scholarly journals Orthogonal tuning of gene expression noise using CRISPR–Cas

2020 ◽  
Author(s):  
Fan Wu ◽  
Jiyoung Shim ◽  
Ting Gong ◽  
Cheemeng Tan
Keyword(s):  
Gene Expression ◽  
Reporter Gene ◽  
Transcription Initiation ◽  
Mrna Translation ◽  
Genetic Circuit ◽  
Control Of Gene Expression ◽  
Gene Expression Noise ◽  
Guide Rnas ◽  
Expression Noise ◽  
Genetic Components

Abstract The control of gene expression noise is important for improving drug treatment and the performance of synthetic biological systems. Previous work has tuned gene expression noise by changing the rate of transcription initiation, mRNA degradation, and mRNA translation. However, these methods are invasive: they require changes to the target genetic components. Here, we create an orthogonal system based on CRISPR-dCas9 to tune gene expression noise. Specifically, we modulate the gene expression noise of a reporter gene in Escherichia coli by incorporating CRISPR activation and repression (CRISPRar) simultaneously in a single cell. The CRISPRar uses a single dCas9 that recognizes two different single guide RNAs (sgRNA). We build a library of sgRNA variants with different expression activation and repression strengths. We find that expression noise and mean of a reporter gene can be tuned independently by CRISPRar. Our results suggest that the expression noise is tuned by the competition between two sgRNAs that modulate the binding of RNA polymerase to promoters. The CRISPRar may change how we tune expression noise at the genomic level. Our work has broad impacts on the study of gene functions, phenotypical heterogeneity, and genetic circuit control.

scholarly journals Translational control of gene expression noise and its relationship to ageing in yeast

FEBS Journal ◽  
2020 ◽  
Author(s):  
Tailise Carolina de Souza‐Guerreiro ◽  
Xiang Meng ◽  
Estelle Dacheux ◽  
Helena Firczuk ◽  
John McCarthy
Keyword(s):  
Gene Expression ◽  
Translational Control ◽  
Control Of Gene Expression ◽  
Gene Expression Noise ◽  
Expression Noise

scholarly journals Observation and Control of Gene Expression Noise: Barrier Crossing Analogies Between Drug Resistance and Metastasis

2020 ◽  
Vol 11 ◽  
Author(s):  
Michael Tyler Guinn ◽  
Yiming Wan ◽  
Sarah Levovitz ◽  
Dongbo Yang ◽  
Marsha R. Rosner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Resistance ◽  
Barrier Crossing ◽  
Control Of Gene Expression ◽  
Gene Expression Noise ◽  
Expression Noise ◽  
Noise Barrier ◽  
And Control

Reduction in gene expression noise by targeted increase in accessibility at gene loci

2021 ◽  
Vol 118 (42) ◽  
pp. e2018640118
Author(s):  
LaTasha C. R. Fraser ◽  
Ryan J. Dikdan ◽  
Supravat Dey ◽  
Abhyudai Singh ◽  
Sanjay Tyagi
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Molecule ◽  
Single Cells ◽  
Global Changes ◽  
Messenger Rnas ◽  
Histone Acetyl Transferase ◽  
Gene Expression Noise ◽  
Expression Noise ◽  
Eukaryotic Genes

Many eukaryotic genes are expressed in randomly initiated bursts that are punctuated by periods of quiescence. Here, we show that the intermittent access of the promoters to transcription factors through relatively impervious chromatin contributes to this “noisy” transcription. We tethered a nuclease-deficient Cas9 fused to a histone acetyl transferase at the promoters of two endogenous genes in HeLa cells. An assay for transposase-accessible chromatin using sequencing showed that the activity of the histone acetyl transferase altered the chromatin architecture locally without introducing global changes in the nucleus and rendered the targeted promoters constitutively accessible. We measured the gene expression variability from the gene loci by performing single-molecule fluorescence in situ hybridization against mature messenger RNAs (mRNAs) and by imaging nascent mRNA molecules present at active gene loci in single cells. Because of the increased accessibility of the promoter to transcription factors, the transcription from two genes became less noisy, even when the average levels of expression did not change. In addition to providing evidence for chromatin accessibility as a determinant of the noise in gene expression, our study offers a mechanism for controlling gene expression noise which is otherwise unavoidable.

scholarly journals Enhancement of gene expression noise due to nonspecific transcription factor binding

2019 ◽  
Author(s):  
Supravat Dey ◽  
Mohammad Soltani ◽  
Abhyudai Singh
Keyword(s):  
Gene Expression ◽  
Stochastic Dynamics ◽  
Gene Expression Noise ◽  
Downstream Target ◽  
High Affinity ◽  
Expression Noise ◽  
Degradation Rates ◽  
Poisson Limit ◽  
Random Fluctuations

ABSTRACTThe genome contains several high-affinity non-functional binding sites for transcription factors (TFs) creating a hidden and unexplored layer of gene regulation. We investigate the role of such “decoy sites” in controlling noise (random fluctuations) in the level of a TF that is synthesized in stochastic bursts. Prior studies have assumed that decoy-bound TFs are protected from degradation, and in this case decoys function to buffer noise. Relaxing this assumption to consider arbitrary degradation rates for both bound/unbound TF states, we find rich noise behaviors. For low-affinity decoys, noise in the level of unbound TF always monotonically decreases to the Poisson limit with increasing decoy numbers. In contrast, for high affinity decoys, noise levels first increase with increasing decoy numbers, before decreasing back to the Poisson limit. Interestingly, while protection of bound TFs from degradation slows the time-scale of fluctuations in the unbound TF levels, decay of bounds TFs leads to faster fluctuations and smaller noise propagation to downstream target proteins. In summary, our analysis reveals stochastic dynamics emerging from nonspecific binding of TFs, and highlight the dual role of decoys as attenuators or amplifiers of gene expression noise depending on their binding affinity and stability of the bound TF.

scholarly journals Single cell 3’UTR analysis identifies changes in alternative polyadenylation throughout neuronal differentiation and in autism

2020 ◽  
Author(s):  
Manuel Göpferich ◽  
Nikhil Oommen George ◽  
Ana Domingo Muelas ◽  
Alex Bizyn ◽  
Rosa Pascual ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Neural Stem Cells ◽  
Single Cell ◽  
Neuronal Differentiation ◽  
Mrna Translation ◽  
Autism Spectrum ◽  
Adult Brain ◽  
Control Of Gene Expression ◽  
Risk Genes

SUMMARYAutism spectrum disorder (ASD) is a neurodevelopmental disease affecting social behavior. Many of the high-confident ASD risk genes relate to mRNA translation. Specifically, many of these genes are involved in regulation of gene expression for subcellular compartmentalization of proteins1. Cis-regulatory motifs that often localize to 3’- and 5’-untranslated regions (UTRs) offer an additional path for posttranscriptional control of gene expression. Alternative cleavage and polyadenylation (APA) affect 3’UTR length thereby influencing the presence or absence of regulatory elements. However, APA has not yet been addressed in the context of neurodevelopmental disorders. Here we used single cell 3’end sequencing to examine changes in 3’UTRs along the differentiation from neural stem cells (NSCs) to neuroblasts within the adult brain. We identified many APA events in genes involved in neurodevelopment, many of them being high confidence ASD risk genes. Further, analysis of 3’UTR lengths in single cells from ASD and healthy individuals detected longer 3’UTRs in ASD patients. Motif analysis of modulated 3’UTRs in the mouse adult neurogenic lineage and ASD-patients revealed enrichment of the cytoplasmic and polyadenylation element (CPE). This motif is bound by CPE binding protein 4 (CPEB4). In human and mouse data sets we observed co-regulation of CPEB4 and the CPEB-binding synaptic adhesion molecule amyloid beta precursor-like protein 1 (APLP1). We show that mice deficient in APLP1 show aberrant regulation of APA, decreased number of neural stem cells, and autistic-like traits. Our findings indicate that APA is used for control of gene expression along neuronal differentiation and is altered in ASD patients.

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