scholarly journals Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence

2018 ◽  
Vol 27 (5) ◽  
pp. 1188-1199 ◽  
Author(s):  
Chathurani Ranathunge ◽  
Gregory L. Wheeler ◽  
Melody E. Chimahusky ◽  
Meaghan M. Kennedy ◽  
Jesse I. Morrison ◽  
...  
Keyword(s):  
Gene Expression ◽  
Potential Role ◽  
Expression Divergence ◽  
Gene Expression Divergence

scholarly journals Microsatellites as Agents of Adaptive Change: An RNA-seq based Comparative Study of Transcriptomes from Five Helianthus Species

2021 ◽  
Author(s):  
Chathurani Ranathunge ◽  
Sreepriya Pramod ◽  
Sébastien Renaut ◽  
Gregory Wheeler ◽  
Andy Perkins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Expression Divergence ◽  
Rna Seq ◽  
Gene Expression Divergence ◽  
Coding Regions ◽  
Regulatory Mutations ◽  
Helianthus Species

Mutations that provide environment dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates and are abundant in both coding and non-coding regions and could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from nine closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5’UTRs and coding regions compared to 3’UTRs and non-coding transcripts among Helianthus spp. Further, allele frequency differences measured by pairwise FST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.

scholarly journals Microsatellites as Agents of Adaptive Change: An RNA-Seq-Based Comparative Study of Transcriptomes from Five Helianthus Species

Symmetry ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 933
Author(s):  
Chathurani Ranathunge ◽  
Sreepriya Pramod ◽  
Sébastien Renaut ◽  
Gregory L. Wheeler ◽  
Andy D. Perkins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Expression Divergence ◽  
Rna Seq ◽  
Gene Expression Divergence ◽  
Coding Regions ◽  
Regulatory Mutations ◽  
Helianthus Species

Mutations that provide environment-dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates achieved through symmetric or asymmetric mutation processes and are abundant in both coding and non-coding regions in positions that could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from five closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5′UTRs and coding regions compared to 3′UTRs and non-coding transcripts among Helianthus spp. Furthermore, allele frequency differences measured by pairwise FST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.

scholarly journals Support for the dominance theory in Drosophila transcriptomes

2018 ◽  
Author(s):  
Ana Llopart ◽  
Evgeny Brud ◽  
Nikale Pettie ◽  
Josep M. Comeron
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Transcriptional Networks ◽  
Expression Divergence ◽  
Gene Expression Divergence ◽  
Genome Wide ◽  
Regulatory Mutations ◽  
Opposite Sex ◽  
High Degree

ABSTRACTInteractions among divergent elements of transcriptional networks from different species can lead to misexpression in hybrids through regulatory incompatibilities, some with the potential to generate sterility. Genes with male-biased expression tend to be overrepresented among genes misexpressed in hybrid males. While the possible contribution of faster-male evolution to this misexpression has been explored, the role of the hemizygous X chromosome (i.e., the dominance theory for transcriptomes) remains yet to be determined. Here we study genome-wide patterns of gene expression in females and males of Drosophila yakuba and D. santomea and their hybrids. We used attached-X stocks to specifically test the dominance theory, and we uncovered a significant contribution of recessive alleles on the X chromosome to hybrid misexpression. Our analysis of gene expression patterns suggests that there is a contribution of weakly deleterious regulatory mutations to gene expression divergence in the sex towards which the expression is biased. In the opposite sex (e.g., genes with female-biased expression analyzed in male transcriptomes), we detect stronger selective constraints on gene expression divergence. Although genes with high degree of male-biased expression show a clear signal of faster-X evolution for gene expression divergence, we also detected slower-X evolution of gene expression in other gene classes (e.g. female-biased genes) that is mediated by significant decreases of cis- and trans-regulatory divergence. The distinct behavior of X-linked genes with high degree of male-biased expression is consistent with these genes experiencing a higher incidence of positively selected regulatory mutations than their autosomal counterparts. We propose that both dominance theory and faster-X evolution of gene expression may be major contributors to hybrid misexpression and possibly the large X-effect in these species.

Speciation and changes in male gene expression in Drosophila

Genome ◽  
2020 ◽  
pp. 1-11
Author(s):  
Bahar Patlar ◽  
Alberto Civetta
Keyword(s):  
Gene Expression ◽  
Reproductive Isolation ◽  
Potential Role ◽  
Regulation Of Gene Expression ◽  
Drosophila Model ◽  
Depth Analysis ◽  
The Impact ◽  
Plastic Responses ◽  
Male Gene

It has long been acknowledged that changes in the regulation of gene expression may account for major organismal differences. However, we still do not fully understand how changes in gene expression evolve and how do such changes influence organisms’ differences. We are even less aware of the impact such changes might have in restricting gene flow between species. Here, we focus on studies of gene expression and speciation in the Drosophila model. We review studies that have identified gene interactions in post-mating reproductive isolation and speciation, particularly those that modulate male gene expression. We also address studies that have experimentally manipulated changes in gene expression to test their effect in post-mating reproductive isolation. We highlight the need for a more in-depth analysis of the role of selection causing disrupted gene expression of such candidate genes in sterile/inviable hybrids. Moreover, we discuss the relevance to incorporate more routinely assays that simultaneously evaluate the potential effects of environmental factors and genetic background in modulating plastic responses in male genes and their potential role in speciation.

P.0900 The potential role of interferon signaling in migraine: a gene expression study

2021 ◽  
Vol 53 ◽  
pp. S661-S662
Author(s):  
S. Kumar ◽  
K. Gecse ◽  
D. Baksa ◽  
X. Gonda ◽  
G. Bagdy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Potential Role ◽  
Gene Expression Study ◽  
Interferon Signaling ◽  
Expression Study

scholarly journals P002 The potential role of IL-33 in inflammatory-associated gut fibrosis: Induction of pro-fibrogenic gene expression and myofibroblast hypertrophy

2012 ◽  
Vol 6 ◽  
pp. S11-S12
Author(s):  
B. Mattioli ◽  
C. De Salvo ◽  
L. Pastorelli ◽  
R.R. Garg ◽  
M. Campieri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Potential Role

scholarly journals Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies

Blood ◽  
2019 ◽  
Vol 134 (24) ◽  
pp. 2195-2208 ◽  
Author(s):  
Daniel Sasca ◽  
Haiyang Yun ◽  
George Giotopoulos ◽  
Jakub Szybinski ◽  
Theo Evan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Potential Role ◽  
Regulation Of Gene Expression ◽  
Specific Gene ◽  
Myeloid Malignancy ◽  
Erythroid Maturation ◽  
Acute Myeloid

Cohesin mutations are common in myeloid malignancy. Sasca et al elucidate the potential role of cohesin loss in myelodysplastic syndrome and acute myeloid leukemia (MDS/AML). They demonstrate that cohesin binding is critical for erythroid-specific gene expression and that reduction in cohesin impairs terminal erythroid maturation and promotes myeloid malignancy.

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