scholarly journals A genome in flux: homoeologous exchanges, subgenome dominance, and gene dosage balance constraints in resynthesized allopolyploid Brassica napus

2021 ◽  
Author(s):  
Kevin A Bird ◽  
J Chris Pires ◽  
Robert VanBuren ◽  
Zhiyong Xiong ◽  
Patrick P. Edger
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Genome Duplication ◽  
Gene Dosage ◽  
Genomic Rearrangements ◽  
Bias Estimation ◽  
Gene Expression Response ◽  
A Genome ◽  
Dosage Balance ◽  
The Impact

Allopolyploidy involves the hybridization of two evolutionary diverged species and the doubling of genomic material. Frequently, allopolyploids exhibit genomic rearrangements that recombine, duplicate, or delete homoeologous regions of the newly formed genome. While decades of investigation have focused on how genome duplication leads to systematic differences in the retention and expression of duplicate genes, the impact of genomic rearrangements on genome evolution has received less attention. We used genomic and transcriptomic data for six independently resynthesized, isogenic Brassica napus lines in the first, fifth, and tenth generation to identify genomic rearrangements and assess their impact on gene expression dynamics related to subgenome dominance and gene dosage constraint. We find that dosage constraints on the gene expression response to polyploidy begin to loosen within the first ten generations of evolution and systematically differ between dominant and non-dominant subgenomes. We also show that genomic rearrangements can bias estimation of homoeolog expression bias, but fail to fully obscure which subgenome is dominantly expressed. Finally, we demonstrate that dosage-sensitive genes exhibit the same kind of coordinated response to homoeologous exchange as they do for genome duplication, suggesting constraint on dosage balance also acts on these changes to gene dosage.

scholarly journals Impact of aging on gene expression response to x-ray irradiation using mouse blood

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Constantinos G. Broustas ◽  
Axel J. Duval ◽  
Sally A. Amundson
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
X Rays ◽  
Gene Expression Response ◽  
X Ray ◽  
The Impact ◽  
Old Mice ◽  
Radiation Biodosimetry ◽  
Young Mice

AbstractAs a radiation biodosimetry tool, gene expression profiling is being developed using mouse and human peripheral blood models. The impact of dose, dose-rate, and radiation quality has been studied with the goal of predicting radiological tissue injury. In this study, we determined the impact of aging on the gene expression profile of blood from mice exposed to radiation. Young (2 mo) and old (21 mo) male mice were irradiated with 4 Gy x-rays, total RNA was isolated from whole blood 24 h later, and subjected to whole genome microarray analysis. Pathway analysis of differentially expressed genes revealed young mice responded to x-ray exposure by significantly upregulating pathways involved in apoptosis and phagocytosis, a process that eliminates apoptotic cells and preserves tissue homeostasis. In contrast, the functional annotation of senescence was overrepresented among differentially expressed genes from irradiated old mice without enrichment of phagocytosis pathways. Pathways associated with hematologic malignancies were enriched in irradiated old mice compared with irradiated young mice. The fibroblast growth factor signaling pathway was underrepresented in older mice under basal conditions. Similarly, brain-related functions were underrepresented in unirradiated old mice. Thus, age-dependent gene expression differences should be considered when developing gene signatures for use in radiation biodosimetry.

Patterns of genome duplication within the Brassica napus genome

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 291-303 ◽  
Author(s):  
I A.P Parkin ◽  
A G Sharpe ◽  
D J Lydiate
Keyword(s):  
Brassica Napus ◽  
Genome Duplication ◽  
Chromosomal Rearrangements ◽  
Centric Fusion ◽  
Linkage Groups ◽  
Gross Chromosomal Rearrangements ◽  
A Genome ◽  
C Genome ◽  
Homologous Locus ◽  
Duplicate Loci

The progenitor diploid genomes (A and C) of the amphidiploid Brassica napus are extensively duplicated with 73% of genomic clones detecting two or more duplicate sequences within each of the diploid genomes. This comprehensive duplication of loci is to be expected in a species that has evolved through a polyploid ancestor. The majority of the duplicate loci within each of the diploid genomes were found in distinct linkage groups as collinear blocks of linked loci, some of which had undergone a variety of rearrangements subsequent to duplication, including inversions and translocations. A number of identical rearrangements were observed in the two diploid genomes, suggesting they had occurred before the divergence of the two species. A number of linkage groups displayed an organization consistent with centric fusion and (or) fission, suggesting this mechanism may have played a role in the evolution of Brassica genomes. For almost every genetically mapped locus detected in the A genome a homologous locus was found in the C genome; the collinear arrangement of these homologous markers allowed the primary regions of homoeology between the two genomes to be identified. At least 16 gross chromosomal rearrangements differentiated the two diploid genomes during their divergence from a common ancestor.Key words: genome evolution, Brassicaeae, polyploidy, homoeologous linkage groups.

scholarly journals The Drosophila Post-mating Response: Gene Expression and Behavioral Changes Reveal Perdurance and Variation in Cross-Tissue Interactions

2020 ◽  
Vol 10 (3) ◽  
pp. 967-983 ◽  
Author(s):  
Nicole R. Newell ◽  
Surjyendu Ray ◽  
Justin E. Dalton ◽  
Julia C. Fortier ◽  
Joyce Y. Kao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Wide Association Study ◽  
Wnt Signaling Pathway ◽  
Dna Polymorphisms ◽  
Female Gonad ◽  
Female Head ◽  
Tissue Interactions ◽  
Examine Gene Expression ◽  
A Genome ◽  
The Impact

Examining cross-tissue interactions is important for understanding physiology and homeostasis. In animals, the female gonad produces signaling molecules that act distally. We examine gene expression in Drosophila melanogaster female head tissues in 1) virgins without a germline compared to virgins with a germline, 2) post-mated females with and without a germline compared to virgins, and 3) post-mated females mated to males with and without a germline compared to virgins. In virgins, the absence of a female germline results in expression changes in genes with known roles in nutrient homeostasis. At one- and three-day(s) post-mating, genes that change expression are enriched with those that function in metabolic pathways, in all conditions. We systematically examine female post-mating impacts on sleep, food preference and re-mating, in the strains and time points used for gene expression analyses and compare to published studies. We show that post-mating, gene expression changes vary by strain, prompting us to examine variation in female re-mating. We perform a genome-wide association study that identifies several DNA polymorphisms, including four in/near Wnt signaling pathway genes. Together, these data reveal how gene expression and behavior in females are influenced by cross-tissue interactions, by examining the impact of mating, fertility, and genotype.

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 Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic

2019 ◽  
Vol 116 (30) ◽  
pp. 14995-15000 ◽  
Author(s):  
Justyna Cholewa-Waclaw ◽  
Ruth Shah ◽  
Shaun Webb ◽  
Kashyap Chhatbar ◽  
Bernard Ramsahoye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rett Syndrome ◽  
Transcription Initiation ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
A Genome ◽  
The Impact

Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here, we integrate quantitative, multidimensional experimental analysis and mathematical modeling to indicate that MeCP2 is a global transcriptional regulator whose binding to DNA creates “slow sites” in gene bodies. We hypothesize that waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shockwaves in nonequilibrium physics transport models. This mechanism differs from conventional gene-regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene-expression patterns are choreographed.

scholarly journals Impact of Gene Dosage on Gene Expression, Biological Processes and Survival in Cervical Cancer: A Genome-Wide Follow-Up Study

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e97842 ◽  
Author(s):  
Ingrid Medina-Martinez ◽  
Valeria Barrón ◽  
Edgar Roman-Bassaure ◽  
Eligia Juárez-Torres ◽  
Mariano Guardado-Estrada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cervical Cancer ◽  
Gene Dosage ◽  
Biological Processes ◽  
Follow Up Study ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Chao Zhou ◽  
Xiaoyun Liu ◽  
Xinglei Li ◽  
Hanlin Zhou ◽  
Sijia Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Duplication ◽  
Chromatin Condensation ◽  
Expression Patterns ◽  
Rice Genome ◽  
Genome Doubling ◽  
Autotetraploid Rice ◽  
A Genome ◽  
Ideal System ◽  
Accessible Chromatin

AbstractEvolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.

scholarly journals Type 2 Diabetes Modifies Skeletal Muscle Gene Expression Response to Gastric Bypass Surgery

2021 ◽  
Author(s):  
Matthew D. Barberio ◽  
G. Lynis Dohm ◽  
Walter J. Pories ◽  
Natalie A. Gadaleta ◽  
Joseph A. Houmard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Type 2 Diabetes ◽  
Skeletal Muscle ◽  
Gastric Bypass ◽  
Clinical Symptoms ◽  
Vastus Lateralis ◽  
Gene Expression Response ◽  
Muscle Health ◽  
The Impact

AbstractRoux-en-Y gastric bypass (RYGB) is an effective treatment for type 2 diabetes mellitus (T2DM) which can result in remission of clinical symptoms, yet mechanisms for improved skeletal muscle health are poorly understood. We sought to define the impact of existing T2DM on RYGB-induced muscle transcriptome changes.MethodsVastus lateralis biopsy transcriptomes were generated pre- and 1-yr post-RYGB in black adult females with (T2D; n = 5, age=51±6 yr, BMI=53.0±5.8 kg/m2) and without (CON; n = 7,43±6 yr,51.0±9.2 kg/m2) T2DM. Insulin, glucose, and HOMA-IR were measured in blood at the same time points. ANCOVA detected differentially expressed genes (p< 0.01, Fold change<|1.2|), which were used to identify enriched biological pathways.ResultsPre-RYGB, 95 probes were downregulated with T2D including subunits of mitochondrial complex I. Post-RYGB, the T2D group had normalized gene expression when compared to their non-diabetic counterparts with only 3 probes remaining significantly different. In the T2D, we identified 52 probes upregulated from pre- to post-RYGB, including NDFUB7 and NDFUA1.ConclusionBlack females with T2DM show extensive down regulation of genes across aerobic metabolism pathways prior to RYGB, which resolves 1 year post-RYGB and is related to improvements in clinical markers. These data support efficacy of RYGB for improving skeletal muscle health, especially in patients with T2DM.

Impact of Trisomy 8 on Expression of Genes Located on Chromosome 8 in Different AML Subgroups.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2034-2034
Author(s):  
Claudia Schoch ◽  
Wolfgang Kern ◽  
Alexander Kohlmann ◽  
Martin Dugas ◽  
Wolfgang Hiddemann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Dosage ◽  
Gene Expression Pattern ◽  
Chromosome 8 ◽  
Support Vector ◽  
Trisomy 8 ◽  
Gene Dosage Effect ◽  
Class Prediction ◽  
Expression Of Genes ◽  
The Impact

Abstract Trisomy 8 is the most frequently observed trisomy in acute myeloid leukemia (AML). It occurs as a sole karyotype abnormality or in addition to other chromosome aberrations. It was the aim of this study to analyze the impact of trisomy 8 on the expression of genes located on chromosome 8 in different AML subgroups. Therefore, gene expression analyses were performed in a total of 567 AML cases using Affymetrix U133A+B oligonucleotide microarrays. The following 14 subgroups were analyzed: +8 sole (n=19), +8 within a complex aberrant karyotype (n=11), +8 with t(15;17) (n=7), +8 and inv(16) (n=3), +8 with t(8;21) (n=3), +8 and 11q23/MLL (n=8), and +8 with other abnormalities (n=10). These were compared to 200 AML with normal karyotype and the following subgroups without trisomy 8: complex aberrant karyotype (n=73), t(15;17) (n=36), inv(16) (n=46), t(8;21) (n=37), 11q23/MLL (n=37), and other abnormalities (n=77). In total 1188 probe sets cover sequences located on chromosome 8 representing 580 genes. A significant higher mean expression of all genes located on chromosome 8 was observed in subgroups with +8 in comparison to their respective control groups (for all comparisons, p<0.05). Significantly higher expressed genes in groups with +8 in comparison to the respective groups without +8 were identified in all comparisons. The number of identified genes ranged from 40 in 11q23/MLL to 326 in trisomy 8 sole vs. normal. There was no common gene significantly overexpressed in all comparisons. Three genes (TRAM1, CHPPR, MGC40214) showed a significantly higher expression in 5 out of 7 comparisons. Between 19 and 107 genes with an exclusive overexpression in trisomy 8 cases in only one subtype comparison were identified. In addition, we performed class prediction using support vector machines (SVM) including all probe sets on the arrays. In one approach all 14 different subgroups were analyzed as one class each. Only 3 out of 61 cases with trisomy 8 were assigned into their correct subclass, while 40 cases were assigned to their corresponding genetic subclass without trisomy 8. In a second approach only two classes were defined: all cases with trisomy 8 combined vs. all cases without trisomy 8. Only 26 out of 61 (42.6%) with trisomy 8 were identified correctly underlining the fact that no distinct gene expression pattern is associated with trisomy 8 in general. Performing SVM only with genes located on chromosome 8 did not improve the correct assignment of cases with trisomy 8 overall. Only cases with trisomy 8 sole were correctly predicted in 58% as compared to 11% in SVM using all genes. In conclusion, overall the gain of chromosome 8 leads to a higher expression of genes located on chromosome 8. However, no consistent pattern of genes was identified which shows a higher expression in all AML subtypes with trisomy 8. This data suggest that the higher expression of genes located on chromosome 8 only in part is directly related to a gene dosage effect. Trisomy 8 may rather provide a platform for a higher expression of chromosome 8 genes which are specifically upregulated by accompanying genetic abnormalities in the respective AML subtypes. Therefore, trisomy 8 does not seem to be an abnormality determining specific disease characteristics such as the well known primary aberrations (t(8;21), inv(16), t(15;17), MLL/11q23) but rather a disease modulating secondary event in addition to primary cytogenetic or moleculargenetic aberrations.

DNA Copy Number Changes Have Gene Dosage Effects with Consequent Impact On Disease Biology and Prognosis in Multiple Myeloma

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3984-3984
Author(s):  
Mehmet Kemal Samur ◽  
Parantu K Shah ◽  
Xujun Wang ◽  
Norman Huang ◽  
Stephane Minvielle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Multiple Myeloma ◽  
Copy Number ◽  
Dosage Effect ◽  
Chromosome 9 ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
A Genome ◽  
The Impact ◽  
Affect Gene Expression

Abstract Abstract 3984 Copy number alterations, deletions and amplifications, are very frequent in multiple myeloma (MM), however, it is less clear how these alterations affect gene expression. We performed a genome-wide analysis of 170 newly-diagnosed uniformly treated MM patients using high-density SNP arrays and Exon ST 1.0 gene expression arrays, and evaluated how copy number alterations affect gene expression in MM. Using SNP array data just over 40% patients had hyperdiploid MM (HMM) while the rest had non-hyperdiploid MM (N-HMM). We used two-step procedure to identify dosage effect scores of genes. At first, for each gene, percentage of copy number altered samples was calculated. Then for each gene percentage of samples that had dosage effect was calculated. Finally dosage effect score for each gene was calculated as a ratio of dosage effect samples percentage to copy number alteration sample percentage. We show that dosage effect in MM is wide-spread and some chromosomal locations are affected by dosage effect more compared to other locations. The dosage effect tracks can be observed at trisomy chromosomes and chromosome 1q, but most explicitly at chromosome 9, 11, 15 and 19. Also for deleted genes, dosage effect can be mostly observed at chromosome 13 and 16q. Separate analysis of HMM and N-HMM patients also showed that HMM patients have higher dosage effect especially in chromosome 15 compared to the others. In addition, relation between dosage effect and gene expression analysis show that the highly expressed genes have significantly higher dosage effect compared to the lowly expressed genes. Also function enrichment analysis showed that genes involved with crucial biological processes including translation, RNA processing and transcription factor genes are enriched in genes with higher dosage effect. Interstingly, dosage resistant genes are enriched in cell death and GTPase processes. These results help us understand the impact of aneuploidy in MM on global gene expression changes. In conclusion, our analysis identifies concordant and discordant gene expression changes associated with DNA copy number alterations, identifying genes and pathways that may play an important role in myeloma disease behavior as well as prognosis. Disclosures: No relevant conflicts of interest to declare.

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