Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Abstract Background: Infestation by tea green leafhoppers, Empoasca (Matsumurasca) onukii , could cause a series of biochemical changes in tea leaves. As a typical cell-rupture feeder, E. onukii secretes proteases while probing with its stylet into the tender shoots of tea plants ( Camellia sinensis ). This study identified and analyzed proteases specifically expressed in the salivary gland (SG) and gut of E. onukii through enzymatic activity assays, complemented with an integrated analysis of transcriptome and proteome data.Results: In total, 129 contigs representing seven types of putative proteases were identified. Transcript abundance of digestive proteases and enzymatic activity assays showed that cathepsin B-like protease, cathepsin L-like protease, and serine proteases (trypsin- and chymotrypsin-like protease) were highly abundant in the gut while moderately abundant in the SG. The abundance pattern of digestive proteases in the SG and gut of E. onukii differed from that of other hemipterans including Nilaparvata lugens , Laodelphax striatellus , Acyrthosiphum pisum , Halyomorpha halys and Nephotettix cincticeps . Phylogenetic analysis showed that aminopeptidase N-like proteins and serine proteases abundant in the SG or gut of hemipterans were distributed to two distinct clusters.Conclusions: Altogether, this study provide insightful information on the digestive system of E. onukii and observed different patterns of proteases abundant in the SG and gut of E. onukii , in comparison with other five hemipteran species. These results will be beneficial in understanding the interaction between tea plants and E. onukii .

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Identification of human genetic variants controlling circular RNA expression

10.1101/472977 ◽

2018 ◽

Author(s):

Ikhlak Ahmed ◽

Thasni Karedath ◽

Fatima M. Al-Dasim ◽

Joel A. Malek

Keyword(s):

Mrna Expression ◽

Sequence Variation ◽

Transcript Abundance ◽

Circular Rna ◽

Circular Rnas ◽

Integrated Analysis ◽

Rna Expression ◽

Rna Regulation ◽

Human Disorders

AbstractCircular RNAs (circRNAs) are abundant in eukaryotic transcriptomes and have been linked to various human disorders. However, understanding genetic control of circular RNA expression is in early stages. Here we present the first integrated analysis of circRNAs and genome sequence variation from lymphoblastoid cell lines of the 1000 genomes project. We identified thousands of circRNAs in the RNA-seq data and show their association with local single nucleotide polymorphic sites, referred to as circQTLs, which influence the circRNA transcript abundance. Strikingly, we found that circQTLs exist independently of eQTLs with most circQTLs having no effect on mRNA expression. Only a fraction of the polymorphic sites are shared and linked to both circRNA and mRNA expression with mostly similar effects on circular and linear RNA. A shared intronic QTL, rs55928920, of HMSD gene drives the circular and linear expression in opposite directions, potentially modulating circRNA levels at the expense of mRNA. Finally, circQTLs and eQTLs are largely independent and exist in separate linkage disequilibrium (LD) blocks with circQTLs highly enriched for functional genomic elements and regulatory regions. This study reveals a previously uncharacterized role of DNA sequence variation in human circular RNA regulation.

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Transcriptomic and proteomic analysis of putative digestive proteases in the salivary gland and gut of Empoasca(Matsumurasca) onukii Matsuda

10.21203/rs.3.rs-25607/v1 ◽

2020 ◽

Author(s):

Ensi Shao ◽

Yujuan Song ◽

Yaomin Wang ◽

Yichen Liao ◽

Yufei Luo ◽

...

Keyword(s):

Salivary Gland ◽

Enzymatic Activity ◽

Serine Proteases ◽

Cathepsin L ◽

Transcript Abundance ◽

Nilaparvata Lugens ◽

Integrated Analysis ◽

Abundance Pattern ◽

Digestive Proteases ◽

Tea Plants

Abstract Background: Infestation by tea green leafhoppers, Empoasca (Matsumurasca) onukii, could cause a series of biochemical changes in tea leaves. As a typical cell-rupture feeder, E. onukii secretes proteases while probing with its stylet into the tender shoots of tea plants (Camellia sinensis). This study identified and analyzed proteases specifically expressed in the salivary gland (SG) and gut of E. onukii through enzymatic activity assays, complemented with an integrated analysis of transcriptome and proteome data.Results: In total, 129 contigs representing seven types of putative proteases were identified. Transcript abundance of digestive proteases and enzymatic activity assays showed that cathepsin B, cathepsin L, and serine proteases (trypsin and chymotrypsin) were highly abundant in the gut while moderately abundant in the SG. The abundance pattern of digestive proteases in the SG and gut of E. onukii differed from that of other hemipterans including Nilaparvata lugens, Laodelphax striatellus, Nephotettix cincticeps and Acyrthosiphum pisum. Phylogenetic analysis showed that aminopeptidase N-like proteins and serine proteases abundant in the SG or gut of hemipterans were distributed to two distinct clusters. Conclusions: Altogether, this study provide insightful information on the digestive system of E. onukii and observed different patterns of proteases abundant in the SG and gut of E. onukii, in comparison with other five hemipteran species. These results will be beneficial in understanding the interaction between tea plants and E. onukii.

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Transcriptomic and proteomic analysis of putative digestive proteases in the salivary gland and gut of Empoasca (Matsumurasca) onukii Matsuda

BMC Genomics ◽

10.1186/s12864-021-07578-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Ensi Shao ◽

Yujuan Song ◽

Yaomin Wang ◽

Yichen Liao ◽

Yufei Luo ◽

...

Keyword(s):

Salivary Gland ◽

Enzymatic Activity ◽

Serine Proteases ◽

Cathepsin L ◽

Transcript Abundance ◽

Nilaparvata Lugens ◽

Integrated Analysis ◽

Abundance Pattern ◽

Digestive Proteases ◽

Tea Plants

Abstract Background Infestation by tea green leafhoppers (Empoasca (Matsumurasca) onukii) can cause a series of biochemical changes in tea leaves. As a typical cell-rupture feeder, E. onukii secretes proteases while using its stylet to probe the tender shoots of tea plants (Camellia sinensis). This study identified and analyzed proteases expressed specifically in the salivary gland (SG) and gut of E. onukii through enzymatic activity assays complemented with an integrated analysis of transcriptomic and proteomic data. Results In total, 129 contigs representing seven types of putative proteases were identified. Transcript abundance of digestive proteases and enzymatic activity assays showed that cathepsin B-like protease, cathepsin L-like protease, and serine proteases (trypsin- and chymotrypsin-like protease) were highly abundant in the gut but moderately abundant in the SG. The abundance pattern of digestive proteases in the SG and gut of E. onukii differed from that of other hemipterans, including Nilaparvata lugens, Laodelphax striatellus, Acyrthosiphum pisum, Halyomorpha halys and Nephotettix cincticeps. Phylogenetic analysis showed that aminopeptidase N-like proteins and serine proteases abundant in the SG or gut of hemipterans formed two distinct clusters. Conclusions Altogether, this study provides insightful information on the digestive system of E. onukii. Compared to five other hemipteran species, we observed different patterns of proteases abundant in the SG and gut of E. onukii. These results will be beneficial in understanding the interaction between tea plants and E. onukii.

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Novel SNPs of the porcine TRIP12 are associated with water holding capacity of meat

Czech Journal of Animal Science ◽

10.17221/7048-cjas ◽

2013 ◽

Vol 58 (No. 11) ◽

pp. 525-533

Author(s):

H.T.P. Loan ◽

E. Murani ◽

S. Maak ◽

S. Ponsuksili ◽

K. Wimmers

Keyword(s):

Thyroid Hormone Receptor ◽

Regulatory Region ◽

Transcript Abundance ◽

Water Holding Capacity ◽

Integrated Analysis ◽

Technological Parameters ◽

Large White ◽

Interacting Protein ◽

Functional Candidate Gene ◽

Water Holding

Degradation of proteins during maturation of meat, mediated by the calpain/calpastatin system and the ubiquitination system, largely affects the tenderness and the water holding capacity (WHC) of meat. The thyroid hormone receptor interacting protein 12 (TRIP12) is known as a HECT domain-containing E3 ubiquitin-protein ligase that recognizes protein substrates for ubiquitination. This study aims to identify polymorphisms of the TRIP12 gene and to evaluate the relationship between genotype, transcript abundance, and meat quality traits in pigs. Two synonymous SNPs (XM_003484315.1:c.2211T>C, c.4957A>C) were identified that segregated among animals of herds of the breed German Landrace (DL, n = 269) and the commercial crossbreed of Pietrain × (German Large White × German Landrace) (PiF1, n = 300). Statistical analysis revealed associations between TRIP12 polymorphisms and the organismal traits related to water holding capacity, i.e. conductivity 45 min postmortem (CON1, P < 0.1) and pH 24 h postmortem (pH24, P < 0.1). Haplotype analysis revealed consistent effects on muscle CON1 in the two populations (P < 0.1). Carriers of the minor alleles C at the two polymorphic sites tended to have higher transcript abundance as well as higher water holding capacity. The integrated analysis of genotypic and haplotypic variation, transcript abundance, and technological parameters of WHC indicates that the XM_003484315.1:c.2211T>C and c.4957A>C of TRIP12 are in linkage disequilibrium with a causal factor located in a cis-regulatory region, which affects in the first instance gene expression and in the second traits related to water holding capacity. Our results provide statistical-genetical evidence supporting TRIP12 as a functional candidate gene for water holding capacity of porcine M. longissimus dorsi.

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