scholarly journals Repeated divergent selection on pigmentation genes in a rapid finch radiation driven by sexual selection

2016 ◽  
Author(s):  
Leonardo Campagna ◽  
Márcio Repenning ◽  
Luis Fabio Silveira ◽  
Carla Suertegaray Fontana ◽  
Pablo L Tubaro ◽  
...  
Keyword(s):  
Biological Diversity ◽  
Phenotypic Diversity ◽  
Regulatory Region ◽  
Bird Species ◽  
Regulatory Elements ◽  
Divergent Selection ◽  
Sexually Selected Traits ◽  
Conserved Genes ◽  
Selected Traits ◽  
Genomic Regions

ABSTRACTThe search for molecular targets of selection is leading to a better understanding of how evolution shapes biological diversity. Instances of recent and rapid speciation are suitable for associating phenotypes with their causal genotypes, because gene flow may homogenize areas of the genome that are not under divergent selection. Locating differentiated genomic regions among taxa allows us to test associations between the genes in these regions and their contributions to phenotypic diversity. Here we study a rapid radiation of nine sympatric bird species known as southern capuchino seedeaters, which are strikingly differentiated in sexually selected characters of male plumage and song. We sequenced the genomes of 72 individuals representing a diverse set of species and associated phenotypes to search for differentiated genomic regions. We asked what genes are harbored in divergent regions and to what extent has selection on the same targets shaped phenotypic diversity across different lineages. Capuchinos show differences in a small proportion of their genomes, yet selection has acted independently on the same targets during the groups’ radiation. Many divergence peaks contain genes involved in the melanogenesis pathway, with the strongest signal originating from a regulatory region upstream of the gene coding for the Agouti-signaling protein. Across all divergence peaks, the most differentiated areas are similarly likely regulatory. Our findings are consistent with selection acting on the same genomic regions in different lineages to shape the evolution of cis-regulatory elements, which control how more conserved genes are expressed and thereby generate diversity in sexually selected traits.

scholarly journals Regulatory elements in the upstream region of metallothionein gene in tilapia species

2021 ◽  
Vol 30 (1) ◽  
pp. 95-103
Author(s):  
Mohammad Shamimul Alam ◽  
Israt Jahan ◽  
Sadniman Rahman ◽  
Hawa Jahan ◽  
Kaniz Fatema
Keyword(s):  
Tissue Specificity ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Metal Resistance ◽  
Genomic Region ◽  
Upstream Region ◽  
Upstream Sequence ◽  
Oreochromis Aureus ◽  
Metallothionein Gene ◽  
Genomic Regions

Tilapia is a hardy fish which can survive in water bodies polluted with heavy metals. Metal resistance is conferred by higher expression of metallothionein gene (mt) in many organisms. Level, time and tissue-specificity of gene expression is regulated through transcription factor binding sites (TFBS) which may be present in the upstream, downstream, or even in the introns of a gene. So, as a candidate regulatory region, the 5’upstream sequence of mt gene in three tilapia species, Oreochromis aureus, O. niloticus and O. mossambicus was studied. The targeted region was PCR-amplified and then sequenced using a pair of custom-designed primer. A total of only 2.7% variation was found in the sequenced genomic region among the three species. Metal-related TFBS were predicted from these sequences. A total of twenty eight TFBS were found in O. aureus and twenty nine in O. mossambicus and O. niloticus. The number of metalrelated TFBS predicted in the targeted sequence was significantly higher compared to that found in randomly selected other genomic regions of same size from O. niloticus genome. Thus, the results suggest the presence of putative regulatory elements in the targeted upstream region which might have important role in the regulation of mt gene function. Dhaka Univ. J. Biol. Sci. 30(1): 95-103, 2021 (January)

Differential methylation tests of regulatory regions

2016 ◽  
Vol 15 (3) ◽  
Author(s):  
Duchwan Ryu ◽  
Hongyan Xu ◽  
Varghese George ◽  
Shaoyong Su ◽  
Xiaoling Wang ◽  
...  
Keyword(s):  
Regulatory Region ◽  
Regulatory Elements ◽  
Genomic Region ◽  
Differential Methylation ◽  
Lymphocytic Leukemia ◽  
Smoothing Methods ◽  
Sample Data ◽  
The Gift ◽  
Average Profile ◽  
Genomic Regions

AbstractDifferential methylation of regulatory elements is critical in epigenetic researches and can be statistically tested. We developed a new statistical test, the generalized integrated functional test (GIFT), that tests for regional differences in methylation based on the methylation percent at each CpG site within a genomic region. The GIFT uses estimated subject-specific profiles with smoothing methods, specifically wavelet smoothing, and calculates an ANOVA-like test to compare the average profile of groups. In this way, possibly correlated CpG sites within the regulatory region are compared all together. Simulations and analyses of data obtained from patients with chronic lymphocytic leukemia indicate that GIFT has good statistical properties and is able to identify promising genomic regions. Further, GIFT is likely to work with multiple different types of experiments since different smoothing methods can be used to estimate the profiles of data without noise. Matlab code for GIFT and sample data are available at

Tests of the positive and functional allometry hypotheses for sexually selected traits in the Jamaican field cricket

2021 ◽  
pp. 104413
Author(s):  
Susan M. Bertram ◽  
Danya D. Yaremchuk ◽  
Mykell L. Reifer ◽  
Amy Villareal ◽  
Matthew J. Muzzatti ◽  
...  
Keyword(s):  
Field Cricket ◽  
Sexually Selected Traits ◽  
Selected Traits

scholarly journals Exploring functionally annotated transcriptional consensus regulatory elements with CONREL

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Davide Dalfovo ◽  
Samuel Valentini ◽  
Alessandro Romanel
Keyword(s):  
Cell Lines ◽  
Web Application ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Levels Of Abstraction ◽  
Binding Motifs ◽  
Extensive Collection ◽  
Transcription Factor Binding Motifs ◽  
Gene Regulatory ◽  
Genomic Regions

Abstract Understanding the interaction between human genome regulatory elements and transcription factors is fundamental to elucidate the structure of gene regulatory networks. Here we present CONREL, a web application that allows for the exploration of functionally annotated transcriptional ‘consensus’ regulatory elements at different levels of abstraction. CONREL provides an extensive collection of consensus promoters, enhancers and active enhancers for 198 cell-lines across 38 tissue types, which are also combined to provide global consensuses. In addition, 1000 Genomes Project genotype data and the ‘total binding affinity’ of thousands of transcription factor binding motifs at genomic regulatory elements is fully combined and exploited to characterize and annotate functional properties of our collection. Comparison with other available resources highlights the strengths and advantages of CONREL. CONREL can be used to explore genomic loci, specific genes or genomic regions of interest across different cell lines and tissue types. The resource is freely available at https://bcglab.cibio.unitn.it/conrel.

scholarly journals Sexually Selected Traits: A Fundamental Framework for Studies on Behavioral Epigenetics

ILAR Journal ◽  
2012 ◽  
Vol 53 (3-4) ◽  
pp. 253-269 ◽  
Author(s):  
E. Jasarevic ◽  
D. C. Geary ◽  
C. S. Rosenfeld
Keyword(s):  
Sexually Selected Traits ◽  
Selected Traits

scholarly journals Two different negative regulatory elements control the transcription of T-cell activation gene 3 in activated mast cells

1997 ◽  
Vol 323 (2) ◽  
pp. 511-519 ◽  
Author(s):  
Chad K. OH ◽  
Markus NEURATH ◽  
Jeong-Je CHO ◽  
Tekli SEMERE ◽  
Dean D. METCALFE
Keyword(s):  
Protein Synthesis ◽  
T Cell ◽  
Mast Cells ◽  
T Cell Activation ◽  
Cell Activation ◽  
Regulatory Region ◽  
Regulatory Elements ◽  
Site Directed Mutagenesis ◽  
Mobility Shift ◽  
Integrin Gene

T-cell activation gene 3 (TCA3) encodes a β-chemokine that is transcriptionally regulated in mast cells; the gene has a functional NF-κB element at positions -194 to -185. The 5´-flanking region of this gene is also known to have a negative regulatory region between -2057 and -1342. To characterize the negative regulatory elements (NREs), this region was sequenced and then digested by HindIII enzyme into two fragments, NRE-1 (-2057 to -1493) and NRE-2 (-1492 to -1342). Both NRE-1 and NRE-2 in the 5´–3´ orientation inhibited chloramphenicol acetyltransferase (CAT)-protein synthesis by a TCA3–CAT construct transfected into mast cells that were then activated. Only NRE-1 inhibited CAT-protein synthesis in the 3´–5´ orientation. Further deletion of the 5´ region of NRE-1 partially abolished the inhibitory activity. Both NRE-1 and NRE-2 inhibited the activity of a CD20–CAT construct independent of cell activation. Electrophoretic mobility shift assays showed DNA–protein complex formation with subsequences (CCCCCATTCT) of NRE-1 (NRE-1a) and (CCATGA) of NRE-2 (NRE-2b). NRE-1a appears to be novel. NRE-2b is identical with a putative silencer motif in the αIIb integrin gene. Site-directed mutagenesis demonstrated that both NRE-1a and NRE-2b are important in the negative regulation of TCA3 promoter activity. In vivo ligation-mediated PCR footprinting of the NRE-2 region revealed protection between -1372 and -1354, which contains NRE-2b. The data thus demonstrate identity of a silencer motif, here termed NRE-2b, in both the αIIb integrin gene and the TCA3, and that this silencer region in mast cells is functional both in vivoand in vitro. Further, evidence is presented that the promoter for TCA3 contains a novel silencer motif, termed NRE-1a, characterized by a CT-rich sequence.

scholarly journals Transcription of the Human 5-Hydroxytryptamine Receptor 2B (HTR2B) Gene Is under the Regulatory Influence of the Transcription Factors NFI and RUNX1 in Human Uveal Melanoma

2018 ◽  
Vol 19 (10) ◽  
pp. 3272 ◽  
Author(s):  
Manel Benhassine ◽  
Sylvain Guérin
Keyword(s):  
Transcription Factors ◽  
Uveal Melanoma ◽  
Serotonin Receptor ◽  
Molecular Mechanisms ◽  
Regulatory Region ◽  
Gene Signature ◽  
Regulatory Elements ◽  
Gene Encoding ◽  
Aberrant Expression ◽  
Factor I

Because it accounts for 70% of all eye cancers, uveal melanoma (UM) is therefore the most common primary ocular malignancy. In this study, we investigated the molecular mechanisms leading to the aberrant expression of the gene encoding the serotonin receptor 2B (HTR2B), one of the most discriminating among the candidates from the class II gene signature, in metastatic and non-metastatic UM cell lines. Transfection analyses revealed that the upstream regulatory region of the HTR2B gene contains a combination of alternative positive and negative regulatory elements functional in HTR2B− but not in HTR23B+ UM cells. We demonstrated that both the transcription factors nuclear factor I (NFI) and Runt-related transcription factor I (RUNX1) interact with regulatory elements from the HTR2B gene to either activate (NFI) or repress (RUNX1) HTR2B expression in UM cells. The results of this study will help understand better the molecular mechanisms accounting for the abnormal expression of the HTR2B gene in uveal melanoma.

scholarly journals Detection and evaluation of selection signatures in sheep

2018 ◽  
Vol 53 (5) ◽  
pp. 527-539 ◽  
Author(s):  
Tiago do Prado Paim ◽  
Patrícia Ianella ◽  
Samuel Rezende Paiva ◽  
Alexandre Rodrigues Caetano ◽  
Concepta Margaret McManus Pimentel
Keyword(s):  
Statistical Methods ◽  
Phenotypic Diversity ◽  
Selection Process ◽  
Genomic Data ◽  
Research Field ◽  
Economic Traits ◽  
Selection Signatures ◽  
Important Species ◽  
Challenges And Opportunities ◽  
Genomic Regions

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

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