Transcription factories
Encyclopedia
In genetics
, a transcription factory is an active gene
transcription
unit that is clustered in a discrete site within the eukaryotic
nucleus
. Such sites can be visualized by allowing engaged polymerase
s to extend their transcripts with tagged precursor
s (Br-UTP or Br-U) and immuno-labeling the tagged nascent RNA
. Transcription factories can also be detected using fluorescence
in situ hybridization or marked by antibodies
directed against RNA polymerase
s. There are ~10,000 factories in the nucleoplasm
of a HeLa
cell, which reflect ~8,000 RNA polymerase II holoenzyme
factories and ~2,000 RNA polymerase III
factories. As most active transcription units are associated with only one polymerase, one estimate suggests a polymerase II factory contains on average ~8 polymerase holoenzymes. The nucleolus
is often considered to be a large RNA polymerase I
factory, although this structure is the site of other activities than just rRNA transcription.
factories in the nucleoplasm
of a HeLa cell, but only 100-300 RNAP II foci per nucleus in erythroid cells like many other tissue
types. The number of transcription factories in tissues is far more restricted than indicated by previous estimates from cultured cells. As an active transcription unit is usually associated with only one Pol II holoenzyme, a polymerase II factory may contain on average ~8 holoenzymes. Colocalization of transcribed genes has not been observed when using cultured fibroblast
-like cells. Differentiated or committed tissue types have a limited number of available transcription sites. Estimates show that erythroid cells express at least 4,000 genes, so many genes are obliged to seek out and share the same factory.
An expressed gene
is preferentially located outside of its chromosome territory, but a closely linked, inactive gene is located inside.
Genetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
, a transcription factory is an active gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
unit that is clustered in a discrete site within the eukaryotic
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
nucleus
Cell nucleus
In cell biology, the nucleus is a membrane-enclosed organelle found in eukaryotic cells. It contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these...
. Such sites can be visualized by allowing engaged polymerase
Polymerase
A polymerase is an enzyme whose central function is associated with polymers of nucleic acids such as RNA and DNA.The primary function of a polymerase is the polymerization of new DNA or RNA against an existing DNA or RNA template in the processes of replication and transcription...
s to extend their transcripts with tagged precursor
Precursor (chemistry)
In chemistry, a precursor is a compound that participates in the chemical reaction that produces another compound. In biochemistry, the term "precursor" is used more specifically to refer to a chemical compound preceding another in a metabolic pathway....
s (Br-UTP or Br-U) and immuno-labeling the tagged nascent RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
. Transcription factories can also be detected using fluorescence
Fluorescence
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation of a different wavelength. It is a form of luminescence. In most cases, emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation...
in situ hybridization or marked by antibodies
Antibody
An antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
directed against RNA polymerase
RNA polymerase
RNA polymerase is an enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. RNA polymerase enzymes are essential to life and are found in all organisms and many viruses...
s. There are ~10,000 factories in the nucleoplasm
Nucleoplasm
Similar to the cytoplasm of a cell, the nucleus contains nucleoplasm or karyoplasm. The nucleoplasm is one of the types of protoplasm, and it is enveloped by the nuclear membrane or nuclear envelope. The nucleoplasm is a highly viscous liquid that surrounds the chromosomes and nucleoli...
of a HeLa
HeLa
A HeLa cell is a cell type in an immortal cell line used in scientific research. It is the oldest and most commonly used human cell line. The line was derived from cervical cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who eventually died of her cancer on October 4, 1951...
cell, which reflect ~8,000 RNA polymerase II holoenzyme
RNA polymerase II holoenzyme
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...
factories and ~2,000 RNA polymerase III
RNA polymerase III
RNA polymerase III transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs. The genes transcribed by RNA Pol III fall in the category of "housekeeping" genes whose expression is required in all cell types and most environmental conditions...
factories. As most active transcription units are associated with only one polymerase, one estimate suggests a polymerase II factory contains on average ~8 polymerase holoenzymes. The nucleolus
Nucleolus
The nucleolus is a non-membrane bound structure composed of proteins and nucleic acids found within the nucleus. Ribosomal RNA is transcribed and assembled within the nucleolus...
is often considered to be a large RNA polymerase I
RNA polymerase I
RNA polymerase I is, in eukaryotes, the enzyme that only transcribes ribosomal RNA , a type of RNA that accounts for over 50% of the total RNA synthesized in a cell....
factory, although this structure is the site of other activities than just rRNA transcription.
RNA polymerase II holoenzyme transcription factory
There are ~8,000 RNA polymerase II holoenzymeRNA polymerase II holoenzyme
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...
factories in the nucleoplasm
Nucleoplasm
Similar to the cytoplasm of a cell, the nucleus contains nucleoplasm or karyoplasm. The nucleoplasm is one of the types of protoplasm, and it is enveloped by the nuclear membrane or nuclear envelope. The nucleoplasm is a highly viscous liquid that surrounds the chromosomes and nucleoli...
of a HeLa cell, but only 100-300 RNAP II foci per nucleus in erythroid cells like many other tissue
Tissue (biology)
Tissue is a cellular organizational level intermediate between cells and a complete organism. A tissue is an ensemble of cells, not necessarily identical, but from the same origin, that together carry out a specific function. These are called tissues because of their identical functioning...
types. The number of transcription factories in tissues is far more restricted than indicated by previous estimates from cultured cells. As an active transcription unit is usually associated with only one Pol II holoenzyme, a polymerase II factory may contain on average ~8 holoenzymes. Colocalization of transcribed genes has not been observed when using cultured fibroblast
Fibroblast
A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework for animal tissues, and plays a critical role in wound healing...
-like cells. Differentiated or committed tissue types have a limited number of available transcription sites. Estimates show that erythroid cells express at least 4,000 genes, so many genes are obliged to seek out and share the same factory.
Gene intranuclear position
The intranuclear position of many genes is correlated with their activity state. During transcription in vivo, distal active genes are dynamically organized into shared nuclear subcompartments and colocalize to the same transcription factory at high frequencies. Movement into or out of these factories results in activation (On) or abatement (Off) of transcription, rather than by recruiting and assembling a transcription complex. Usually, genes migrate to preassembled factories for transcription.An expressed gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
is preferentially located outside of its chromosome territory, but a closely linked, inactive gene is located inside.