIbeta-mediated DNA strand breaks and gene proximity". Proc. Natl. Acad. Sci. U.S.A. 109 (23): 8989–8994. Bibcode:2012PNAS..109.8989C. doi: 10.1073/pnas.1204406109 . PMC   3384169 . PMID   22615413.
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