Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene &lt;i&gt;TRDMT1&lt;/i&gt;

Abstract. The tRNA modification gene in eukaryotes is relatively conservative. As an important modification gene, the TRDMT1 gene plays an important role in maintaining tRNA structural maintenance and reducing mistranslation of protein translation by methylation of specific tRNA subpopulations. Mouse and zebrafish TRDMT1 knockout experiments indicate that it may mediate growth and development through tRNA modification. However, there are no systematic reports on the function of tRNA-modified genes in livestock. In this study, Qinchuan cattle DNA pool sequencing technology was used. A G>C mutation in the −1223 bp position upstream of the TRDMT1 translation initiator codon was found. At this locus, the dual-luciferase assay indicated that different genotypes cause differences in transcriptional activity (P<0.05). Our experiment detected a natural genetic variation of a tRNA modification gene TRDMT1, which may provide potential natural molecular materials for the study of tRNA modification.

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Inherited Differences in Crossing Over and Gene Conversion Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽

10.1093/genetics/159.4.1573 ◽

2001 ◽

Vol 159 (4) ◽

pp. 1573-1593

Author(s):

Muhammad Saleem ◽

Bernard C Lamb ◽

Eviatar Nevo

Keyword(s):

Genetic Variation ◽

Gene Conversion ◽

Spontaneous Mutation ◽

Crossing Over ◽

Natural Genetic Variation ◽

Evolution Canyon ◽

Wild Strains ◽

Sordaria Fimicola ◽

First And Second Generation ◽

Consistent Direction

Abstract Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II.

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Inherited and Environmentally Induced Differences in Mutation Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽

10.1093/genetics/149.1.87 ◽

1998 ◽

Vol 149 (1) ◽

pp. 87-99

Author(s):

Bernard C Lamb ◽

Muhammad Saleem ◽

William Scott ◽

Nina Thapa ◽

Eviatar Nevo

Keyword(s):

Genetic Variation ◽

Spontaneous Mutation ◽

The South ◽

Natural Genetic Variation ◽

The North ◽

Ascospore Germination ◽

Evolution Canyon ◽

Two Generations ◽

Wild Strains ◽

Sordaria Fimicola

Abstract We have studied whether there is natural genetic variation for mutation frequencies, and whether any such variation is environment-related. Mutation frequencies differed significantly between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. Strains from the harsher, drier, south-facing slope had higher frequencies of new spontaneous mutations and of accumulated mutations than strains from the milder, lusher, north-facing slope. Collective total mutation frequencies over many loci for ascospore pigmentation were 2.3, 3.5 and 4.4% for three strains from the south-facing slope, and 0.9, 1.1, 1.2, 1.3 and 1.3% for five strains from the north-facing slope. Some of this between-slope difference was inherited through two generations of selfing, with average spontaneous mutation frequencies of 1.9% for south-facing slope strains and 0.8% for north-facing slope strains. The remainder was caused by different frequencies of mutations arising in the original environments. There was also significant heritable genetic variation in mutation frequencies within slopes. Similar between-slope differences were found for ascospore germination-resistance to acriflavine, with much higher frequencies in strains from the south-facing slope. Such inherited variation provides a basis for natural selection for optimum mutation rates in each environment.

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PBRM1 Cooperates with YTHDF2 to Control HIF-1α Protein Translation

Cells ◽

10.3390/cells10061425 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1425

Author(s):

Alena Shmakova ◽

Mark Frost ◽

Michael Batie ◽

Niall S. Kenneth ◽

Sonia Rocha

Keyword(s):

Protein Expression ◽

Cellular Response ◽

Transcriptional Activity ◽

Mrna Translation ◽

Protein Translation ◽

Signalling Pathways ◽

Independent Function ◽

Protein Levels ◽

Associated Proteins ◽

Core Components

PBRM1, a component of the chromatin remodeller SWI/SNF, is often deleted or mutated in human cancers, most prominently in renal cancers. Core components of the SWI/SNF complex have been shown to be important for the cellular response to hypoxia. Here, we investigated how PBRM1 controls HIF-1α activity. We found that PBRM1 is required for HIF-1α transcriptional activity and protein levels. Mechanistically, PBRM1 is important for HIF-1α mRNA translation, as absence of PBRM1 results in reduced actively translating HIF-1α mRNA. Interestingly, we found that PBRM1, but not BRG1, interacts with the m6A reader protein YTHDF2. HIF-1α mRNA is m6A-modified, bound by PBRM1 and YTHDF2. PBRM1 is necessary for YTHDF2 binding to HIF-1α mRNA and reduction of YTHDF2 results in reduced HIF-1α protein expression in cells. Our results identify a SWI/SNF-independent function for PBRM1, interacting with HIF-1α mRNA and the epitranscriptome machinery. Furthermore, our results suggest that the epitranscriptome-associated proteins play a role in the control of hypoxia signalling pathways.

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Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut

Current Biology ◽

10.1016/j.cub.2021.04.046 ◽

2021 ◽

Author(s):

Fan Zhang ◽

Jessica L. Weckhorst ◽

Adrien Assié ◽

Ciara Hosea ◽

Christopher A. Ayoub ◽

...

Keyword(s):

Genetic Variation ◽

Caenorhabditis Elegans ◽

Natural Genetic Variation

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Karyo-morphological characterization of natural genetic variation in some threatenedCymbidiumspecies of Northeast India

Caryologia ◽

10.1080/00087114.2010.10589713 ◽

2010 ◽

Vol 63 (1) ◽

pp. 99-105 ◽

Cited By ~ 10

Author(s):

Santosh Kumar Sharma ◽

Khedasana Rajkumari ◽

Suman Kumaria ◽

Pramod Tandon ◽

Satyawada Rama Rao

Keyword(s):

Genetic Variation ◽

Northeast India ◽

Morphological Characterization ◽

Natural Genetic Variation

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Differential Masking of Natural Genetic Variation by miR-9a in Drosophila

Genetics ◽

10.1534/genetics.115.183822 ◽

2015 ◽

Vol 202 (2) ◽

pp. 675-687 ◽

Cited By ~ 11

Author(s):

Justin J. Cassidy ◽

Alexander J. Straughan ◽

Richard W. Carthew

Keyword(s):

Genetic Variation ◽

Natural Genetic Variation

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The Tomato (Solanum Lycopersicum cv. Micro-Tom) Natural Genetic Variation Rg1 and the DELLA Mutant Procera Control the Competence Necessary to Form Adventitious Roots and Shoots

Journal of Experimental Botany ◽

10.1093/jxb/ers221 ◽

2012 ◽

Vol 63 (15) ◽

pp. 5689-5703 ◽

Cited By ~ 30

Author(s):

Simone Lombardi-Crestana ◽

Mariana da Silva Azevedo ◽

Geraldo Felipe Ferreira e Silva ◽

Lílian Ellen Pino ◽

Beatriz Appezzato-da-Glória ◽

...

Keyword(s):

Genetic Variation ◽

Solanum Lycopersicum ◽

Adventitious Roots ◽

Natural Genetic Variation

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Substrate-Specific Effects of Natural Genetic Variation on Proteasome Activity

10.1101/2021.11.23.469794 ◽

2021 ◽

Author(s):

Mahlon Collins ◽

Randi R. Avery ◽

Frank W Albert

Keyword(s):

Genetic Variation ◽

Protein Degradation ◽

Dynamic Control ◽

Cellular Protein ◽

Proteasome Activity ◽

Heritable Variation ◽

Natural Genetic Variation ◽

Specific Effects ◽

Regulatory Particle

The bulk of targeted cellular protein degradation is performed by the proteasome, a multi-subunit complex consisting of the 19S regulatory particle, which binds, unfolds, and translocates substrate proteins, and the 20S core particle, which degrades them. Protein homeostasis requires precise, dynamic control of proteasome activity. To what extent genetic variation creates differences in proteasome activity is almost entirely unknown. Using the ubiquitin-independent degrons of the ornithine decarboxylase and Rpn4 proteins, we developed reporters that provide high-throughput, quantitative measurements of proteasome activity in vivo in genetically diverse cell populations. We used these reporters to characterize the genetic basis of variation in proteasome activity in the yeast Saccharomyces cerevisiae. We found that proteasome activity is a complex, polygenic trait, shaped by variation throughout the genome. Genetic influences on proteasome activity were predominantly substrate-specific, suggesting that they primarily affect the function or activity of the 19S regulatory particle. Our results demonstrate that individual genetic differences create heritable variation in proteasome activity and suggest that genetic effects on proteasomal protein degradation may be an important source of variation in cellular and organismal traits.

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