Transcriptional bursting
Encyclopedia
Transcriptional bursting, also known as transcriptional pulsing, is a fundamental property of genes from bacteria to humans. Transcription
of genes, the process which transforms the stable code written in DNA
into the mobile RNA
message can occur in "bursts" or "pulses". This phenomenon has recently come to light with the advent of new technologies, such as MS2 tagging
, to detect RNA production in single cells, allowing precise measurements of RNA number, or RNA appearance at the gene. Other, more widespread techniques, such as Northern Blotting, Microarrays, RT-PCR and RNA-Seq
, measure bulk RNA levels from homogenous population extracts. These techniques lose dynamic information from individual cells, and give the impression transcription is a continuous smooth process. The reality is that transcription is irregular, with strong periods of activity, interspersed by long periods of inactivity. Averaged over millions of cells, this appears continuous. But at the individual cell level, there is considerable variability, and for most genes, very little activity at any one time.
Bursting may result from the stochastic nature of biochemical events superimposed upon a 2 or more step fluctuation. In its most simple form, the gene can exist in 2 states, one where activity is negligible and one where there is a certain probability of activation. Only in the second state does transcription readily occur. Whilst the nuclear and signaling landscapes of complex eukaryotic nuclei are likely to favour more than two simple states- for example, there are over twenty post-translational modifications of nucleosomes known, this simple two step model perhaps provides a reasonable intellectual framework for understanding the changing probabilities affecting transcription. It seems likely that some rudimentary eukaryotes have genes which do not show bursting. The genes are always in the permissive state, with a simple probability describing the numbers of RNAs generated.
What do the repressive and permissive states represent? An attractive idea is that the repressed state is a closed chromatin
conformation whilst the permissive state is an open one. Another hypothesis is that the fluctuations reflect transition between bound pre-initiation complexes (permissive) and dissociated ones (restrictive). Bursts may also result from bursty signalling, cell cycle effects or movement of chromatin to and from transcription factories
.
The bursting phenomenon, as opposed to simple probabilistic models of transcription, can account for the high variability (see transcriptional noise
) in gene expression occurring between cells in isogenic populations. This variability in turn can have tremendous consequences on cell behaviour, and must be mitigated or integrated. In certain contexts, such as the survival of microbes in rapidly changing stressful environments, or several types of scattered differentiation, the variability may be essential. Variability also impacts upon the effectiveness of clinical treatment, with resistance of bacteria to antibiotics demonstrably caused by non-genetic differences. Variability in gene expression may also contribute to resistance of sub-populations of cancer cells to chemotherapy.
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...
of genes, the process which transforms the stable code written in DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
into the mobile RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
message can occur in "bursts" or "pulses". This phenomenon has recently come to light with the advent of new technologies, such as MS2 tagging
MS2 tagging
Techniques based upon the interaction of the MS2 bacteriophage coat protein with a stem loop structure from the phage genome. Used for biochemical purification of RNA-protein complexes and partnered to GFP for detection of RNA in living cells...
, to detect RNA production in single cells, allowing precise measurements of RNA number, or RNA appearance at the gene. Other, more widespread techniques, such as Northern Blotting, Microarrays, RT-PCR and RNA-Seq
RNA-Seq
RNA-seq, also called "Whole Transcriptome Shotgun Sequencing" and dubbed "a revolutionary tool for transcriptomics", refers to the use of high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content, a technique that is quickly becoming...
, measure bulk RNA levels from homogenous population extracts. These techniques lose dynamic information from individual cells, and give the impression transcription is a continuous smooth process. The reality is that transcription is irregular, with strong periods of activity, interspersed by long periods of inactivity. Averaged over millions of cells, this appears continuous. But at the individual cell level, there is considerable variability, and for most genes, very little activity at any one time.
Bursting may result from the stochastic nature of biochemical events superimposed upon a 2 or more step fluctuation. In its most simple form, the gene can exist in 2 states, one where activity is negligible and one where there is a certain probability of activation. Only in the second state does transcription readily occur. Whilst the nuclear and signaling landscapes of complex eukaryotic nuclei are likely to favour more than two simple states- for example, there are over twenty post-translational modifications of nucleosomes known, this simple two step model perhaps provides a reasonable intellectual framework for understanding the changing probabilities affecting transcription. It seems likely that some rudimentary eukaryotes have genes which do not show bursting. The genes are always in the permissive state, with a simple probability describing the numbers of RNAs generated.
What do the repressive and permissive states represent? An attractive idea is that the repressed state is a closed chromatin
Chromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
conformation whilst the permissive state is an open one. Another hypothesis is that the fluctuations reflect transition between bound pre-initiation complexes (permissive) and dissociated ones (restrictive). Bursts may also result from bursty signalling, cell cycle effects or movement of chromatin to and from transcription factories
Transcription factories
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 polymerases to extend their transcripts with tagged precursors and immuno-labeling the tagged nascent RNA...
.
The bursting phenomenon, as opposed to simple probabilistic models of transcription, can account for the high variability (see transcriptional noise
Transcriptional noise
A primary cause of the variability in gene expression occurring between cells in isogenic populations . A major source of transcriptional noise is likely to be transcriptional bursting although other sources of heterogeneity, such as unequal separation of cell contents at mitosis are also likely...
) in gene expression occurring between cells in isogenic populations. This variability in turn can have tremendous consequences on cell behaviour, and must be mitigated or integrated. In certain contexts, such as the survival of microbes in rapidly changing stressful environments, or several types of scattered differentiation, the variability may be essential. Variability also impacts upon the effectiveness of clinical treatment, with resistance of bacteria to antibiotics demonstrably caused by non-genetic differences. Variability in gene expression may also contribute to resistance of sub-populations of cancer cells to chemotherapy.