Transcriptional burst kinetics are linked to short term transcriptional memory

Transcriptional bursting is thought to be a stochastic process that allows the dynamic regulation of most genes. The random telegraph model assumes the existence of two states, ON and OFF. However recent studies indicate the presence of additional ON states, suggesting that bursting kinetics and their regulation can be quite complex. We have developed a system to study transcriptional bursting in the context of p53 biology using the endogenous p21 gene tagged with MS2 in human cells. Remarkably, we find that transcriptional bursts from the p21 gene contain multiple ON and OFF states that can be regulated by elevation of p53 levels. Distinct ON states are characterized by differences in burst duration, classified as Short and Long, with long bursts associated with higher Pol II initiation rates. Importantly, the different ON states display memory effects that allow us to predict the likelihood of properties of future bursting events. Long bursting events result in faster re-activation, longer subsequent bursts and higher transcriptional output in the future compared to short bursts. Bursting memory persists up to 2 hours suggesting a stable inheritable promoter architecture. Bursting memory at the p21 gene is the strongest under basal conditions and is suppressed by UV and inhibition of H3K9me1/2, which also increase transcriptional noise. Stabilization of p53 by Nutlin-3a partially reverses suppression of bursting memory suggesting that higher p53 levels may be a key in enforcing memory under conditions of cellular stress. Overall our data uncover a new found bursting property termed Short-Term Transcriptional Memory (STTM) that has the potential to fine-tune transcriptional output at the p21 gene.

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A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory

Molecular and Cellular Biology ◽

10.1128/mcb.00372-16 ◽

2016 ◽

Vol 37 (4) ◽

Cited By ~ 2

Author(s):

Aimee Iberg-Badeaux ◽

Samuel Collombet ◽

Benoit Laurent ◽

Chris van Oevelen ◽

Kuo-Kai Chin ◽

...

Keyword(s):

Transcription Factor ◽

Rna Polymerase Ii ◽

Target Genes ◽

Short Term Memory ◽

Epigenetic Mechanism ◽

Short Term ◽

Term Memory ◽

Pol Ii ◽

Transcriptional Memory

ABSTRACT Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in postmitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM) and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli. We find that a pulse of transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) induces LTTM on a subset of target genes that survives nine cell divisions. The chromatin landscape at genes that acquire LTTM is more repressed than at those genes that do not exhibit memory, akin to a latent state. We show through chromatin immunoprecipitation (ChIP) and chemical inhibitor studies that RNA polymerase II (Pol II) elongation is important for establishing memory in this model but that Pol II itself is not retained as part of the memory mechanism. More generally, our work reveals that a transcription factor involved in lineage specification can induce LTTM and that failure to rerepress chromatin is one epigenetic mechanism underlying transcriptional memory.

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PhoQ is an unsaturated fatty acid receptor that fine-tunes Salmonella pathogenic traits

Science Signaling ◽

10.1126/scisignal.aaz3334 ◽

2020 ◽

Vol 13 (628) ◽

pp. eaaz3334 ◽

Cited By ~ 1

Author(s):

María Ayelén Carabajal ◽

Gastón Viarengo ◽

Lucía Yim ◽

Adriana Martínez-Sanguiné ◽

Javier F. Mariscotti ◽

...

Keyword(s):

Unsaturated Fatty Acids ◽

Wild Type ◽

Short Term ◽

Geometrical Isomers ◽

Gut Colonization ◽

Spatiotemporal Expression ◽

Systemic Dissemination ◽

Periplasmic Domain ◽

Fine Tune ◽

Autokinase Activity

The Salmonella enterica PhoP/PhoQ two-component signaling system coordinates the spatiotemporal expression of key virulence factors that confer pathogenic traits. Through biochemical and structural analyses, we found that the sensor histidine kinase PhoQ acted as a receptor for long-chain unsaturated fatty acids (LCUFAs), which induced a conformational change in the periplasmic domain of the PhoQ protein. This resulted in the repression of PhoQ autokinase activity, leading to inhibition of the expression of PhoP/PhoQ-dependent genes. Recognition of the LCUFA linoleic acid (LA) by PhoQ was not stereospecific because positional and geometrical isomers of LA equally inhibited PhoQ autophosphorylation, which was conserved in multiple S. enterica serovars. Because orally acquired Salmonella encounters conjugated LA (CLA), a product of the metabolic conversion of LA by microbiota, in the human intestine, we tested how short-term oral administration of CLA affected gut colonization and systemic dissemination in a mouse model of Salmonella-induced colitis. Compared to untreated mice, CLA-treated mice showed increased gut colonization by wild-type Salmonella, as well as increased dissemination to the spleen. In contrast, the inability of the phoP strain to disseminate systemically remained unchanged by CLA treatment. Together, our results reveal that, by inhibiting PhoQ, environmental LCUFAs fine-tune the fate of Salmonella during infection. These findings may aid in the design of new anti-Salmonella therapies.

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Short-term acclimation of the photosynthetic electron transfer chain to changing light: a mathematical model

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0223 ◽

2014 ◽

Vol 369 (1640) ◽

pp. 20130223 ◽

Cited By ~ 36

Author(s):

Oliver Ebenhöh ◽

Geoffrey Fucile ◽

Giovanni Finazzi ◽

Jean-David Rochaix ◽

Michel Goldschmidt-Clermont

Keyword(s):

Mathematical Model ◽

Molecular Mechanisms ◽

Photosynthetic Apparatus ◽

Light Acclimation ◽

State Transitions ◽

Photochemical Quenching ◽

Short Term ◽

Dynamic Regulation ◽

Relative Contribution ◽

Photosynthetic Eukaryotes

Photosynthetic eukaryotes house two photosystems with distinct light absorption spectra. Natural fluctuations in light quality and quantity can lead to unbalanced or excess excitation, compromising photosynthetic efficiency and causing photodamage. Consequently, these organisms have acquired several distinct adaptive mechanisms, collectively referred to as non-photochemical quenching (NPQ) of chlorophyll fluorescence, which modulates the organization and function of the photosynthetic apparatus. The ability to monitor NPQ processes fluorometrically has led to substantial progress in elucidating the underlying molecular mechanisms. However, the relative contribution of distinct NPQ mechanisms to variable light conditions in different photosynthetic eukaryotes remains unclear. Here, we present a mathematical model of the dynamic regulation of eukaryotic photosynthesis using ordinary differential equations. We demonstrate that, for Chlamydomonas , our model recapitulates the basic fluorescence features of short-term light acclimation known as state transitions and discuss how the model can be iteratively refined by comparison with physiological experiments to further our understanding of light acclimation in different species.

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Dynamic regulation of transcription factors by nucleosome remodeling

eLife ◽

10.7554/elife.06249 ◽

2015 ◽

Vol 4 ◽

Cited By ~ 57

Author(s):

Ming Li ◽

Arjan Hada ◽

Payel Sen ◽

Lola Olufemi ◽

Michael A Hall ◽

...

Keyword(s):

Direct Evidence ◽

Nucleosome Positioning ◽

Regulation Of Transcription ◽

Dynamic Regulation ◽

Major Barrier ◽

Nucleosome Remodeling ◽

Chromatin Remodelers ◽

Promoter Architecture ◽

Sequence Elements ◽

Dna Template

The chromatin landscape and promoter architecture are dominated by the interplay of nucleosome and transcription factor (TF) binding to crucial DNA sequence elements. However, it remains unclear whether nucleosomes mobilized by chromatin remodelers can influence TFs that are already present on the DNA template. In this study, we investigated the interplay between nucleosome remodeling, by either yeast ISW1a or SWI/SNF, and a bound TF. We found that a TF serves as a major barrier to ISW1a remodeling, and acts as a boundary for nucleosome repositioning. In contrast, SWI/SNF was able to slide a nucleosome past a TF, with concurrent eviction of the TF from the DNA, and the TF did not significantly impact the nucleosome positioning. Our results provide direct evidence for a novel mechanism for both nucleosome positioning regulation by bound TFs and TF regulation via dynamic repositioning of nucleosomes.

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Separation of presynaptic Cav2 and Cav1 channel function in synaptic vesicle exo- and endocytosis by the membrane anchored Ca2+ pump PMCA

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2106621118 ◽

2021 ◽

Vol 118 (28) ◽

pp. e2106621118

Author(s):

Niklas Krick ◽

Stefanie Ryglewski ◽

Aylin Pichler ◽

Arthur Bikbaev ◽

Torsten Götz ◽

...

Keyword(s):

Synaptic Vesicle ◽

Neurotransmitter Release ◽

Calcium Currents ◽

Short Term ◽

Triggered Release ◽

Presynaptic Terminals ◽

Dynamic Regulation ◽

Short Term Plasticity ◽

Separate Control ◽

Active Zones

Synaptic vesicle (SV) release, recycling, and plastic changes of release probability co-occur side by side within nerve terminals and rely on local Ca2+ signals with different temporal and spatial profiles. The mechanisms that guarantee separate regulation of these vital presynaptic functions during action potential (AP)–triggered presynaptic Ca2+ entry remain unclear. Combining Drosophila genetics with electrophysiology and imaging reveals the localization of two different voltage-gated calcium channels at the presynaptic terminals of glutamatergic neuromuscular synapses (the Drosophila Cav2 homolog, Dmca1A or cacophony, and the Cav1 homolog, Dmca1D) but with spatial and functional separation. Cav2 within active zones is required for AP-triggered neurotransmitter release. By contrast, Cav1 localizes predominantly around active zones and contributes substantially to AP-evoked Ca2+ influx but has a small impact on release. Instead, L-type calcium currents through Cav1 fine-tune short-term plasticity and facilitate SV recycling. Separate control of SV exo- and endocytosis by AP-triggered presynaptic Ca2+ influx through different channels demands efficient measures to protect the neurotransmitter release machinery against Cav1-mediated Ca2+ influx. We show that the plasma membrane Ca2+ ATPase (PMCA) resides in between active zones and isolates Cav2-triggered release from Cav1-mediated dynamic regulation of recycling and short-term plasticity, two processes which Cav2 may also contribute to. As L-type Cav1 channels also localize next to PQ-type Cav2 channels within axon terminals of some central mammalian synapses, we propose that Cav2, Cav1, and PMCA act as a conserved functional triad that enables separate control of SV release and recycling rates in presynaptic terminals.

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Differential ATAC-seq and ChIP-seq peak detection using ROTS

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab059 ◽

2021 ◽

Vol 3 (3) ◽

Author(s):

Thomas Faux ◽

Kalle T Rytkönen ◽

Mehrad Mahmoudian ◽

Niklas Paulin ◽

Sini Junttila ◽

...

Keyword(s):

Chromatin Modification ◽

Synthetic Data ◽

Peak Detection ◽

Detection Methods ◽

Test Statistics ◽

Chromatin States ◽

One Step ◽

Transcriptional Output ◽

Fine Tune ◽

Peak Caller

Abstract Changes in cellular chromatin states fine-tune transcriptional output and ultimately lead to phenotypic changes. Here we propose a novel application of our reproducibility-optimized test statistics (ROTS) to detect differential chromatin states (ATAC-seq) or differential chromatin modification states (ChIP-seq) between conditions. We compare the performance of ROTS to existing and widely used methods for ATAC-seq and ChIP-seq data using both synthetic and real datasets. Our results show that ROTS outperformed other commonly used methods when analyzing ATAC-seq data. ROTS also displayed the most accurate detection of small differences when modeling with synthetic data. We observed that two-step methods that require the use of a separate peak caller often more accurately called enrichment borders, whereas one-step methods without a separate peak calling step were more versatile in calling sub-peaks. The top ranked differential regions detected by the methods had marked correlation with transcriptional differences of the closest genes. Overall, our study provides evidence that ROTS is a useful addition to the available differential peak detection methods to study chromatin and performs especially well when applied to study differential chromatin states in ATAC-seq data.

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Short-term in vitro glutamine restriction differentially impacts the chromosomal stability of transformed and non-transformed cells

Mutagenesis ◽

10.1093/mutage/geaa026 ◽

2020 ◽

Author(s):

Ling Yan ◽

Ziru Zhao ◽

Xiaoran Wang ◽

Ting Lyu ◽

Jianfei Li ◽

...

Keyword(s):

Chromosomal Instability ◽

Building Blocks ◽

Transformed Cells ◽

Short Term ◽

Cellular Energy ◽

Chromosomal Stability ◽

Huvec Cells ◽

Fine Tune ◽

A375 Cells

Abstract Glutamine (Gln) is a non-essential amino acid central for generating building blocks and cellular energy in tumours and rapidly proliferating non-transformed cells. However, the influence of Gln on regulating chromosomal stability of transformed and non-transformed cells remain poorly understand. We hypothesised that Gln is required for maintaining a homeostatic level of chromosomal stability. To this end, transformed cells HeLa and A375 and non-transformed cells NCM460 and HUVEC cells were intervened with varying concentrations of Gln (10, 1, 0.1 and 0.01 mM), with or without cisplatin (0.1 µg/ml), for 24 h. The cytokinesis-block micronucleus (MN) assay was used to determine chromosomal instability (CIN), the extent of which is reflected by the frequency of MN, nucleoplasmic bridge (NPB) and nuclear bud (NB). We demonstrated an unexpected decrease in the spontaneous rate of MN, but not NPB and NB, after Gln restriction in HeLa and A375 cells. Gln restriction reduced cisplatin-induced MN, but not NPB and NB, in HeLa and A375 cells. We further revealed that Gln restriction suppressed the proliferation of HeLa cells with high CIN induced by nocodazole, partially explaining why Gln restriction decreased the frequency of spontaneous and cisplatin-induced MN in transformed cells. In contrast, Gln restriction increased MN and NB, but not NPB, in NCM460 cells. In HUVEC cells, Gln restriction increased MN, NPB and NB. Meanwhile, Gln restriction sensitised NCM460 cells to cisplatin-induced genotoxicity. A similar but more pronounced pattern was observed in HUVEC cells. Collectively, these results suggest that the in vitro influences of Gln metabolism on CIN depend on cellular contexts: Transformed cells require high Gln to fine tune their CIN in an optimal rate to maximise genomic heterogeneity and fitness, whereas non-transformed cells need high Gln to prevent CIN.

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Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells

Nature Communications ◽

10.1038/s41467-021-21591-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Costanza Borrelli ◽

Tomas Valenta ◽

Kristina Handler ◽

Karelia Vélez ◽

Alessandra Gurtner ◽

...

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Intestinal Epithelial ◽

Epithelial Stem Cells ◽

Unfolded Protein ◽

Modulation Of Gene Expression ◽

Protein Response ◽

Transcriptional Output ◽

Fine Tune ◽

Stem Cell Pool

AbstractThe homeostasis of the gut epithelium relies upon continuous renewal and proliferation of crypt-resident intestinal epithelial stem cells (IESCs). Wnt/β-catenin signaling is required for IESC maintenance, however, it remains unclear how this pathway selectively governs the identity and proliferative decisions of IESCs. Here, we took advantage of knock-in mice harboring transgenic β-catenin alleles with mutations that specifically impair the recruitment of N- or C-terminal transcriptional co-factors. We show that C-terminally-recruited transcriptional co-factors of β-catenin act as all-or-nothing regulators of Wnt-target gene expression. Blocking their interactions with β-catenin rapidly induces loss of IESCs and intestinal homeostasis. Conversely, N-terminally recruited co-factors fine-tune β-catenin’s transcriptional output to ensure proper self-renewal and proliferative behaviour of IESCs. Impairment of N-terminal interactions triggers transient hyperproliferation of IESCs, eventually resulting in exhaustion of the self-renewing stem cell pool. IESC mis-differentiation, accompanied by unfolded protein response stress and immune infiltration, results in a process resembling aberrant “villisation” of intestinal crypts. Our data suggest that IESC-specific Wnt/β-catenin output requires selective modulation of gene expression by transcriptional co-factors.

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Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance

10.1101/649285 ◽

2019 ◽

Author(s):

Anton J.M. Larsson ◽

Björn Reinius ◽

Tina Jacob ◽

Tim Dalessandri ◽

Gert-Jan Hendriks ◽

...

Keyword(s):

Allelic Imbalance ◽

Expression Patterns ◽

Monoallelic Expression ◽

Biological Noise ◽

Burst Frequency ◽

Large Numbers ◽

Single Cell Rna Sequencing ◽

Transcriptional Bursting ◽

Burst Kinetics ◽

Shed Light

AbstractTranscriptional bursts render substantial biological noise in cellular transcriptomes. Here, we investigated the theoretical extent of monoallelic expression resulting from transcriptional bursting and how it compared to the amounts of monoallelic expression of autosomal genes observed in single-cell RNA-sequencing (scRNA-seq) data. We found that transcriptional bursting can explain frequent observations of autosomal monoallelic gene expression in cells. Importantly, the burst frequency largely determined the fraction of cells with monoallelic expression, whereas both burst frequency and size contributed to allelic imbalance. Allelic observations deviate from the expected when analysed across heterogeneous groups of cells, suggesting that allelic modelling can provide an unbiased assessment of heterogeneity within cells. Finally, large numbers of cells are required for analyses of allelic imbalance to avoid confounding observations from transcriptional bursting. Altogether, our results shed light on the implications of transcriptional burst kinetics on allelic expression patterns and phenotypic variation between cells.

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Short-Term Regulation of BOD Upsets in an Estuary

Journal of Dynamic Systems Measurement and Control ◽

10.1115/1.3426980 ◽

1976 ◽

Vol 98 (1) ◽

pp. 30-31 ◽

Cited By ~ 1

Author(s):

R. K. Jain ◽

M. M. Denn

Keyword(s):

Water Quality ◽

Optimal Control ◽

Control Theory ◽

Optimal Control Theory ◽

Local Dynamic ◽

Short Term ◽

Dynamic Regulation

Local dynamic regulation of BOD upsets in an estuary is considered using optimal control theory. It is concluded that such regulation is not a feasible means of maintaining water quality.

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