An Integrated Analysis of miRNAs and Methylated Genes Encoding mRNAs and lncRNAs in Sheep Breeds with Different Fecundity

AbstractBackgroundThe genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization.ResultsWe performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.ConclusionsThis study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.

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Characterizing disease progression of nonalcoholic steatohepatitis in Leptin-deficient rats by integrated transcriptome analysis

Experimental Biology and Medicine ◽

10.1177/1535370220976530 ◽

2020 ◽

pp. 153537022097653

Author(s):

Ping Lu ◽

Guang Yang ◽

Lichun Jiang ◽

Wen He ◽

Wanwan Wu ◽

...

Keyword(s):

Nonalcoholic Steatohepatitis ◽

Fatty Acid Synthase ◽

Macrophage Polarization ◽

Nuclear Factor Κb ◽

Integrated Analysis ◽

Cytokines And Chemokines ◽

Genes Encoding ◽

Elevated Expression ◽

Chemokine Ligand ◽

Hepatic Transcriptome

Nonalcoholic steatohepatitis (NASH) is an aggressive liver disease threatening human health, yet no medicine is developed to treat this disease. In this study, we first discovered that Leptin mutant rats ( LepΔI14/ΔI14) exhibit characteristic NASH phenotypes including steatosis, lymphocyte infiltration, and ballooning after postnatal week 16. We then examined NASH progression by performing an integrated analysis of hepatic transcriptome in Leptin-deficient rats from postnatal 4 to 48 weeks. Initially, simple steatosis in LepΔI14/ΔI14 rats were observed with increased expression of the genes encoding for rate-limiting enzymes in lipid metabolism such as acetyl-CoA carboxylase and fatty acid synthase. When NASH phenotypes became well developed at postnatal week 16, we found gene expression changes in insulin resistance, inflammation, reactive oxygen species and endoplasmic reticulum stress. As NASH phenotypes further progressed with age, we observed elevated expression of cytokines and chemokines including C-C motif chemokine ligand 2, tumor necrosis factor ɑ, interleukin-6, and interleukin-1β together with activation of the c-Jun N-terminal kinase and nuclear factor-κB pathways. Histologically, livers in LepΔI14/ΔI14 rats exhibited increased cell infiltration of MPO+ neutrophils, CD8+ T cells, CD68+ hepatic macrophages, and CCR2+ inflammatory monocyte-derived macrophages associated with macrophage polarization from M2 to M1. Subsequent cross-species comparison of transcriptomes in human, rat, and mouse NASH models indicated that Leptin-deficient rats bear more similarities to human NASH patients than previously established mouse NASH models. Taken together, our study suggests that LepΔI14/ΔI14 rats are a valuable pre-clinical rodent model to evaluate NASH drug safety and efficacy.

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Application of PCR Technique to Detect Polymorphism of the KRTAP1.1 Gene in Three Sheep Breeds - A Review

10.5772/intechopen.96941 ◽

2021 ◽

Author(s):

Theopoline Omagano Itenge

Keyword(s):

Genetic Variation ◽

New Zealand ◽

Base Pair ◽

Wool Fibre ◽

Length Variation ◽

Typing Method ◽

Sheep Breeds ◽

Genes Encoding ◽

Associated Proteins

The quality of wool and pelt products depends on the quality of the wool and pelt grown on farm. Genes coding for the proteins involved in the structural components of wool fibre; keratin intermediate filaments (KRTs) and keratin keratin-associated proteins (KAPs) have been extensively researched. The KAPs form a matrix in which the KRTs are embedded. In sheep, KRTAP1.1 (previously B2A) is one of the four genes encoding proteins that make up the KAP1.n family. The ovine KRTAP1.1 gene is clustered with the KRTAP1.3 and KRTAP1.4 genes on chromosome 11. In this chapter, the Polymerase Chain Reaction (PCR) – Applied Fragment Length Polymorphism (AFLP) typing method used to detect polymorphism in the KRTAP1.1 gene is reviewed. Three length variation KRTAP1.1 alleles; named A, B and C, of the lengths 341 base pair, 311 base pair and 281 base pair, respectively have been reported in three sheep breeds; Romney sheep of New Zealand, Merino sheep of New Zealand and Swakara sheep of Namibia. Genetic variation within the KRTs and KAPs can be further exploited to determine as to whether such variation impacts on wool quality. The presence of genetic variation within KRTs and KAPs offers opportunities for the development of gene markers affecting wool and pelt quality traits.

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Integrated Analysis of mRNA and microRNA Elucidates the Regulation of Glycyrrhizic Acid Biosynthesis in Glycyrrhiza uralensis Fisch

International Journal of Molecular Sciences ◽

10.3390/ijms21093101 ◽

2020 ◽

Vol 21 (9) ◽

pp. 3101

Author(s):

Yanni Li ◽

Caixia Chen ◽

Zhenzhen Xie ◽

Jing Xu ◽

Bin Wu ◽

...

Keyword(s):

Glycyrrhizic Acid ◽

High Throughput Sequencing ◽

Bioactive Compound ◽

Integrated Analysis ◽

Structural Genes ◽

Acid Biosynthesis ◽

Chinese Herbal ◽

Genes Encoding ◽

New Varieties ◽

Ga Biosynthesis

Licorice (Glycyrrhiza) is a staple Chinese herbal medicine in which the primary bioactive compound is glycyrrhizic acid (GA), which has important pharmacological functions. To date, the structural genes involved in GA biosynthesis have been identified. However, the regulation of these genes in G. uralensis has not been elucidated. In this study, we performed a comprehensive analysis based on the transcriptome and small RNAome by high-throughput sequencing. In total, we identified 18 structural GA genes and 3924 transporter genes. We identified genes encoding 2374 transporters, 1040 transcription factors (TFs), 262 transcriptional regulators (TRs) and 689 protein kinases (PKs), which were coexpressed with at least one structural gene. We also identified 50,970 alternative splicing (AS) events, in which 17 structural genes exhibited AS. Finally, we also determined that miRNAs potentially targeted 4 structural genes, and 318, 8, and 218 miRNAs potentially regulated 150 TFs, 34 TRs, and 88 PKs, respectively, related to GA. Overall, the results of this study helped to elucidate the gene expression and regulation of GA biosynthesis in G. uralensis, provided a theoretical basis for the synthesis of GA via synthetic biology, and laid a foundation for the cultivation of new varieties of licorice with high GA content.

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DNA methylation in satellite repeats disorders

Essays in Biochemistry ◽

10.1042/ebc20190028 ◽

2019 ◽

Vol 63 (6) ◽

pp. 757-771 ◽

Cited By ~ 4

Author(s):

Claire Francastel ◽

Frédérique Magdinier

Keyword(s):

Dna Methylation ◽

Human Genome ◽

Repetitive Dna ◽

Dna Sequences ◽

Satellite Repeats ◽

Tremendous Progress ◽

Genes Encoding ◽

Dna Elements ◽

Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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