Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model plant species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants

Hanseniaspora Uvarum ◽

Premature Termination Codons ◽

Gene Transcripts ◽

Abstract Background Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Results Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon transcription through the exposure of the callus to live cultures of an endemic grapevine yeast, Hanseniaspora uvarum. We found that only 1.7%-2.5% of total annotated TE loci were transcribed, of which 5%-10% of these were full-length, and the expressed TE loci exhibited a strong location bias towards expressed genes. These tendencies were also observed in Arabidopsis thaliana wild-type and ibm2, but not in ddm1 mutant. Moreover, differentially expressed TE loci in the grapevine model tended to share expression patterns with co-localised differentially expressed genes. Utilising nanopore cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified low levels of full-length transcripts deriving from structurally autonomous TE loci in the grapevine model. Conclusion Our observations in two disparate plant models representing clonally and seed propagated plant species reveal a closely connected transcriptional relationship between TEs and co-localised genes, particularly when the epigenetic silencing system is intact. We found that the stress treatment alone was insufficient to induce large-scale full-length transcription from structurally competent TE loci, a necessity for non-autonomous and autonomous mobilisation.

miRNA Expression Characterizes Histological Subtypes and Metastasis in Penile Squamous Cell Carcinoma

Cancers ◽

10.3390/cancers13061480 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1480

Author(s):

Hiresh Ayoubian ◽

Joana Heinzelmann ◽

Sebastian Hölters ◽

Oybek Khalmurzaev ◽

Alexey Pryalukhin ◽

...

Keyword(s):

Microarray Data ◽

Expression Patterns ◽

Hpv Infection ◽

Histological Subtypes ◽

Specific Expression ◽

Tissue Samples ◽

Qrt Pcr ◽

Differentially Expressed Mirnas ◽

Although microRNAs are described as promising biomarkers in many tumor types, little is known about their role in PSCC. Thus, we attempted to identify miRNAs involved in tumor development and metastasis in distinct histological subtypes considering the impact of HPV infection. In a first step, microarray analyses were performed on RNA from formalin-fixed, paraffin-embedded tumor (22), and normal (8) tissue samples. Microarray data were validated for selected miRNAs by qRT-PCR on an enlarged cohort, including 27 tumor and 18 normal tissues. We found 876 significantly differentially expressed miRNAs (p ≤ 0.01) between HPV-positive and HPV-negative tumor samples by microarray analysis. Although no significant differences were detected between normal and tumor tissue in the whole cohort, specific expression patterns occurred in distinct histological subtypes, such as HPV-negative usual PSCC (95 differentially expressed miRNAs, p ≤ 0.05) and HPV-positive basaloid/warty subtypes (247 differentially expressed miRNAs, p ≤ 0.05). Selected miRNAs were confirmed by qRT-PCR. Furthermore, microarray data revealed 118 miRNAs (p ≤ 0.01) that were significantly differentially expressed in metastatic versus non-metastatic usual PSCC. The lower expression levels for miR-137 and miR-328-3p in metastatic usual PSCC were validated by qRT-PCR. The results of this study confirmed that specific miRNAs could serve as potential diagnostic and prognostic markers in single PSCC subtypes and are associated with HPV-dependent pathways.

Ecological Impacts of Megaprojects: Species Succession and Functional Composition

Plants ◽

10.3390/plants10112411 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2411

Author(s):

Hamada E. Ali ◽

Solveig Franziska Bucher

Keyword(s):

Plant Species ◽

Large Scale ◽

Invasive Plant ◽

Species Traits ◽

Natural Vegetation ◽

Ecological Impacts ◽

Imperata Cylindrica ◽

Dry Matter Content ◽

Large Scale Disturbance ◽

Land-use changes have huge impacts on natural vegetation, especially megaprojects, as the vegetation layer is destroyed in the course of construction works affecting the plant community composition and functionality. This large-scale disturbance might be a gateway for the establishment of invasive plant species, which can outcompete the natural flora. In contrast, species occurring in the area before the construction are not able to re-establish. In this study, we analyzed the impact of a pipeline construction on a wetland nature reserve located in northern Egypt. Therefore, we analyzed the plant species occurrence and abundance and measured each plant species’ traits before the construction in 2017 as well as on multiple occasions up to 2 years after the construction had finished on altogether five sampling events. We found that the construction activity led to the establishment of an invasive species which previously did not occur in the area, namely, Imperata cylindrica, whereas five species (Ipomoea carnea, Pluchea dioscoridis, Polygonum equisetiforme, Tamarix nilotica, and Typha domingensis) could not re-establish after the disturbance. The functionality of ecosystems assessed via the analysis of plant functional traits (plant height, specific leaf area, and leaf dry matter content) changed within species over all sampling events and within the community showing a tendency to approximate pre-construction values. Functional dispersion and Rao’s quadratic diversity were higher after the megaproject than before. These findings are important to capture possible re-establishment and recovery of natural vegetation after construction and raise awareness to the impact of megaprojects, especially in areas which are high priority for conservation.

Toxoplasma infection alters dopamine-sensitive behaviors and host gene expression patterns associated with neuropsychiatric disease

10.1101/2021.08.16.456298 ◽

2021 ◽

Author(s):

Graham L. Cromar ◽

Jonathan Epp ◽

Ana Popovic ◽

Yusing Gu ◽

Violet Ha ◽

...

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Neurocognitive Disorders ◽

Gene Expression Patterns ◽

Low Grade ◽

Cocaine Exposure ◽

Multiple Testing Correction ◽

ABSTRACTToxoplasma gondii is a single celled parasite thought to infect 1 in 3 worldwide. During chronic infection, T. gondii can migrate to the brain where it promotes low-grade neuroinflammation with the capacity to induce changes in brain morphology and behavior. Consequently, infection with T. gondii has been linked with a number of neurocognitive disorders including schizophrenia (SZ), dementia, and Parkinson’s disease. Beyond neuroinflammation, infection with T. gondii can modulate the production of neurotransmitters, such as dopamine. To further dissect these pathways and examine the impact of altered dopaminergic sensitivity in T. gondii-infected mice on both behavior and gene expression, we developed a novel mouse model, based on stimulant-induced (cocaine) hyperactivity. Employing this model, we found that infection with T. gondii did not alter fear behavior but did impact motor activity and neuropsychiatric-related behaviurs. While both behaviors may help reduce predator avoidance, consistent with previous studies, the latter finding is reminiscent of neurocognitive disorders. Applying RNASeq to two relevant brain regions, striatum and hippocampus, we identified a broad upregulation of immune responses. However, we also noted significant associations with more meaningful neurologically relevant terms were masked due to the sheer number of terms incorporated in multiple testing correction. We therefore performed a more focused analysis using a curated set of neurologically relevant terms revealing significant associations across multiple pathways. We also found that T. gondii and cocaine treatments impacted the expression of similar functional pathways in the hippocampus and striatum although, as indicated by the low overlap among differentially expressed genes, largely via different proteins. Furthermore, while most differentially expressed genes reacted to a single condition and were mostly upregulated, we identified gene expression patterns indicating unexpected interactions between T. gondii infection and cocaine exposure. These include sets of genes which responded to cocaine exposure but not upon cocaine exposure in the context of T. gondii infection, suggestive of a neuroprotective effect advantageous to parasite persistence. Given its ability to uncover such complex relationships, we propose this novel model offers a new perspective to dissect the molecular pathways by which T. gondii infection contributes to neuropsychiatric disorders such as schizophrenia.

Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

10.21203/rs.3.rs-22487/v1 ◽

2020 ◽

Author(s):

Ayyappa Kumar Sista Kameshwar ◽

Julang Li

Keyword(s):

Gene Expression ◽

Litter Size ◽

Large Scale ◽

Expression Patterns ◽

Genetic Selection ◽

Follicular Development ◽

Oocyte Quality ◽

Metadata Analysis

Abstract Background : Litter size is a very important production index in the livestock industry, which is controlled by various complex physiological processes. To understand and reveal the common gene expression patterns involved in controlling prolificacy, we have performed a large-scale metadata analysis of five genome-wide transcriptome datasets of pig and sheep ovary samples obtained from high and low litter groups, respectively. We analyzed separately each transcriptome dataset using GeneSpring v14.8 software by implementing standard, generic analysis pipelines and further compared the list of most significant and differentially expressed genes obtained from each dataset to identify genes that are found to be common and significant across all the studies. Results : We have observed a total of 62 differentially expressed genes common among more than two gene expression datasets. The KEGG pathway analysis of most significant genes has shown that they are involved in metabolism, the biosynthesis of lipids, cholesterol and steroid hormones, immune system, cell growth and death, cancer-related pathways and signal transduction pathways. Of these 62 genes, we further narrowed the list to the 25 most significant genes by focusing on the ones with fold change >1.5 and p<0.05. These genes are CYP11A1, HSD17B2, STAR, SCARB1, IGSF8, MSMB, SERPINA1 , FAM46C, HEXA, PTTG1, TIMP1, FAM167B, CCNG1, FAXDC2, HMGCS1, L2HGDH, Lipin1, MME, MSMO1, PARM1, PTGFR, SLC22A4, SLC35F5, CCNA2, CENPU, CEP55, RASSF2, and SLC16A3 . Conclusions : Interestingly, comparing the list of genes with the list of genes obtained from our literature search analysis, we found only three genes in common. These genes are HEXA, PTTG1, and TIMP1. Our finding points to the potential of a few genes that may be important for ovarian follicular development and oocyte quality. Future studies revealing the function of these genes will further our understanding of how litter size is controlled in the ovary while also providing insight on genetic selection of high litter gilts.

Identification And Characterization

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

Nucleic Acids Research ◽

10.1093/nar/gkl507 ◽

2006 ◽

Vol 34 (14) ◽

pp. 3917-3928 ◽

Cited By ~ 30

Author(s):

Jun-ichi Takeda ◽

Yutaka Suzuki ◽

Mitsuteru Nakao ◽

Roberto A. Barrero ◽

Kanako O. Koyanagi ◽

...

Keyword(s):

Alternative Splicing ◽

Large Scale ◽

Human Gene ◽

Full Length ◽

Splicing Variants ◽

Gene Transcripts ◽

Gene Set- and Pathway- Centered Knowledge Discovery Assigns Transcriptional Activation Patterns in Brain, Blood, and Colon Cancer

International Journal of Knowledge Discovery in Bioinformatics ◽

10.4018/ijkdb.2014070104 ◽

2014 ◽

Vol 4 (2) ◽

pp. 46-69 ◽

Cited By ~ 8

Author(s):

Lilit Nersisyan ◽

Henry Löffler-Wirth ◽

Arsen Arakelyan ◽

Hans Binder

Keyword(s):

Knowledge Discovery ◽

Transcriptional Activation ◽

Regulatory Networks ◽

Expression Patterns ◽

Flow Analysis ◽

B Cell Lymphoma ◽

Biological Knowledge ◽

Self Organizing Maps ◽

Gene Set ◽

Genome-wide ‘omics'-assays provide a comprehensive view on the molecular landscapes of healthy and diseased cells. Bioinformatics traditionally pursues a ‘gene-centered' view by extracting lists of genes differentially expressed or methylated between healthy and diseased states. Biological knowledge mining is then performed by applying gene set techniques using libraries of functional gene sets obtained from independent studies. This analysis strategy neglects two facts: (i) that different disease states can be characterized by a series of functional modules of co-regulated genes and (ii) that the topology of the underlying regulatory networks can induce complex expression patterns that require analysis methods beyond traditional genes set techniques. The authors here provide a knowledge discovery method that overcomes these shortcomings. It combines machine learning using self-organizing maps with pathway flow analysis. It extracts and visualizes regulatory modes from molecular omics data, maps them onto selected pathways and estimates the impact of pathway-activity changes. The authors illustrate the performance of the gene set and pathway signal flow methods using expression data of oncogenic pathway activation experiments and of patient data on glioma, B-cell lymphoma and colorectal cancer.

Probing the Honey Bee Diet-Microbiota-Host Axis Using Pollen Restriction and Organic Acid Feeding

Insects ◽

10.3390/insects11050291 ◽

2020 ◽

Vol 11 (5) ◽

pp. 291

Author(s):

Vincent A. Ricigliano ◽

Kirk E. Anderson

Keyword(s):

Organic Acid ◽

Honey Bee ◽

Expression Patterns ◽

Feeding Behaviors ◽

Fermentation Products ◽

Bacterial Fermentation ◽

Bee Health ◽

Gene Transcripts ◽

Microbial metabolites are considered important drivers of diet-based microbiota influence on the host, however, mechanistic models are confounded by interactions between diet, microbiota function, and host physiology. The honey bee harbors a simple microbiota that produces organic acids as fermentation products of dietary nectar and pollen, making it a model for gut microbiota research. Herein, we demonstrate that bacterial abundance in the honey bee gut is partially associated with the anterior rectum epithelium. We used dietary pollen restriction and organic acid feeding treatments to obtain information about the role of undigested pollen as a microbiota growth substrate and the impact of bacterial fermentation products on honey bee enteroendocrine signaling. Pollen restriction markedly reduced total and specific bacterial 16S rRNA abundance in the anterior rectum but not in the ileum. Anterior rectum expression levels of bacterial fermentative enzyme gene transcripts (acetate kinase, lactate dehydrogenase, and hydroxybutyryl-CoA dehydrogenase) were reduced in association with diet-induced microbiota shifts. To evaluate the effects of fermentative metabolites on host enteroendocrine function, pollen-restricted bees were fed an equimolar mixture of organic acid sodium salts (acetate, lactate, butyrate, formate, and succinate). Organic acid feeding significantly impacted hindgut enteroendocrine signaling gene expression, rescuing some effects of pollen restriction. This was specifically manifested by tissue-dependent expression patterns of neuropeptide F and allatostatin pathways, which are implicated in energy metabolism and feeding behaviors. Our findings provide new insights into the diet-microbiota-host axis in honey bees and may inform future efforts to improve bee health through diet-based microbiota manipulations.

Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals ◽

10.3390/ani9060387 ◽

2019 ◽

Vol 9 (6) ◽

pp. 387 ◽

Cited By ~ 6

Author(s):

Zengkui Lu ◽

Mingxing Chu ◽

Qing Li ◽

Meilin Jin ◽

Xiaojuan Fei ◽

...

Keyword(s):

Heat Stress ◽

Stress Responses ◽

Large Scale ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Transcriptomic Analysis ◽

P Value ◽

Comprehensive Overview

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

Primary cancer cell culture: mammary-optimized vs conditional reprogramming

Endocrine Related Cancer ◽

10.1530/erc-16-0071 ◽

2016 ◽

Vol 23 (7) ◽

pp. 535-554 ◽

Cited By ~ 5

Author(s):

Ahmad M Alamri ◽

Keunsoo Kang ◽

Svenja Groeneveld ◽

Weisheng Wang ◽

Xiaogang Zhong ◽

...

Keyword(s):

Culture Condition ◽

Expression Patterns ◽

Primary Cultures ◽

Cell Isolation ◽

Specific Gene ◽

Primary Cancer ◽

Mesenchymal Transition ◽

The impact of different culture conditions on biology of primary cancer cells is not always addressed. Here, conditional reprogramming (CRC) was compared with mammary-optimized EpiCult-B (EpiC) for primary mammary epithelial cell isolation and propagation, allograft generation, and genome-wide transcriptional consequences using cancer and non-cancer mammary tissue from mice with different dosages of Brca1 and p53. Selective comparison to DMEM was included. Primary cultures were established with all three media, but CRC was most efficient for initial isolation (P<0.05). Allograft development was faster using cells grown in EpiC compared with CRC (P<0.05). Transcriptome comparison of paired CRC and EpiC cultures revealed 1700 differentially expressed genes by passage 20. CRC promoted Trp53 gene family upregulation and increased expression of epithelial differentiation genes, whereas EpiC elevated expression of epithelial–mesenchymal transition genes. Differences did not persist in allografts where both methods yielded allografts with relatively similar transcriptomes. Restricting passage (<7) reduced numbers of differentially expressed genes below 50. In conclusion, CRC was most efficient for initial cell isolation but EpiC was quicker for allograft generation. The extensive culture-specific gene expression patterns that emerged with longer passage could be limited by reducing passage number when both culture transcriptomes were equally similar to that of the primary tissue. Defining impact of culture condition and passage on the transcriptome of primary cells could assist experimental design and interpretation. For example, differences that appear with passage and culture condition are potentially exploitable for comparative studies targeting specific biological networks in different transcriptional environments.

The mechanism and detection of alternative splicing events in circular RNAs

PeerJ ◽

10.7717/peerj.10032 ◽

2020 ◽

Vol 8 ◽

pp. e10032

Author(s):

Xiaohan Li ◽

Bing Zhang ◽

Fuyu Li ◽

Kequan Yu ◽

Yunfei Bai

Keyword(s):

Alternative Splicing ◽

Large Scale ◽

Single Gene ◽

Expression Patterns ◽

Functional Characterization ◽

Full Length ◽

Circular Rnas ◽

Specific Expression ◽

Enrichment Protocol

Circular RNAs (circRNAs) are considered as functional biomolecules with tissue/development-specific expression patterns. Generally, a single gene may generate multiple circRNA variants by alternative splicing, which contain different combinations of exons and/or introns. Due to the low abundance of circRNAs as well as overlapped with their linear counterparts, circRNA enrichment protocol is needed prior to sequencing. Compared with numerous algorithms, which use back-splicing reads for detection and functional characterization of circRNAs, original bioinformatic analyzing tools have been developed to large-scale determination of full-length circRNAs and accurate quantification. This review provides insights into the complexity of circRNA biogenesis and surveys the recent progresses in the experimental and bioinformatic methodologies that focus on accurately full-length circRNAs identification.