Analysis of protein-protein interaction network based on transcriptome profiling of ovine granulosa cells identifies candidate genes in cyclic recruitment of ovarian follicles

Talebi, Reza; Ahmadi, Ahmad; Afraz, Fazlollah

doi:10.1186/s40781-018-0171-y

Cited by 11 publications

(3 citation statements)

References 31 publications

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“…SLC39A9 may be an important gene in the early stages of NDV infection and may play an important role in the chickens’ adaptive immune response. Another gene, ACTN1 has been connected to phagocytosis and the immune system [44].…”

Section: Discussionmentioning

confidence: 99%

Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

Walugembe

Mushi

Amuzu-Aweh

et al. 2019

Genes

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Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in addition to growth rate. We estimated genetic parameters and conducted genome-wide association study analyses by genotyping 1399 chickens using the Affymetrix 600K chicken SNP chip. Estimates of heritability of the evaluated traits were moderate (0.18–0.35). Five quantitative trait loci (QTL) associated with growth and/or response to NDV were identified by single-SNP analyses, with some regions explaining ≥1% of genetic variance based on the Bayes-B method. Immune related genes, such as ETS1, TIRAP, and KIRREL3, were located in regions associated with viral load at 6 dpi. The moderate estimates of heritability and identified QTL indicate that NDV response traits may be improved through selective breeding of chickens to enhance increased NDV resistance and vaccine efficacy in Tanzanian local ecotypes.

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Section: Discussionmentioning

confidence: 99%

Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

Walugembe

Mushi

Amuzu-Aweh

et al. 2019

Genes

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“…We identified candidate genes associated with immune response ( BCAP29 [ 55 ], ATP8B4 [ 56 ]), reproductive traits ( CC2D1B ) [ 57 ], teat number ( SYNDIG1L ) [ 58 ], and horn phenotype ( RXFP2 ) [ 12 ]. The upregulation of critical genes during the follicular phase reflects the immune system’s role in follicular recruitment, while endocrine changes throughout the estrous cycle regulate immune gene expression, affecting follicular atresia and recruitment [ 59 ]. The immune system precisely regulates follicle development and maturation, influenced by the ovarian microenvironment [ 60 ].…”

Section: Discussionmentioning

confidence: 99%

Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds

Zhong,

Hou,

Zhao

et al. 2024

BMC Genomics

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Hu sheep (HS), a breed of sheep carrying the FecB mutation gene, is known for its “year-round estrus and multiple births” and is an ideal model for studying the high fecundity mechanisms of livestock. Through analyzing and comparing the genomic selection features of Hu sheep and other sheep breeds, we identified a series of candidate genes that may play a role in Hu sheep’s high fecundity mechanisms. In this study, we conducted whole-genome resequencing on six breeds and screened key mutations significantly correlated with high reproductive traits in sheep. Notably, the CC2D1B gene was selected by the fixation index (FST) and the cross-population composite likelihood ratio (XP-CLR) methods in HS and other five breeds. It was worth noting that the CC2D1B gene in HS was different from that in other sheep breeds, and seven missense mutations have been identified. Furthermore, the linkage disequilibrium (LD) analysis revealed a strong linkage disequilibrium in this specific gene region. Subsequently, by performing different grouping based on FecB genotypes in Hu sheep, genome-wide selective signal analysis screened several genes related to reproduction, such as BMPR1B and PPM1K. Besides, FST analysis identified functional genes related to reproductive traits, including RHEB, HSPA2, PPP1CC, HVCN1, and CCDC63. Additionally, a missense mutation was found in the CCDC63 gene and the haplotype was different between the high reproduction (HR) group and low reproduction (LR) group in HS. In summary, we discovered genetic differentiation among six distinct breeding sheep breeds at the whole genome level. Additionally, we identified a set of genes which were associated with reproductive performance in Hu sheep and visualized how these genes differed in different breeds. These findings laid a theoretical foundation for understanding genetic mechanisms behind high prolific traits in sheep.

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“…PPI networks were constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) Version 11.5 (https://www.string-db.org/ accessed on 23 December 2022) and Cytoscape 3.9.1 software [34]. The PPI network was constructed based on information obtained from experiments and predicted from gene neighborhood, gene fusions, gene co-occurrence (with a 0.4 medium confidence score as the analysis parameter), and additional information, such as co-expression and text mining [35]. GO and pathway annotation of PPI networks were also analyzed and visualized using ClueGO version 2.5.9/CluePedia version 1.5.9 plugins from Cytoscape software [36].…”

Section: Ppi Network Construction and The Identification Of Hub Genesmentioning

confidence: 99%

RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in Neurospora crassa

Yu,

Veerana,

Ketya

et al. 2023

JoF

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While the biological role of naturally occurring nitric oxide (NO) in filamentous fungi has been uncovered, the underlying molecular regulatory networks remain unclear. In this study, we conducted an analysis of transcriptome profiles to investigate the initial stages of understanding these NO regulatory networks in Neurospora crassa, a well-established model filamentous fungus. Utilizing RNA sequencing, differential gene expression screening, and various functional analyses, our findings revealed that the removal of intracellular NO resulted in the differential transcription of 424 genes. Notably, the majority of these differentially expressed genes were functionally linked to processes associated with carbohydrate and amino acid metabolism. Furthermore, our analysis highlighted the prevalence of four specific protein domains (zinc finger C2H2, PLCYc, PLCXc, and SH3) in the encoded proteins of these differentially expressed genes. Through protein–protein interaction network analysis, we identified eight hub genes with substantial interaction connectivity, with mss-4 and gel-3 emerging as possibly major responsive genes during NO scavenging, particularly influencing vegetative growth. Additionally, our study unveiled that NO scavenging led to the inhibition of gene transcription related to a protein complex associated with ribosome biogenesis. Overall, our investigation suggests that endogenously produced NO in N. crassa likely governs the transcription of genes responsible for protein complexes involved in carbohydrate and amino acid metabolism, as well as ribosomal biogenesis, ultimately impacting the growth and development of hyphae.

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Analysis of protein-protein interaction network based on transcriptome profiling of ovine granulosa cells identifies candidate genes in cyclic recruitment of ovarian follicles

Cited by 11 publications

References 31 publications

Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

Genetic Analyses of Tanzanian Local Chicken Ecotypes Challenged with Newcastle Disease Virus

Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds

RNA-Seq-Based Transcriptome Analysis of Nitric Oxide Scavenging Response in Neurospora crassa

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