scholarly journals Genomic decoding of neuronal depolarization by stimulus-specific NPAS4 heterodimers

2019 ◽  
Author(s):  
G. Stefano Brigidi ◽  
Michael G. B. Hayes ◽  
Andrea L. Hartzell ◽  
Lorane Texari ◽  
Pei-Ann Lin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Action Potential ◽  
Regulate Gene Expression ◽  
Synaptic Inputs ◽  
Different Types ◽  
Genomic Regulation ◽  
External Stimuli ◽  
Regulate Gene

SUMMARYCells regulate gene expression in response to salient external stimuli. In neurons, depolarization leads to the expression of inducible transcription factors (ITFs) that direct subsequent gene regulation. Depolarization encodes both a neuron’s action potential (AP) output and synaptic inputs, via excitatory postsynaptic potentials (EPSPs). However, it is unclear if different types of depolarizing signals can be transformed by an ITF into distinct modes of genomic regulation. Here, we show that APs and EPSPs in the murine hippocampus trigger two spatially segregated and molecularly distinct mechanisms that lead to the expression of the ITF NPAS4. These two pathways culminate in the assembly of unique, stimulus-specific NPAS4 heterodimers that exhibit distinctive DNA binding patterns. Thus, NPAS4 independently communicates increases in a neuron’s spiking output and synaptic inputs to the nucleus, enabling gene regulation to be tailored to the type of depolarizing activity experienced by a neuron.

scholarly journals Arabidopsis heat shock transcription factor HSFA7b positively mediates salt stress tolerance by binding to an E-box-like motif to regulate gene expression

2019 ◽  
Vol 70 (19) ◽  
pp. 5355-5374 ◽  
Author(s):  
Dandan Zang ◽  
Jingxin Wang ◽  
Xin Zhang ◽  
Zhujun Liu ◽  
Yucheng Wang
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Heat Shock ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Ion Homeostasis ◽  
Cellulose Synthase ◽  
Regulate Gene Expression ◽  
E Box ◽  
Regulate Gene

Abstract Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

scholarly journals Transcript degradation and codon usage regulate gene expression in a lytic phage

2019 ◽  
Author(s):  
Benjamin R. Jack ◽  
Daniel R. Boutz ◽  
Matthew L. Paff ◽  
Bartram L. Smith ◽  
Claus O. Wilke
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Computational Models ◽  
Regulatory Elements ◽  
Mechanistic Modeling ◽  
Host Cells ◽  
Bacteriophage T7 ◽  
Lytic Phage ◽  
Regulate Gene Expression ◽  
Regulate Gene

AbstractMany viral genomes are small, containing only single- or double-digit numbers of genes and relatively few regulatory elements. Yet viruses successfully execute complex regulatory programs as they take over their host cells. Here, we propose that some viruses regulate gene expression via a carefully balanced interplay between transcription, translation, and transcript degradation. As our model system, we employ bacteriophage T7, whose genome of approximately 60 genes is well annotated and for which there is a long history of computational models of gene regulation. We expand upon prior modeling work by implementing a stochastic gene expression simulator that tracks individual transcripts, polymerases, ribosomes, and RNases participating in the transcription, translation, and transcript-degradation processes occurring during a T7 infection. By combining this detailed mechanistic modeling of a phage infection with high throughput gene expression measurements of several strains of bacteriophage T7, evolved and engineered, we can show that both the dynamic interplay between transcription and transcript degradation, and between these two processes and translation, appear to be critical components of T7 gene regulation. Our results point to a generic gene regulation strategy that may have evolved in many other viruses. Further, our results suggest that detailed mechanistic modeling may uncover the biological mechanisms at work in both evolved and engineered virus variants.

scholarly journals Sensing, Signaling, and Secretion: A Review and Analysis of Systems for Regulating Host Interaction in Wolbachia

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 813 ◽  
Author(s):  
Amelia R. I. Lindsey
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Molecular Mechanisms ◽  
Host Cells ◽  
Promising Candidate ◽  
Regulate Gene Expression ◽  
Host Interaction ◽  
Female Germline ◽  
Intracellular Infections ◽  
Regulate Gene

Wolbachia (Anaplasmataceae) is an endosymbiont of arthropods and nematodes that resides within host cells and is well known for manipulating host biology to facilitate transmission via the female germline. The effects Wolbachia has on host physiology, combined with reproductive manipulations, make this bacterium a promising candidate for use in biological- and vector-control. While it is becoming increasingly clear that Wolbachia’s effects on host biology are numerous and vary according to the host and the environment, we know very little about the molecular mechanisms behind Wolbachia’s interactions with its host. Here, I analyze 29 Wolbachia genomes for the presence of systems that are likely central to the ability of Wolbachia to respond to and interface with its host, including proteins for sensing, signaling, gene regulation, and secretion. Second, I review conditions under which Wolbachia alters gene expression in response to changes in its environment and discuss other instances where we might hypothesize Wolbachia to regulate gene expression. Findings will direct mechanistic investigations into gene regulation and host-interaction that will deepen our understanding of intracellular infections and enhance applied management efforts that leverage Wolbachia.

Glucose induces increases in levels of the transcriptional repressor Id2 via the hexosamine pathway

2006 ◽  
Vol 290 (4) ◽  
pp. E599-E606 ◽  
Author(s):  
Line Mariann Grønning ◽  
Rommaneeya Tingsabadh ◽  
Kristine Hardy ◽  
Knut Thomas Dalen ◽  
Parmjit S. Jat ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Transcriptional Repressor ◽  
Hormone Sensitive Lipase ◽  
Alternative Mechanism ◽  
Regulate Gene Expression ◽  
Glucose Levels ◽  
Hexosamine Pathway ◽  
Effect Of Glucose ◽  
Regulate Gene

Changes in glucose levels are known to directly alter gene expression. A number of previous studies have found that these effects are in part mediated by modulating the levels and the activity of transcription factors. We have investigated an alternative mechanism by which glucose might regulate gene expression by modulating levels of a transcriptional repressor. We have focused on Id2, which is a protein that indirectly regulates gene expression by sequestering certain transcription factors and preventing them from forming functional dimers. Id2 targets include the class A basic helix-loop-helix transcription factors and the sterol regulatory element-binding protein (SREBP)-1. We demonstrate that increases in glucose levels cause a rapid increase in levels of Id2 in J774.2 macrophages, and a number of lines of evidence indicate that this is via the hexosamine pathway because 1) the effect of glucose requires glutamine; 2) the effect of glucose is mimicked by low levels of glucosamine; 3) the effect of glucose is inhibited by azaserine, an inhibitor of glutamine:fructose-6-phosphate amidotransferase (GFAT); and 4) adenoviral mediated overexpression of GFAT increases levels of Id2. We go on to show that increases in Id2 can have functional effects on metabolic genes, because Id2 blocked the SREBP-1-induced induction of hormone-sensitive lipase (HSL) promoter activity, whereas Id2 alone does not modulate activity of the HSL promoter. In summary, these studies define a new mechanism by which glucose uses the hexosamine pathway to regulate gene expression by increasing levels of a transcriptional repressor.

scholarly journals Challenges of Decoding Transcription Factor Dynamics in Terms of Gene Regulation

Cells ◽  
2018 ◽  
Vol 7 (9) ◽  
pp. 132 ◽  
Author(s):  
Erik Martin ◽  
Myong-Hee Sung
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Cell Biology ◽  
Extrinsic Factors ◽  
Regulate Gene Expression ◽  
Technological Advances ◽  
Experimental Approaches ◽  
Intrinsic And Extrinsic Factors ◽  
Regulate Gene

Technological advances are continually improving our ability to obtain more accurate views about the inner workings of biological systems. One such rapidly evolving area is single cell biology, and in particular gene expression and its regulation by transcription factors in response to intrinsic and extrinsic factors. Regarding the study of transcription factors, we discuss some of the promises and pitfalls associated with investigating how individual cells regulate gene expression through modulation of transcription factor activities. Specifically, we discuss four leading experimental approaches, the data that can be obtained from each, and important considerations that investigators should be aware of when drawing conclusions from such data.

scholarly journals Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14

2015 ◽  
Vol 43 (3) ◽  
pp. 1469-1484 ◽  
Author(s):  
Yong-Qiang Ning ◽  
Ze-Yang Ma ◽  
Huan-Wei Huang ◽  
Huixian Mo ◽  
Ting-ting Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Flowering Time ◽  
Histone Demethylase ◽  
Regulate Gene Expression ◽  
Nac Transcription Factors ◽  
Regulate Gene

scholarly journals Transcription Factor ANAC074 Binds to NRS1, NRS2, or MybSt1 Element in Addition to the NACRS to Regulate Gene Expression

2018 ◽  
Vol 19 (10) ◽  
pp. 3271
Author(s):  
Lin He ◽  
Jingyu Xu ◽  
Yucheng Wang ◽  
Kejun Yang
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Biological Processes ◽  
Regulate Gene Expression ◽  
Cis Element ◽  
Stress Responsive Genes ◽  
Regulate Gene ◽  
Gus Assays

NAC (NAM, ATAF1/2, and CUC2) transcription factors play important roles in many biological processes, and mainly bind to the NACRS with core sequences “CACG” or “CATGTG” to regulate gene expression. However, whether NAC proteins can bind to other motifs without these core sequences remains unknown. In this study, we employed a Transcription Factor-Centered Yeast one Hybrid (TF-Centered Y1H) screen to study the motifs recognized by ANAC074. In addition to the NACRS core cis-element, we identified that ANAC074 could bind to MybSt1, NRS1, and NRS2. Y1H and GUS assays showed that ANAC074 could bind the promoters of ethylene responsive genes and stress responsive genes via the NRS1, NRS2, or MybSt1 element. ChIP study further confirmed that the bindings of ANAC074 to MybSt1, NRS1, and NRS2 actually occurred in Arabidopsis. Furthermore, ten NAC proteins from different NAC subfamilies in Arabidopsis thaliana were selected and confirmed to bind to the MybSt1, NRS1, and NRS2 motifs, indicating that they are recognized commonly by NACs. These findings will help us to further reveal the functions of NAC proteins.

scholarly journals Transcript degradation and codon usage regulate gene expression in a lytic phage†

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Benjamin R Jack ◽  
Daniel R Boutz ◽  
Matthew L Paff ◽  
Bartram L Smith ◽  
Claus O Wilke
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Computational Models ◽  
Regulatory Elements ◽  
Mechanistic Modeling ◽  
Host Cells ◽  
Bacteriophage T7 ◽  
Lytic Phage ◽  
Regulate Gene Expression ◽  
Regulate Gene

Abstract Many viral genomes are small, containing only single- or double-digit numbers of genes and relatively few regulatory elements. Yet viruses successfully execute complex regulatory programs as they take over their host cells. Here, we propose that some viruses regulate gene expression via a carefully balanced interplay between transcription, translation, and transcript degradation. As our model system, we employ bacteriophage T7, whose genome of approximately sixty genes is well annotated and for which there is a long history of computational models of gene regulation. We expand upon prior modeling work by implementing a stochastic gene expression simulator that tracks individual transcripts, polymerases, ribosomes, and ribonucleases participating in the transcription, translation, and transcript-degradation processes occurring during a T7 infection. By combining this detailed mechanistic modeling of a phage infection with high-throughput gene expression measurements of several strains of bacteriophage T7, evolved and engineered, we can show that both the dynamic interplay between transcription and transcript degradation, and between these two processes and translation, appear to be critical components of T7 gene regulation. Our results point to targeted degradation as a generic gene regulation strategy that may have evolved in many other viruses. Further, our results suggest that detailed mechanistic modeling may uncover the biological mechanisms at work in both evolved and engineered virus variants.

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