Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck

Klees, Selina; Schlüter, Johanna-Sophie; Schellhorn, Jendrik; Bertram, Hendrik; Kurzweg, Antje Christine; Ramzan, Faisal; Schmitt, Armin O.; Gültaş, Mehmet

doi:10.3390/biology11020219

Cited by 4 publications

(6 citation statements)

References 94 publications

(185 reference statements)

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“…In this chapter, I discuss the methods applied in this thesis and the biological relevance of the results of my four publications, as described in the previous chapters. This chapter is partly based on the original publications [1][2][3][4].…”

Section: Discussionmentioning

confidence: 99%

“…In this chapter, I conclude my work and provide an outlook for future studies. This chapter is partly based on the original publications [1][2][3][4].…”

Section: Discussionmentioning

confidence: 99%

“…Lastly, I introduce the two application projects of my thesis, the oil content and -quality based on the oil crop Brassica napus L. and the immune response of chicken and duck after an infection with avian influenza. In the following four chapters, I provide my publications relevant for this thesis [1][2][3][4].…”

Section: Structure Of the Thesismentioning

confidence: 99%

“…In this study of different B. napus cultivars, I demonstrate the application of rSNPs together with multi-omics data to perform a systematic analysis of the complex interplay between rSNPs, TFs, and differentially expressed genes (DEGs) in vegetative and floral tissues underlying rapeseed oil content and -quality [4] (see Figure 1.3). In Chapter 6, I present a study in which I investigated the transcriptional gene regulation controlling the expression of genes induced by an infection with avian influenza in chicken and duck [2]. This uncovered master regulators that could stimulate an effective immune response in ducks following viral infection, while being dysfunctional in chicken.…”

Section: Structure Of the Thesismentioning

confidence: 99%

“…However, while the detection of rSNPs was rather straight-forward for the two rapeseed cultivars that share one reference genome, it is not as straight-forward in two different species with different reference genomes. In order to address this, I was involved in another study 2 , in which we investigated the role of SNPs that are shared between chicken and duck at orthologous positions, which can be referred to as coincident SNPs (coSNPs) [277]. In particular, we investigated coSNPs in promoters of the duck DEGs, differentially expressed after avian influenza infection, which were also investigated in this study (Chapter 6).…”

Section: Avian Influenza In Chicken and Duckmentioning

confidence: 99%

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Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

Wilhelmi

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Transcriptional regulation of gene expression in higher organisms is fundamental for numerous biological processes. These processes are mainly controlled by a special class of regulatory proteins, the transcription factors (TFs), and their combinatorial interplay. Various genetic programs, such as environmental adaptation, tissue development, or disease control, are governed by the binding of TFs to short DNA motifs, called transcription factor binding sites (TFBS), in the regulatory regions of their target genes. Single nucleotide polymorphisms (SNPs) located in promoter regions can alter TFBSs leading to a change in the binding affinity of TFs and, thus, affect gene expression. Such SNPs are referred to as regulatory SNPs (rSNPs). In recent years, rSNPs have come into the focus of research, and the underlying mechanisms resulting in a differential gene expression have been studied for many specific traits and diseases mainly in humans or model organisms, but also in agricultural species. However, these studies mostly concentrate on single regulatory variants and do not include systematic analyses. Thus, there is still a lack of such comprehensive analyses and genome-wide collections of rSNPs, and to date, only few tools and databases are available for livestock or crop species. In this work, I developed a pipeline for the detection of rSNPs and created the databases agReg-SNPdb and agReg-SNPdb-Plants, storing genome-wide collections of rSNPs and their predicted effects on TF binding for agricultural animal and plant species, respectively. agReg-SNPdb includes seven livestock and domestic species, namely cattle, pig, chicken, sheep, horse, goat, and dog and agReg-SNPdb-Plants includes 13 crop species and subspecies, namely African rice, Asian rice (with its subspecies Indica and Japonica), barley, bread wheat, durum wheat, grape, maize, rapeseed, sorghum, sunflower, tomato, and wild rice. Out of all species stored in agReg-SNPdb-Plants, rapeseed holds a special role. In contrast to the remaining species, where I used the data from Ensembl Plants as basis, in rapeseed, to date, there is no genome-wide collection of SNPs available. Therefore, I used a previously published data set based on different resequenced Brassica napus L. cultivars for the identification of rSNPs in agReg-SNPdb-Plants. Based on this data set, I investigated the regulatory mechanisms in two cultivars, namely Zhongshuang11 (ZS11), a so-called double-low accession with low content of erucic acid and glucosinolate, which is characterized by high oil content, and Zhongyou821 (ZY821), a so-called double-high accession with high content of erucic acid and glucosinolate, which is characterized by low oil content. In this way, I demonstrate the application of rSNPs together with multi-omics data to perform a systematic analysis of the complex interplay between rSNPs, TFs, and differentially expressed genes (DEGs) in four tissues (flower, leaf, stem, and root) which are underlying the oil content and -quality in rapeseed. viii Es hat mir großen Spaß ...

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Section: Discussionmentioning

confidence: 99%

“…In this chapter, I conclude my work and provide an outlook for future studies. This chapter is partly based on the original publications [1][2][3][4].…”

Section: Discussionmentioning

confidence: 99%

Section: Structure Of the Thesismentioning

confidence: 99%

Section: Structure Of the Thesismentioning

confidence: 99%

Section: Avian Influenza In Chicken and Duckmentioning

confidence: 99%

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Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

Wilhelmi

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CircMYO1B/miR-155 pathway is a common mechanism of stress-induced immunosuppression affecting immune response to three vaccines in chicken

Tian,

Wen,

Zhang

et al. 2024

International Immunopharmacology

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Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks

Bertram

Klees

Rajavel

et al. 2023

Biology

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Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as IκBα, STAT1/STAT3, GSK-3β, or p53) and related key signaling pathways (such as NF-κB, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.

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Comparative Investigation of Gene Regulatory Processes Underlying Avian Influenza Viruses in Chicken and Duck

Cited by 4 publications

References 94 publications

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

Investigation of the Regulatory Processes of Gene Expression in Animal and Plant Sciences

CircMYO1B/miR-155 pathway is a common mechanism of stress-induced immunosuppression affecting immune response to three vaccines in chicken

Comparative Investigation of Coincident Single Nucleotide Polymorphisms Underlying Avian Influenza Viruses in Chickens and Ducks

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