scholarly journals Genomics of coloration in natural animal populations

2017 ◽  
Vol 372 (1724) ◽  
pp. 20160337 ◽  
Author(s):  
Luis M. San-Jose ◽  
Alexandre Roulin
Keyword(s):  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Model Species ◽  
Animal Coloration ◽  
Sequencing Technologies ◽  
Animal Populations ◽  
Genome Wide ◽  
General Relevance ◽  
Genetic Structures

Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools. This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.

Inherited skin disease

2020 ◽  
pp. 5602-5611
Author(s):  
Thiviyani Maruthappu ◽  
David P. Kelsell
Keyword(s):  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Skin Diseases ◽  
Association Studies ◽  
Sequencing Technologies ◽  
Ectodermal Dysplasias ◽  
Genome Wide ◽  
Whole Exome ◽  
Common Skin ◽  
Immune Related Genes

Considerable advances in our understanding of inherited skin diseases have been made over the last decade as a result of high throughput sequencing technologies, including next generation sequencing and whole exome sequencing. The genetic basis of a myriad of monogenic epidermal disorders and syndromes including blistering diseases, ichthyoses, palmoplantar keratodermas, and the ectodermal dysplasias have now been elucidated. However, most patients referred from primary care to the dermatology clinic will be seeking treatment for a few common skin disorders such as psoriasis, eczema, and acne. The genetic basis of these disorders is rather more complex, but progress has been made through genome-wide association studies, which, for example, have linked susceptibility variants in the gene for filaggrin (FLG) and SPINK5 to atopic eczema, and IL23R and many other immune-related genes to psoriasis.

scholarly journals Genome-wide miRNA analysis and integrated network for flavonoid biosynthesis in Osmanthus fragrans

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yong Shi ◽  
Heng Xia ◽  
Xiaoting Cheng ◽  
Libin Zhang
Keyword(s):  
Secondary Metabolites ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Flavonoid Biosynthesis ◽  
Integrated Network ◽  
Osmanthus Fragrans ◽  
Flavonoid Synthesis ◽  
Genome Wide

AbstractBackgroundOsmanthus fragransis an important economical plant containing multiple secondary metabolites including flavonoids and anthocyanins. During the past years, the roles of miRNAs in regulating the biosynthesis of secondary metabolites in plants have been widely investigated. However, few studies on miRNA expression profiles and the potential roles in regulating flavonoid biosynthesis have been reported inO. fragrans.ResultsIn this study, we used high-throughput sequencing technology to analyze the expression profiles of miRNAs in leaf and flower tissues ofO. fragrans. As a result, 106 conserved miRNAs distributed in 47 families and 88 novel miRNAs were identified. Further analysis showed there were 133 miRNAs differentially expressed in leaves and flowers. Additionally, the potential target genes of miRNAs as well as the related metabolic pathways were predicted. In the end, flavonoid content was measured in flower and leaf tissues and potential role of miR858 in regulating flavonoid synthesis was illustrated inO. fragrans.ConclusionsThis study not only provided the genome-wide miRNA profiles in the flower and leaf tissue ofO. fragrans, but also investigated the potential regulatory role of miR858a in flavonoid synthesis inO. fragrans. The results specifically indicated the connection of miRNAs to the regulation of secondary metabolite biosynthesis in non-model economical plant.

scholarly journals Genetic architecture and heritability of early-life telomere length in a wild passerine

2021 ◽  
Author(s):  
Michael Pepke ◽  
Thomas Kvalnes ◽  
Sarah Lundregan ◽  
Winnie Boner ◽  
Pat Monaghan ◽  
...  
Keyword(s):  
Body Size ◽  
Telomere Length ◽  
Early Life ◽  
Genetic Basis ◽  
Skeletal Development ◽  
Cellular Growth ◽  
Phenotypic Correlation ◽  
Animal Populations ◽  
Genome Wide ◽  
Genomic Regions

Early-life telomere length (TL) is associated with fitness in a range of organisms. Little is known about the genetic basis of variation in TL in wild animal populations, but to understand the evolutionary and ecological significance of TL it is important to quantify the relative importance of genetic and environmental variation in TL. In this study, we measured TL in 2746 house sparrow nestlings sampled across 20 years and used an animal model to show that there is a small heritable component of early-life TL (h2=0.04), but with a strong component of maternal inheritance. Variation in TL among individuals was mainly driven by environmental (year) variance, but also brood and parental effects. We did not find evidence for a negative genetic correlation underlying the observed negative phenotypic correlation between TL and structural body size. Thus, TL may evolve independently of body size and the negative phenotypic correlation is likely to be caused by non-genetic environmental effects. We further used genome‐wide association analysis to identify genomic regions associated with TL variation. We identified several putative genes underlying TL variation; these have been inferred to be involved in oxidative stress, cellular growth, skeletal development, cell differentiation and tumorigenesis in other species. Together, our results show that TL is a lowly heritable, polygenic trait which is strongly affected by environmental conditions in a free-living bird.

scholarly journals Splicing dysregulation as a driver of breast cancer

2018 ◽  
Vol 25 (9) ◽  
pp. R467-R478 ◽  
Author(s):  
Abigail Read ◽  
Rachael Natrajan
Keyword(s):  
Breast Cancer ◽  
High Throughput Sequencing ◽  
Predictive Biomarkers ◽  
Therapy Resistance ◽  
Complete Understanding ◽  
Molecular Abnormalities ◽  
Sequencing Technologies ◽  
Large Repertoire ◽  
Positive Breast Cancer

Breast cancer is known to be a heterogeneous disease driven by a large repertoire of molecular abnormalities, which contribute to its diverse clinical behaviour. Despite the success of targeted therapy approaches for breast cancer patient management, there is still a lack of the molecular understanding of aggressive forms of the disease and clinical management of these patients remains difficult. The advent of high-throughput sequencing technologies has paved the way for a more complete understanding of the molecular make-up of the breast cancer genome. As such, it is becoming apparent that disruption of canonical splicing within breast cancer governs its clinical progression. In this review, we discuss the role of dysregulation of spliceosomal component genes and associated factors in the progression of breast cancer, their role in therapy resistance and the use of quantitative isoform expression as potential prognostic and predictive biomarkers with a particular focus on oestrogen receptor-positive breast cancer.

High Throughput Sequencing Following Cross-Linked Immune Precipitation (HITS-CLIP) of Argonaute (AGO) Identifies Mir-9 As a Regulator of MMP2 in the Marrow Microenvironment (ME)

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2392-2392 ◽  
Author(s):  
Ilango Balakrishnan ◽  
Xiaodong Yang ◽  
Beverly Torok-Storb ◽  
Jay Hesselberth ◽  
Manoj M Pillai
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Stromal Cells ◽  
False Positive ◽  
High Throughput Sequencing ◽  
Regulation Of Gene Expression ◽  
Negative Results ◽  
Genome Wide ◽  
Direct Binding

Abstract Abstract 2392 There is increasing recognition of the role of small noncoding RNAs in post-transcriptional regulation of gene expression in diverse tissues of eukaryotic organisms including vertebrates. MicroRNAs (miRNAs) are the best studied amongst these small RNAs and are thought to act by binding to the 3' untranslated regions (3' UTRs) of mature mRNAs in a sequence-specific fashion and preventing the initiation of peptide translation and/ or initiating mRNA degradation. Recent evidence suggests that miRNA-based regulation might involve binding to regions other than 3' UTRs including coding regions. Current approaches to defining miRNA-mRNA interactions are mostly restricted to those based on bio-informatic prediction, protein down-regulation following in-vitro transfection of miRNA precursors and luciferase assays to determine binding to 3' UTRs. None of these methods however show direct interaction between a specific miRNA and its purported target RNA. Bio-informatics-based approaches are also prone to false positive and negative results given the short length of sequence matching, and reliance on heuristics and cross-species conservation. Newer genome-wide approaches like HITS-CLIP (High Throughput Sequencing following Cross Linked Immuno Precipitation, or CLIP-Seq) overcome some of these limitations by directly isolating the miRNA-mRNA interactome bound to argonaute (AGO), a critical component of the rna-induced silencing complex (RISC)1. HITS-CLIP utilizes the ability of ultraviolet (UV) light to cross-link RNAs to proteins in their close proximity. The crosslinked miRNA-mRNA-Ago complexes are then isolated and the RNA reverse transcribed to cDNA libraries and sequenced by next generation sequencing (NGS). Given the widespread role of miRNAs in several vertebrate tissues, we hypothesized that miRNA-regulation of gene expression is operant in the hematopoietic microenvironment (ME) and thus contributes to regulation of hematopoiesis. We hence used HITS-CLIP to analyze the miRNA-mRNA interactome of three key cellular components of the ME: stromal cells, endothelium and macrophages. We have previously reported on the use of the stromal cell lines Hs27a and Hs5 to define specific functional niches within the ME. Hs27a can functionally support primitive hematopoietic stem and progenitor cells (HSPC) in cobblestone areas (CSAs) and express high levels of factors known to support HSPC such as SDF1, Jagged1 and Angiopoietin1. In contrast, Hs5 drives HSPC to mature lineages and secretes high levels of cytokines like IL1, IL6 and GCSF. Human umbilical vein endothelial cells (HUVECs) and MCSF-treated CD14+ cells were utilized for the endothelial and macrophage cultures respectively. The HITS-CLIP datasets from each of these populations were enriched for a putative binding site for miR-9 in the coding region of Matrix Metalloproteinase 2 (MMP2) mRNA. MMP2 belongs to a family of endopeptidases critical in the remodeling of extracellular matrix in several tissues and in the egress/ homing of HSPC to their functional niches in the ME. Functional binding of miR-9 to MMP2 was validated by Western-blotting of stromal cells transfected with miR-9 which revealed > 50% reduction of protein levels when compared to control-transfected cells. This was also confirmed by gelatin zymography which showed significantly reduced MMP2 activity in stromal cells transfected with miR-9. Finally, to confirm direct binding of miR-9 to the putative binding region on the MMP2 transcript, we cloned this microRNA responsive region (MRE) downstream of the Renilla luciferase gene and assayed its activity by luciferase assays. MiR-9 transfection down-regulated luciferase activity > 50% confirming direct binding to the MRE. Our results show that genome-wide approaches such as HITS-CLIP can be used to define in vivo miRNA-mRNA interactions in the ME and should be considered in studies that define such interactions given the significant false-positive and false negative results associated with approaches based on bio-informatics alone. The approach can also define specific interactions between miRNAs and mRNAs such as MMP2, of relevance to regulation of the hematopoietic ME. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Identification and characterization of salt-tolerance relative miRNAs in Procambarus clarkii by high-throughput sequencing

ExRNA ◽  
2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Fangfang Jin ◽  
Yuling Sun
Keyword(s):  
Salt Tolerance ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Economic Losses ◽  
Srna Library ◽  
Genome Wide ◽  
A Genome

Abstract Procambarus clarkii is one of the important economic species in China and has been served as tasty food in recent years after being introduced to Nanjing. Significant problems of environment factors, such as salinity, pH and temperature, especially salinity, has the potential to result in significant economic losses in many crayfish-producing farms in China. miRNAs are a kind of ~ 22 nucleotide small non coding RNAs which were encoded by plants, animals and some viruses with functions in RNA silencing or post-transcription regulation. We constructed four sRNA library of P. clarkia from different tissues and treatments by using high-throughput sequencing technology. A total of 101 conserved miRNAs and two novel pre-miRNAs were identified and RT-qPCR were further performed to confirm existence of part of identified miRNAs. A genome wide expression profile of salt-tolerance miRNAs was proved and three miRNAs were further validated by RT-qPCR with dynamic response to different salinity stages. The study of miRNAs in P. clarkia can help us better understanding the role of miRNAs in salt-tolerance in P. clarkia.

scholarly journals On the origin of species: insights from the ecological genomics of lake whitefish

2010 ◽  
Vol 365 (1547) ◽  
pp. 1783-1800 ◽  
Author(s):  
Louis Bernatchez ◽  
Sébastien Renaut ◽  
Andrew R. Whiteley ◽  
Nicolas Derome ◽  
Julie Jeukens ◽  
...  
Keyword(s):  
Research Programme ◽  
Adaptive Divergence ◽  
Population Divergence ◽  
Ecological Genomics ◽  
Model Species ◽  
Sequencing Technologies ◽  
Sympatric Forms ◽  
Genomic Tools

In contrast to the large amount of ecological information supporting the role of natural selection as a main cause of population divergence and speciation, an understanding of the genomic basis underlying those processes is in its infancy. In this paper, we review the main findings of a long-term research programme that we have been conducting on the ecological genomics of sympatric forms of whitefish ( Coregonus spp.) engaged in the process of speciation. We present this system as an example of how applying a combination of approaches under the conceptual framework of the theory of adaptive radiation has yielded substantial insight into evolutionary processes in a non-model species. We also discuss how the joint use of recent biotechnological developments will provide a powerful means to address issues raised by observations made to date. Namely, we present data illustrating the potential offered by combining next generation sequencing technologies with other genomic approaches to reveal the genomic bases of adaptive divergence and reproductive isolation. Given increasing access to these new genomic tools, we argue that non-model species studied in their ecological context such as whitefish will play an increasingly important role in generalizing knowledge of speciation.

scholarly journals Incorporation of DNA methylation into eQTL mapping in African Americans

2020 ◽  
Author(s):  
Anmol Singh ◽  
Yizhen Zhong ◽  
Layan Nahlawi ◽  
C. Sehwan Park ◽  
Tanima De ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
African Americans ◽  
Genetic Basis ◽  
Critical Role ◽  
Eqtl Analysis ◽  
Biliary Cirrhosis ◽  
Eqtl Mapping ◽  
Genome Wide

Epigenetics is a reversible molecular mechanism that plays a critical role in many developmental, adaptive, and disease processes. DNA methylation has been shown to regulate gene expression and the advent of high throughput technologies has made genome-wide DNA methylation analysis possible. We investigated the effect of DNA methylation in eQTL mapping (methylation-adjusted eQTLs), by incorporating DNA methylation as a SNP-based covariate in eQTL mapping in African American derived hepatocytes. We found that the addition of DNA methylation uncovered new eQTLs and eGenes. Previously discovered eQTLs were significantly altered by the addition of DNA methylation data suggesting that methylation may modulate the association of SNPs to gene expression. We found that methylation-adjusted eQTLs which were less significant compared to PC-adjusted eQTLs were enriched in lipoprotein measurements (FDR = 0.0040), immune system disorders (FDR = 0.0042), and liver enzyme measurements (FDR = 0.047), suggesting a role of DNA methylation in regulating the genetic basis of these phenotypes. Our methylation-adjusted eQTL analysis also uncovered novel SNP-gene pairs. For example, our study found the SNP, rs11546996, was associated to PNKP. In a previous GWAS, this SNP was associated with primary biliary cirrhosis although the causal gene was thought to be SPIB. Our methylation-adjusted method potentially adds new understanding to the genetic basis of complex diseases that disproportionally affect African Americans.

scholarly journals Genome-wide characterization of RNA editing in chicken: lack of evidence for non-A-to-I events

2014 ◽  
Author(s):  
Laure Frésard ◽  
Sophie Leroux ◽  
Pierre-François Roux ◽  
C Klopp ◽  
Stéphane Fabre ◽  
...  
Keyword(s):  
Rna Editing ◽  
High Throughput Sequencing ◽  
Nucleotide Substitutions ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Level Increase ◽  
Functional Consequences ◽  
Genome Screening ◽  
Editing Level

RNA editing corresponds to a post-transcriptional nucleotide change in the RNA sequence, creating an alternative nucleotide, not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is more and more described in mammals, notably since the availability of next generation sequencing technologies allowing a whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken are still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, to understand to what extent this phenomenon is conserved in vertebrates. We performed RNA and DNA sequencing from 8 embryos. Being aware of common pitfalls inherent to sequence analyses leading to false positive discovery, we stringently filtered our datasets and found less than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual editing level increase with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, and provide support of an absence of non A-to-I events from the chicken transcriptome.

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