scholarly journals Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change In Arabidopsis thaliana

2019 ◽  
Author(s):  
Barney Potter ◽  
Michael J. Song ◽  
Jeff J. Doyle ◽  
Jeremy E. Coate
Keyword(s):  
Arabidopsis Thaliana ◽  
Gene Product ◽  
Gene Dosage ◽  
Gene Families ◽  
Gene Copy ◽  
Haploid Induction ◽  
Transcriptional Responses ◽  
Individual Gene ◽  
Dosage Balance ◽  
Transcriptome Size

AbstractThe Gene Balance Hypothesis postulates that there is selection on gene copy number (gene dosage) to preserve stoichiometric balance among interacting proteins. This presupposes that gene product abundance is governed by gene dosage, and that the way in which gene product abundance is governed by gene dosage is consistent for all genes in a dosage-sensitive network or complex. Gene dosage responses, however, have rarely been quantified and the available data suggest that they are highly variable. We sequenced the transcriptomes of two synthetic autopolyploid accessions of Arabidopsis thaliana and their diploid progenitors, as well as one natural tetraploid and its synthetic diploid produced via haploid induction, to estimate transcriptome size and gene dosage responses immediately following ploidy change. We demonstrate that overall transcriptome size does not exhibit a simple doubling in response to genome doubling, and that individual gene dosage responses are highly variable in all three accessions, indicating that expression is not strictly coupled with gene dosage. Nonetheless, putatively dosage-sensitive gene groups (GO terms, metabolic networks, gene families, and predicted interacting protein pairs) exhibit both smaller and more coordinated dosage responses than do putatively dosage-insensitive gene groups, suggesting that constraints on dosage balance operate immediately following whole genome duplication. This supports the hypothesis that duplicate gene retention patterns are shaped by selection to preserve dosage balance.

scholarly journals Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos

2021 ◽  
Vol 376 (1833) ◽  
pp. 20200102 ◽  
Author(s):  
Michail Rovatsos ◽  
Tony Gamble ◽  
Stuart V. Nielsen ◽  
Arthur Georges ◽  
Tariq Ezaz ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Gene Dosage ◽  
Regulatory Mechanisms ◽  
Gene Copy ◽  
Male And Female ◽  
Gene Dose ◽  
Female Heterogamety ◽  
Dosage Balance ◽  
Male Heterogamety

Differentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here, we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32–72 Ma, one species in particular, Burton's legless lizard ( Lialis burtonis ), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

scholarly journals Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number

2021 ◽  
Author(s):  
Francesca B Lopez ◽  
Antoine Fort ◽  
Luca Tadini ◽  
Aline V Probst ◽  
Marcus McHale ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Genome Editing ◽  
Dosage Compensation ◽  
Copy Number ◽  
Gene Dosage ◽  
Rrna Genes ◽  
Gene Copy ◽  
Transcript Levels ◽  
Rdna Copy ◽  
Rdna Copy Number

Abstract The 45S rRNA genes (rDNA) are amongst the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as ‘back-up’ copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte we reduced 45S rDNA copy number to a plateau of ∼10%. Two independent lines had rDNA copy numbers reduced by up to 90% at the T7 generation, named Low Copy Number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates and steady-state levels remained the same as wild type plants. Gene dosage compensation of rRNA transcript levels was associated with reduction of silencing histone marks at rDNA loci and altered Nucleolar Organiser Region 2 organization. While overall genome integrity of LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines. Transcriptome analysis of LCN seedlings identified several shared dysregulated genes and pathways in both independent lines. Cas9 genome editing of rRNA repeats to generate LCN lines provides a powerful technique to elucidate rDNA dosage compensation mechanisms and impacts of low rDNA copy number on genome stability, development, and cellular processes.

Do male and female heterogamety really differ in expression regulation? Lack of global dosage balance in pygopodid geckos

2020 ◽  
Author(s):  
Michail Rovatsos ◽  
Tony Gamble ◽  
Stuart V. Nielsen ◽  
Arthur Georges ◽  
Tariq Ezaz ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Gene Dosage ◽  
Regulatory Mechanisms ◽  
Gene Copy ◽  
Male And Female ◽  
Gene Dose ◽  
Female Heterogamety ◽  
Dosage Balance ◽  
Male Heterogamety

AbstractDifferentiation of sex chromosomes is thought to have evolved with cessation of recombination and subsequent loss of genes from the degenerated partner (Y and W) of sex chromosomes, which in turn leads to imbalance of gene dosage between sexes. Based on work with traditional model species, theory suggests that unequal gene copy numbers lead to the evolution of mechanisms to counter this imbalance. Dosage compensation, or at least achieving dosage balance in expression of sex-linked genes between sexes, has largely been documented in lineages with male heterogamety (XX/XY sex determination), while ZZ/ZW systems are assumed to be usually associated with the lack of chromosome-wide gene dose regulatory mechanisms. Here we document that although the pygopodid geckos evolved male heterogamety with a degenerated Y chromosome 32-72 million years ago, one species in particular, Burton’s legless lizard (Lialis burtonis), does not possess dosage balance in the expression of genes in its X-specific region. We summarize studies on gene dose regulatory mechanisms in animals and conclude that there is in them no significant dichotomy between male and female heterogamety. We speculate that gene dose regulatory mechanisms are likely to be related to the general mechanisms of sex determination instead of type of heterogamety.

scholarly journals PATACSDB - The database of polyA translational attenuators in coding sequences

2015 ◽  
Author(s):  
Malgorzata Habich ◽  
Sergej Djuranovic ◽  
Pawel Szczesny
Keyword(s):  
Gene Dosage ◽  
Interesting Case ◽  
Minimal Length ◽  
Regulatory Mechanisms ◽  
Coding Sequences ◽  
Translation Apparatus ◽  
Recent Addition ◽  
Dosage Balance ◽  
The Stability ◽  
Eukaryotic Genomes

Recent addition to the repertoire of gene expression regulatory mechanisms are polyadenylate (polyA) tracks encoding for poly-lysine runs in protein sequences. Such tracks stall translation apparatus and induce frameshifting independently of the effects of charged nascent poly-lysine sequence on the ribosome exit channel. As such they substantially influence the stability of mRNA and amount of protein produced from a given transcript. Single base changes in these regions are enough to exert a measurable response on both protein and mRNA abundance, and makes each of these sequences potentially interesting case studies for effects of synonymous mutation, gene dosage balance and natural frameshifting. Here we present the PATACSDB, a resource that contain comprehensive list of polyA tracks from over 250 eukaryotic genomes. Our data is based on Ensembl genomic database of coding sequences and filtered with algorithm of 12A-1 which selects sequences of polyA tracks with a minimal length of 12 A's allowing for one mismatched base. The PATACSDB database is accesible at: http://sysbio.ibb.waw.pl/patacsdb. Source code is available for download from GitHub repository at http://github.com/habich/PATACSDB, including the scripts to recreate the database from the scratch on user's own computer.

scholarly journals On the Mode of Gene-Dosage Compensation in Drosophila

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 729-736
Author(s):  
Irina Arkhipova ◽  
Jingjing Li ◽  
Matthew Meselson
Keyword(s):  
X Chromosome ◽  
Dosage Compensation ◽  
Gene Dosage ◽  
Gene Activity ◽  
Gene Copy ◽  
Drosophila Pseudoobscura ◽  
A Site ◽  
Reduced Activity ◽  
Per Gene

A procedure is described for determining the mode and magnitude of gene-dosage compensation of transformed genes. It involves measurement of the ratio of the activity of a gene inserted at X-linked sites to the activity of the same gene inserted at autosomal sites. Applying the procedure to the Drosophila pseudoobscura Hsp82 gene inserted at ectopic sites in D. melanogaster and taking gene activity as proportional to the amount of transcript per gene copy, we conclude that (1) in both adults and larvae the gene is not compensated at autosomal sites or at a site in β-heterochromatin at the base of the X chromosome and is fully compensated at euchromatic X-chromosomal sites; (2) inappropriate normalization is responsible for a claim that the gene is compensated at autosomal sites; and (3) the observed compensation operates mainly or entirely by heightened activity of X-linked genes in males, rather than by reduced activity in females.

Abstract 229: Increased Ace Gene Dosage Reduces Ace2 Activity in Diabetic Mice Kidney: Involvement of Ace/ace2 Balance on the Development of Diabetic Nephropathy

Hypertension ◽  
2013 ◽  
Vol 62 (suppl_1) ◽  
Author(s):  
Nadia S Bertoncello ◽  
Roseli P Moreira ◽  
Rodrigo Yokota ◽  
Rodolfo M Rosa ◽  
Danielle Y Arita ◽  
...  
Keyword(s):  
Body Weight ◽  
Diabetic Nephropathy ◽  
Gene Dosage ◽  
Weight Ratio ◽  
Gene Copy ◽  
Diabetic Mice ◽  
Body Weight Ratio ◽  
Ace Gene ◽  
Kidney Involvement ◽  
Ace Activity

The mechanisms underlying the link between high constitutive levels of ACE and diabetic nephropathy has not been completely understood, but an imbalance between angiotensin I (ACE) and II (ACE2) converting enzymes homeostasis has been described in diabetic kidney disease. The aim of this study was to evaluate ACE/ACE2 homeostasis in kidney from diabetic mice presenting increased dosage of ACE gene. Male mice (3 months old) genetically engineered to harbor one or three copies of the ACE gene were made diabetic (streptozotocin - STZ, 50 mg/Kg) and randomly assigned into: 1-copy control (1CC), 1-copy diabetic (1CD), 3-copy control (3CC) and 3-copy diabetic. At the end of experimental period body weight was evaluated and kidney was excised. Kidney-to-body weight ratio and ACE and ACE 2 activities were determined using specific substrates (ZPhe-HL and 7-Mca-APK(Dnp), respectively) (Two way ANOVA + Tukey test; P<0.05). Diabetes increased blood glucose (1CD : 436 ± 25 vs. 1CC: 90 ± 2; 3CD: 556 ± 6 vs. 3CC: 112 ± 4 mg/dL) and kidney-to-body weight ratio (1CD: 7.5 ± 0.2 vs. 1CC: 5.8 ± 0.2; 3CD: 7.8 ± 0.1 vs. 3CC: 5.8 ± 0.1 mg/g) with no influence of ACE genotype. As expected, renal ACE activity was directly related to ACE gene copy number in control group (3CC: 9.4 ± 2.11 vs. 1CC:5.6 ± 0.9 mU/mg protein). Renal ACE activity was decreased in diabetic groups (1CD: 3.6 ± 0.2 vs. 1CC: 5.6 ± 0.9; 3CD: 2.3 ± 0.4 vs. 3CC: 9.4 ± 2.1 mU/mg protein) with no influence of ACE genotype. Under physiological condition, renal ACE2 activity remained unchanged regardless of the ACE genotype (1CC: 1.9 ± 0.2 = 3CC: 1.4 ± 0.1 μM/min/mg). However upon a pathological stimulus, renal ACE2 activity was efficiently increased only in 1CD group, but not in 3CD, as compared with the others (1CD: 5.1 ± 0.9 vs. 1CC: 1.9 ± 0.2 = 3CC: 1.4 ± 0.1 = 3CD: 2.2 ± 0.2 μM/min/mg). Taken together, our results show for the first time, that susceptibility for the development of diabetic nephropathy associated with increased ACE gene dosage may be, at least in part, caused by a decrease on renal ACE2 activity. This may result in increased local levels of angiotensin II and decreased angiotensin (1-7), leading to altered glomerular permeability and albuminuria, functional alterations presented by 3CD animals. Financial Support: FAPESP, CAPES, CNPq.

scholarly journals The Flavoproteome of the Model Plant Arabidopsis thaliana

2020 ◽  
Vol 21 (15) ◽  
pp. 5371 ◽  
Author(s):  
Patrick Schall ◽  
Lucas Marutschke ◽  
Bernhard Grimm
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcriptional Control ◽  
Gene Families ◽  
Flavin Mononucleotide ◽  
Biotic And Abiotic Stress ◽  
Homologous Genes ◽  
Model Plant Arabidopsis Thaliana ◽  
Metabolic Activities ◽  
Flavin Binding ◽  
Plant Arabidopsis Thaliana

Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are essential cofactors for enzymes, which catalyze a broad spectrum of vital reactions. This paper intends to compile all potential FAD/FMN-binding proteins encoded by the genome of Arabidopsis thaliana. Several computational approaches were applied to group the entire flavoproteome according to (i) different catalytic reactions in enzyme classes, (ii) the localization in subcellular compartments, (iii) different protein families and subclasses, and (iv) their classification to structural properties. Subsequently, the physiological significance of several of the larger flavoprotein families was highlighted. It is conclusive that plants, such as Arabidopsis thaliana, use many flavoenzymes for plant-specific and pivotal metabolic activities during development and for signal transduction pathways in response to biotic and abiotic stress. Thereby, often two up to several homologous genes are found encoding proteins with high protein similarity. It is proposed that these gene families for flavoproteins reflect presumably their need for differential transcriptional control or the expression of similar proteins with modified flavin-binding properties or catalytic activities.

scholarly journals Tranosema rostrale ichnovirus repeat element genes display distinct transcriptional patterns in caterpillar and wasp hosts

2009 ◽  
Vol 90 (6) ◽  
pp. 1505-1514 ◽  
Author(s):  
Asieh Rasoolizadeh ◽  
Catherine Béliveau ◽  
Don Stewart ◽  
Conrad Cloutier ◽  
Michel Cusson
Keyword(s):  
Fat Body ◽  
Gene Dosage ◽  
Choristoneura Fumiferana ◽  
Gene Families ◽  
Transcript Abundance ◽  
Repeat Element ◽  
Open Reading Frames ◽  
Regulation Of Transcription ◽  
Lepidopteran Host ◽  
Reading Frames

The endoparasitic wasp Tranosema rostrale transmits an ichnovirus to its lepidopteran host, Choristoneura fumiferana, during parasitization. As shown for other ichnoviruses, the segmented dsDNA genome of the T. rostrale ichnovirus (TrIV) features several multi-gene families, including the repeat element (rep) family, whose products display no known similarity to non-ichnovirus proteins, except for a homologue encoded by the genome of the Helicoverpa armigera granulovirus; their functions remain unknown. This study applied linear regression of efficiency analysis to real-time PCR quantification of transcript abundance for all 17 TrIV rep open reading frames (ORFs) in parasitized and virus-injected C. fumiferana larvae, as well as in T. rostrale ovaries and head–thorax complexes. Although transcripts were detected for most rep ORFs in infected caterpillars, two of them clearly outnumbered the others in whole larvae, with a tendency for levels to drop over time after infection. The genome segments bearing the three most highly expressed rep genes in parasitized caterpillars were present in higher proportions than other rep-bearing genome segments in TrIV DNA, suggesting a possible role for gene dosage in the regulation of transcription level. TrIV rep genes also showed important differences in the relative abundance of their transcripts in specific tissues (cuticular epithelium, the fat body, haemocytes and the midgut), implying tissue-specific roles for individual members of this gene family. Significantly, no rep transcripts were detected in T. rostrale head–thorax complexes, whereas some were abundant in ovaries. There, the transcription pattern was completely different from that observed in infected caterpillars, suggesting that some rep genes have wasp-specific functions.

New Horizons for Dissecting Epistasis in Crop Quantitative Trait Variation

2020 ◽  
Vol 54 (1) ◽  
pp. 287-307
Author(s):  
Sebastian Soyk ◽  
Matthias Benoit ◽  
Zachary B. Lippman
Keyword(s):  
Genetic Variation ◽  
Quantitative Trait ◽  
Gene Dosage ◽  
Gene Mutations ◽  
Cumulative Effect ◽  
Developmental Pathways ◽  
Trait Variation ◽  
Individual Gene ◽  
New Horizons ◽  
New Strategies

Uncovering the genes, variants, and interactions underlying crop diversity is a frontier in plant genetics. Phenotypic variation often does not reflect the cumulative effect of individual gene mutations. This deviation is due to epistasis, in which interactions between alleles are often unpredictable and quantitative in effect. Recent advances in genomics and genome-editing technologies are elevating the study of epistasis in crops. Using the traits and developmental pathways that were major targets in domestication and breeding, we highlight how epistasis is central in guiding the behavior of the genetic variation that shapes quantitative trait variation. We outline new strategies that illuminate how quantitative epistasis from modified gene dosage defines background dependencies. Advancing our understanding of epistasis in crops can reveal new principles and approaches to engineering targeted improvements in agriculture.

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