Discontinuous transcription

Smirnov, Evgeny; Hornáček, Matúš; Vacı́k, Tomáš; Cmarko, Dušan; Raška, Ivan

doi:10.1080/19491034.2017.1419112

Cited by 8 publications

(12 citation statements)

References 118 publications

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“…After this procedure, the total transcription signal in the nucleoplasm showed symptoms of fluctuations with two discernible, though not very distinct, peaks (Fig 6). Evaluating these results, we have to keep in mind that various nucleoplasmic genes in the same cell display a wide range of transcriptional kinetic behavior (reviewed in Smirnov et al [1]). [4, 10, 55, 56] Moreover, some of these genes are expressed in typical bursts with long periods of silence, during which they cannot be detected by FU incorporation.…”

Section: Discussionmentioning

confidence: 99%

“…Numerous studies show that genes in all kinds of organisms, from prokaryotes to mammals, can be transcribed in short bursts or pulses alternated by periods of silence (reviewed in Smirnov et al [1]) The probability of such mode of expression was suggested long ago;[2] now it seems that the discontinuous transcription is a common feature of the gene expression, at least in mammalian cells. [3–12] The periodical switches of the promoter between the active and “refractory” states may be crucial in the efficient regulation of the gene expression.…”

Section: Introductionmentioning

confidence: 99%

“…The discontinuous character of transcription has been detected by various methods (reviewed in Smirnov et al [1]) The number of transcripts produced in a certain (sufficiently short) period of time may be determined with high precision by single molecule RNA fluorescence in situ hybridisation (smFISH). [19–21] The results of such quantification alone provide indirect, but valuable information for modelling the expression kinetics in a cell population or tissue, when the studied gene is supposed to be transcriptionally active in all the cells.…”

Section: Introductionmentioning

confidence: 99%

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Discontinuous transcription of ribosomal DNA in human cells

Smirnov

Trošan

Cabral

et al. 2019

Preprint

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21Numerous studies show that various genes in all kinds of organisms are transcribed 22 discontinuously, i.e. in short bursts or pulses with periods of inactivity between them. But it 2 23 remains unclear whether ribosomal DNA (rDNA), represented by multiple copies in every cell, is 24 also expressed in such manner. In this work, we synchronized the pol I activity in the populations 25 of tumour derived as well as normal human cells by cold block and release. Then using special 26 software for analysis of the microscopic images, we measured the intensity of transcription signal 27 revealed by incorporated 5-fluorouridine (FU) in the nucleoli at different time points after the 28 release. We found that the ribosomal genes in the human cells are transcribed discontinuously with 29 periods ranging from 45 min to 75 min. Our data indicate that the dynamics of rDNA transcription 30 follows the undulating pattern, in which the bursts are alternated by periods of rare transcription 31 events. 32 33 Keywords: nucleoli, rDNA, FC/DFC units, discontinuous transcription, bursting 34 35 Introduction 36 Numerous studies show that genes in all kinds of organisms, from prokaryotes to mammals, 37 can be transcribed in short bursts or pulses alternated by periods of silence (reviewed in Smirnov 38 et al. [1]) The probability of such mode of expression was suggested long ago;[2] now it seems that 39 the discontinuous transcription is a common feature of the gene expression, at least in mammalian 40 cells.[3-12] The periodical switches of the promoter between the active and "refractory" states may 41 be crucial in the efficient regulation of the gene expression.[13-17] General considerations suggest 42 even more significant role of the phenomenon in the dynamic organization of the cell, since the 43 pulsing mode of one process is likely to be a cause and a consequence of pulsing in other processes.44 Thus, RNA processing, which is closely linked to the RNA synthesis, seems to be discontinuous.[9] 45 A spontaneous heterogeneity of gene expression occasioned by transcriptional fluctuations may 3 46 influence cell behaviour in changing environmental conditions and in the course of 47 differentiation.[18] 48 The discontinuous character of transcription has been detected by various methods 49 (reviewed in Smirnov et al. [1]) The number of transcripts produced in a certain (sufficiently short) 50 period of time may be determined with high precision by single molecule RNA fluorescence in situ 51 hybridisation (smFISH).[19-21] The results of such quantification alone provide indirect, but 52 valuable information for modelling the expression kinetics in a cell population or tissue, when the 53 studied gene is supposed to be transcriptionally active in all the cells. Methods based on the allele-54 sensitive single-cell RNA sequencing also allow to reveal and characterize the transcription 55 bursting.[22] To monitor gene expression in real time, cells are transfected with constructs 56 providing a fluorescent signal that corresponds to the ex...

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Discontinuous transcription of ribosomal DNA in human cells

Smirnov

Trošan

Cabral

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Numerous studies show that genes in all kinds of organisms, from prokaryotes to mammals, can be transcribed in short bursts or pulses alternated by periods of silence (reviewed in Smirnov et al [1]) The probability of such mode of expression was suggested long ago; [2] now it seems that the discontinuous transcription is a common feature of the gene expression, at least in mammalian cells. [3][4][5][6][7][8][9][10][11][12] The periodical switches of the promoter between the active and "refractory" states may be crucial in the efficient regulation of the gene expression.…”

Section: Introductionmentioning

confidence: 99%

“…[9] A spontaneous heterogeneity of gene expression occasioned by transcriptional fluctuations may influence cell behaviour in changing environmental conditions and in the course of differentiation. [18] The discontinuous character of transcription has been detected by various methods (reviewed in Smirnov et al [1]) The number of transcripts produced in a certain (sufficiently short) period of time may be determined with high precision by single molecule RNA fluorescence in situ hybridisation (smFISH). [19][20][21] The results of such quantification alone provide indirect, but valuable information for modelling the expression kinetics in a cell population or tissue, when the studied gene is supposed to be transcriptionally active in all the cells.…”

Section: Introductionmentioning

confidence: 99%

Discontinuous transcription of ribosomal DNA in human cells

et al. 2020

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Numerous studies show that various genes in all kinds of organisms are transcribed discontinuously, i.e. in short bursts or pulses with periods of inactivity between them. But it remains unclear whether ribosomal DNA (rDNA), represented by multiple copies in every cell, is also expressed in such manner. In this work, we synchronized the pol I activity in the populations of tumour derived as well as normal human cells by cold block and release. Our experiments with 5-fluorouridine (FU) and BrUTP confirmed that the nucleolar transcription can be efficiently and reversibly arrested at +4˚C. Then using special software for analysis of the microscopic images, we measured the intensity of transcription signal (incorporated FU) in the nucleoli at different time points after the release. We found that the ribosomal genes in the human cells are transcribed discontinuously with periods ranging from 45 min to 75 min. Our data indicate that the dynamics of rDNA transcription follows the undulating pattern, in which the bursts are alternated by periods of rare transcription events.

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Frequency modulation of a bacterial quorum sensing response

et al. 2022

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In quorum sensing, bacteria secrete or release small molecules into the environment that, once they reach a certain threshold, trigger a behavioural change in the population. As the concentration of these so-called autoinducers is supposed to reflect population density, they were originally assumed to be continuously produced by all cells in a population. However, here we show that in the α-proteobacterium Sinorhizobium meliloti expression of the autoinducer synthase gene is realized in asynchronous stochastic pulses that result from scarcity and, presumably, low binding affinity of the key activator. Physiological cues modulate pulse frequency, and pulse frequency in turn modulates the velocity with which autoinducer levels in the environment reach the threshold to trigger the quorum sensing response. We therefore propose that frequency-modulated pulsing in S. meliloti represents the molecular mechanism for a collective decision-making process in which each cell’s physiological state and need for behavioural adaptation is encoded in the pulse frequency with which it expresses the autoinducer synthase gene; the pulse frequencies of all members of the population are then integrated in the common pool of autoinducers, and only once this vote crosses the threshold, the response behaviour is initiated.

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Discontinuous transcription

Cited by 8 publications

References 118 publications

Discontinuous transcription of ribosomal DNA in human cells

Discontinuous transcription of ribosomal DNA in human cells

Discontinuous transcription of ribosomal DNA in human cells

Frequency modulation of a bacterial quorum sensing response

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