scholarly journals Resolving noise-control conflict by gene duplication

2019 ◽  
Author(s):  
Michal Chapal ◽  
Sefi Mintzer ◽  
Sagie Brodsky ◽  
Miri Carmi ◽  
Naama Barkai

AbstractGene duplication promotes adaptive evolution in two principle ways: allowing one duplicate to evolve a new function and resolving adaptive conflicts by splitting ancestral functions between the duplicates. In an apparent departure from both scenarios, low-expressing transcription factor (TF) duplicates commonly regulate similar sets of genes and act in overlapping conditions. To examine for possible benefits of such apparently redundant duplicates, we examined the budding yeast duplicated stress regulators Msn2 and Msn4. We show that Msn2,4 indeed function as one unit, inducing the same set of target genes in overlapping conditions, yet this two-factor composition allows its expression to be both environmental-responsive and with low-noise, thereby resolving an adaptive conflict that inherently limits expression of single genes. Our study exemplified a new model for evolution by gene duplication whereby duplicates provide adaptive benefit through cooperation, rather than functional divergence: attaining two-factor dynamics with beneficial properties that cannot be achieved by a single gene.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 277-277 ◽  
Author(s):  
Camila O. dos Santos ◽  
Duonan Yu ◽  
Julio Amigo ◽  
Eugene Kandros ◽  
Eric R Valentine ◽  
...  

Abstract MicroRNAs (miRNAs) regulate tissue development by destabilizing cellular mRNAs or blocking their translation. We previously described two conserved erythroid miRNAs, miR144 and miR451, which are encoded by a single gene locus that is regulated by the essential hematopoietic transcription factor GATA-1. Morpholino-induced inhibition of miR451 impairs erythropoiesis in zebrafish. To gain further insight into miR144/451, we deleted the locus in mice. Mutant animals are born at the normal Mendelian ratio and exhibit no obvious structural defects. At baseline, loss of miR 144/451 causes mild anemia and reticulocytosis with moderate abnormalities in erythrocyte morphology. However, compared to littermate controls, miR144/451 null animals exhibit 33% greater depletion of circulating erythrocytes after phenylhydrazine-induced oxidant stress. At baseline, the mutant erythrocytes exhibit increased levels of reactive oxidant species, exquisite sensitivity to hydrogen peroxide induced hemolysis, and 50% reduced catalase activity compared to controls. Catalase is a downstream effector in an erythroid anti-oxidant program regulated by the forkhead transcription factor Foxo3a. In the mutant erythroblasts, mRNAs encoding catalase and glutathione peroxidase 1, another Foxo3a-regulated anti-oxidant, were reduced 2 and 1.7 fold, respectively. Messenger RNAs encoding several additional Foxo3a target genes, including Cdkn1b and Btg1 were also significantly reduced. Quantitative confocal fluorescence microscopy demonstrated that although total cellular Foxo3a protein was similar in wt and miR144/451 null erythroblasts, nuclear Foxo3a was reduced by 40% in miR144/451 null erythroblasts with a corresponding relocation of the protein to the cytoplasm. To explain this, we showed that miR451 (but not miR144) directly blocks translation of Ywhaz mRNA encoding 14-3-3 zeta, a cytoplasmic protein that sequesters Foxo3a away from the nucleus. In agreement, 14-3-3 zeta protein is upregulated by approximately 2-fold higher levels in miR144/451 null erythroblasts. Together, our findings suggest a model in which miR451 represses 14-3-3 zeta expression, which releases Foxo3a for translocation to the nucleus, thereby activating an anti-oxidant program of gene expression. This illustrates a new miRNA-regulated pathway through which erythroid cells are protected against oxidant stress.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.


2021 ◽  
Vol 22 (15) ◽  
pp. 8193
Author(s):  
Daniel Pérez-Cremades ◽  
Ana B. Paes ◽  
Xavier Vidal-Gómez ◽  
Ana Mompeón ◽  
Carlos Hermenegildo ◽  
...  

Background/Aims: Estrogen has been reported to have beneficial effects on vascular biology through direct actions on endothelium. Together with transcription factors, miRNAs are the major drivers of gene expression and signaling networks. The objective of this study was to identify a comprehensive regulatory network (miRNA-transcription factor-downstream genes) that controls the transcriptomic changes observed in endothelial cells exposed to estradiol. Methods: miRNA/mRNA interactions were assembled using our previous microarray data of human umbilical vein endothelial cells (HUVEC) treated with 17β-estradiol (E2) (1 nmol/L, 24 h). miRNA–mRNA pairings and their associated canonical pathways were determined using Ingenuity Pathway Analysis software. Transcription factors were identified among the miRNA-regulated genes. Transcription factor downstream target genes were predicted by consensus transcription factor binding sites in the promoter region of E2-regulated genes by using JASPAR and TRANSFAC tools in Enrichr software. Results: miRNA–target pairings were filtered by using differentially expressed miRNAs and mRNAs characterized by a regulatory relationship according to miRNA target prediction databases. The analysis identified 588 miRNA–target interactions between 102 miRNAs and 588 targets. Specifically, 63 upregulated miRNAs interacted with 295 downregulated targets, while 39 downregulated miRNAs were paired with 293 upregulated mRNA targets. Functional characterization of miRNA/mRNA association analysis highlighted hypoxia signaling, integrin, ephrin receptor signaling and regulation of actin-based motility by Rho among the canonical pathways regulated by E2 in HUVEC. Transcription factors and downstream genes analysis revealed eight networks, including those mediated by JUN and REPIN1, which are associated with cadherin binding and cell adhesion molecule binding pathways. Conclusion: This study identifies regulatory networks obtained by integrative microarray analysis and provides additional insights into the way estradiol could regulate endothelial function in human endothelial cells.


Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 466
Author(s):  
Weiwei Du ◽  
Yarui Xi ◽  
Kiichi Harada ◽  
Yumei Zhang ◽  
Keiko Nagashima ◽  
...  

Research shows that the intensity impact factors of wood, such as late timber ratio, volume density and the intensity of itself, correlate with the width of wood annual rings. Therefore, extracting wood annual ring information from wood images is helpful for evaluating wood quality. During the past few years, many researchers have conducted defect detection by studying the information of wood images. However, there are few in-depth studies on the statistics and calculation of wood annual ring information. This study proposes a new model combining the Total Variation (TV) algorithm and the improved Hough transform to accurately measure the wood annual ring information. The TV algorithm is used to suppress image noise, and the Hough transform is for detecting the center of the wood image. Moreover, the edges of wood annual rings are extracted, and the statistical ring information is calculated. The experimental results show that the new model has good denoising capability, clearly extract the edges of wood annual rings and calculate the related parameters from the indoor wood images of the processed logs and the unprocessed low-noise logs.


2021 ◽  
Vol 12 (3) ◽  
Author(s):  
Vishwanie S. Budhram-Mahadeo ◽  
Matthew R. Solomons ◽  
Eeshan A. O. Mahadeo-Heads

AbstractMetabolic and cardiovascular diseases are highly prevalent and chronic conditions that are closely linked by complex molecular and pathological changes. Such adverse effects often arise from changes in the expression of genes that control essential cellular functions, but the factors that drive such effects are not fully understood. Since tissue-specific transcription factors control the expression of multiple genes, which affect cell fate under different conditions, then identifying such regulators can provide valuable insight into the molecular basis of such diseases. This review explores emerging evidence that supports novel and important roles for the POU4F2/Brn-3b transcription factor (TF) in controlling cellular genes that regulate cardiometabolic function. Brn-3b is expressed in insulin-responsive metabolic tissues (e.g. skeletal muscle and adipose tissue) and is important for normal function because constitutive Brn-3b-knockout (KO) mice develop profound metabolic dysfunction (hyperglycaemia; insulin resistance). Brn-3b is highly expressed in the developing hearts, with lower levels in adult hearts. However, Brn-3b is re-expressed in adult cardiomyocytes following haemodynamic stress or injury and is necessary for adaptive cardiac responses, particularly in male hearts, because male Brn-3b KO mice develop adverse remodelling and reduced cardiac function. As a TF, Brn-3b regulates the expression of multiple target genes, including GLUT4, GSK3β, sonic hedgehog (SHH), cyclin D1 and CDK4, which have known functions in controlling metabolic processes but also participate in cardiac responses to stress or injury. Therefore, loss of Brn-3b and the resultant alterations in the expression of such genes could potentially provide the link between metabolic dysfunctions with adverse cardiovascular responses, which is seen in Brn-3b KO mutants. Since the loss of Brn-3b is associated with obesity, type II diabetes (T2DM) and altered cardiac responses to stress, this regulator may provide a new and important link for understanding how pathological changes arise in such endemic diseases.


2020 ◽  
Author(s):  
Seungwoo Cha ◽  
Chang Pyo Hong ◽  
Hyun Ah Kang ◽  
Ji-Sook Hahn

Abstract Gcr1, an important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1U and Gcr1S, produced from un-spliced and spliced transcripts, respectively. In this study, by generating strains expressing only Gcr1U or Gcr1S using the CRISPR/Cas9 system, we elucidate differential activation mechanisms of these two isoforms. The Gcr1U monomer forms an active complex with its coactivator Gcr2 homodimer, whereas Gcr1S acts as a homodimer without Gcr2. The USS domain, 55 residues at the N-terminus existing only in Gcr1U, inhibits dimerization of Gcr1U and even acts in trans to inhibit Gcr1S dimerization. The Gcr1S monomer inhibits the metabolic switch from fermentation to respiration by directly binding to the ALD4 promoter, which can be restored by overexpression of the ALD4 gene, encoding a mitochondrial aldehyde dehydrogenase required for ethanol utilization. Gcr1U and Gcr1S regulate almost the same target genes, but show unique activities depending on growth phase, suggesting that these isoforms play differential roles through separate activation mechanisms depending on environmental conditions.


2014 ◽  
Vol 966 ◽  
pp. 83-92 ◽  
Author(s):  
Zanariah Hashim ◽  
Shao Thing Teoh ◽  
Takeshi Bamba ◽  
Eiichiro Fukusaki

2004 ◽  
Vol 101 (28) ◽  
pp. 10458-10463 ◽  
Author(s):  
A. W. Bruce ◽  
I. J. Donaldson ◽  
I. C. Wood ◽  
S. A. Yerbury ◽  
M. I. Sadowski ◽  
...  

Genomics ◽  
2017 ◽  
Vol 109 (2) ◽  
pp. 75-82 ◽  
Author(s):  
Mirana Ramialison ◽  
Ashley J. Waardenberg ◽  
Nicole Schonrock ◽  
Tram Doan ◽  
Danielle de Jong ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document