scholarly journals Application of the gene dosage balance hypothesis to auxin-related ribosomal mutants in Arabidopsis

2010 ◽  
Vol 5 (4) ◽  
pp. 450-452 ◽  
Author(s):  
Abel Rosado ◽  
Natasha V. Raikhel
Keyword(s):  
Gene Dosage ◽  
Balance Hypothesis ◽  
Dosage Balance

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 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 Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance

2019 ◽  
Author(s):  
Alison Mullis ◽  
Zhaolian Lu ◽  
Yu Zhan ◽  
Tzi-Yuan Wang ◽  
Judith Rodriguez ◽  
...  
Keyword(s):  
Concerted Evolution ◽  
Ribosomal Proteins ◽  
Ribosome Biogenesis ◽  
Gene Dosage ◽  
High Growth ◽  
Fungal Species ◽  
Physiological Data ◽  
Ribosomal Protein Genes ◽  
Cellular Machinery ◽  
Dosage Balance

ABSTRACTRibosomal proteins (RPs) genes encode structure components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. How the RP genes were duplicated and maintained in these fungal species, and their functional significance remains unresolved. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages. The RP duplicates in two of them, budding yeast and Mucoromycota, were mainly created by whole genome duplication (WGD) events. However, in fission yeasts, duplicate RP genes were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs in each species have been homogenized by repeated gene conversion, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased RP transcription abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consuming sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.

scholarly journals Grass MicroRNA Gene Paleohistory Unveils New Insights into Gene Dosage Balance in Subgenome Partitioning after Whole-Genome Duplication

2012 ◽  
Vol 24 (5) ◽  
pp. 1776-1792 ◽  
Author(s):  
Michael Abrouk ◽  
Rongzhi Zhang ◽  
Florent Murat ◽  
Aili Li ◽  
Caroline Pont ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Whole Genome ◽  
Microrna Gene ◽  
Dosage Balance

scholarly journals Gene Dosage Balance in Cellular Pathways

Genetics ◽  
2004 ◽  
Vol 168 (1) ◽  
pp. 569-574 ◽  
Author(s):  
Reiner A. Veitia
Keyword(s):  
Gene Dosage ◽  
Dosage Balance ◽  
Cellular Pathways

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.

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 Dominance and gene dosage balance in health and disease: why levels matter!

2009 ◽  
Vol 220 (2) ◽  
pp. 174-185 ◽  
Author(s):  
Reiner A. Veitia ◽  
James A. Birchler
Keyword(s):  
Gene Dosage ◽  
Health And Disease ◽  
Dosage Balance

Evolutionary constraints imposed by gene dosage balance

10.2741/3010 ◽  
2008 ◽  
Vol Volume (13) ◽  
pp. 4373 ◽  
Author(s):  
Han Liang
Keyword(s):  
Gene Dosage ◽  
Evolutionary Constraints ◽  
Dosage Balance

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.

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