Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation

The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification.

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A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqz006 ◽

2019 ◽

Vol 2 (1) ◽

Author(s):

Nelly F Mostajo ◽

Marie Lataretu ◽

Sebastian Krautwurst ◽

Florian Mock ◽

Daniel Desirò ◽

...

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Large Scale ◽

Viral Infections ◽

Gene Expression Regulation ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Regulatory Processes ◽

Genome Annotations ◽

Host Virus Interactions

Abstract Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.

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Comparison of phenol-based and alternative RNA isolation methods for gene expression analyses

Journal of the Serbian Chemical Society ◽

10.2298/jsc091223084j ◽

2010 ◽

Vol 75 (8) ◽

pp. 1053-1061 ◽

Cited By ~ 2

Author(s):

Ksenija Jakovljevic ◽

Milena Spasic ◽

Emina Malisic ◽

Jelena Dobricic ◽

Ana Krivokuca ◽

...

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Whole Blood ◽

Gene Expression Analysis ◽

Expression Patterns ◽

Rna Extraction ◽

Rna Isolation ◽

Specific Gene ◽

Isolation Methods ◽

Gene Expression Analyses

The widespread use of gene expression analyses has been limited by the lack of a critical evaluation of the methods used to extract nucleic acids from human tissues. For evaluating gene expression patterns in whole blood or leukocytes, the method of RNA isolation needs to be considered as a critical variable in the design of the experiment. Quantitative real-time PCR (qPCR) is widely used for the quantification of gene expression in today?s clinical practice. Blood samples as a preferred RNA source for qPCR should be carefully handled and prepared to not inhibit gene expression analyses. The present study was designed to compare the frequently used guanidine thiocyanate-phenol-chloroformbased method (TRI Reagent?) with two alternative RNA isolation methods (6100 PrepStation and QIAamp?) from whole blood or leukocytes for the purpose of gene expression analysis in chronic myeloid leukemia (CML) patients. Based on the results of this study, for the best combination of yield and RNA extraction purity, taking into account the necessary amount of the clinical sample and performance time, the protocol using phenol-based TRI Reagent? for RNA extraction from leukocytes is suggested as the most suitable protocol for this specific gene expression analysis.

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Prognostic value and co-expression patterns of metabolic pathways in cancers

BMC Genomics ◽

10.1186/s12864-020-07251-0 ◽

2020 ◽

Vol 21 (S11) ◽

Author(s):

Dan Zhang ◽

Yan Guo ◽

Ni Xie

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Metabolic Pathway ◽

Metabolic Pathways ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Cancer Prognosis ◽

Gene Expressions ◽

Pathway Gene ◽

Pathway Expression

Abstract Background Abnormal metabolic pathways have been considered as one of the hallmarks of cancer. While numerous metabolic pathways have been studied in various cancers, the direct link between metabolic pathway gene expression and cancer prognosis has not been established. Results Using two recently developed bioinformatics analysis methods, we evaluated the prognosis potential of metabolic pathway expression and tumor-vs-normal dysregulations for up to 29 metabolic pathways in 33 cancer types. Results show that increased metabolic gene expression within tumors corresponds to poor cancer prognosis. Meta differential co-expression analysis identified four metabolic pathways with significant global co-expression network disturbance between tumor and normal samples. Differential expression analysis of metabolic pathways also demonstrated strong gene expression disturbance between paired tumor and normal samples. Conclusion Taken together, these results strongly suggested that metabolic pathway gene expressions are disturbed after tumorigenesis. Within tumors, many metabolic pathways are upregulated for tumor cells to activate corresponding metabolisms to sustain the required energy for cell division.

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Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)

Genes ◽

10.3390/genes12030417 ◽

2021 ◽

Vol 12 (3) ◽

pp. 417

Author(s):

Fulei Mo ◽

Nian Zhang ◽

Youwen Qiu ◽

Lingjun Meng ◽

Mozhen Cheng ◽

...

Keyword(s):

Abiotic Stress ◽

Cold Stress ◽

Gene Family ◽

Solanum Lycopersicum ◽

Expression Analysis ◽

Gene Evolution ◽

Expression Patterns ◽

Pcr Analysis ◽

Whole Genome ◽

Cis Elements

F-box genes play an important role in the growth and development of plants, but there are few studies on its role in a plant’s response to abiotic stresses. In order to further study the functions of F-box genes in tomato (Solanum lycopersicum, Sl), a total of 139 F-box genes were identified in the whole genome of tomato using bioinformatics methods, and the basic information, transcript structure, conserved motif, cis-elements, chromosomal location, gene evolution, phylogenetic relationship, expression patterns and the expression under cold stress, drought stress, jasmonic acid (JA) treatment and salicylic acid (SA) treatment were analyzed. The results showed that SlFBX genes were distributed on 12 chromosomes of tomato and were prone to TD (tandem duplication) at the ends of chromosomes. WGD (whole genome duplication), TD, PD (proximal duplication) and TRD (transposed duplication) modes seem play an important role in the expansion and evolution of tomato SlFBX genes. The most recent divergence occurred 1.3042 million years ago, between SlFBX89 and SlFBX103. The cis-elements in SlFBX genes’ promoter regions were mainly responded to phytohormone and abiotic stress. Expression analysis based on transcriptome data and qRT-PCR (Real-time quantitative PCR) analysis of SlFBX genes showed that most SlFBX genes were differentially expressed under abiotic stress. SlFBX24 was significantly up-regulated at 12 h under cold stress. This study reported the SlFBX gene family of tomato for the first time, providing a theoretical basis for the detailed study of SlFBX genes in the future, especially the function of SlFBX genes under abiotic stress.

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Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

BMC Plant Biology ◽

10.1186/s12870-021-03356-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ming Ma ◽

Qiming Chen ◽

Huizhen Dong ◽

Shaoling Zhang ◽

Xiaosan Huang

Keyword(s):

Transcription Factors ◽

Expression Analysis ◽

Leucine Zipper ◽

Expression Patterns ◽

Purifying Selection ◽

Whole Genome ◽

Virus Induced Gene Silencing ◽

Abiotic Stress Response ◽

Whole Genome Duplications ◽

Genome Duplications

Abstract Background Transcription factors (TFs) are involved in many important biological processes, including cell stretching, histological differentiation, metabolic activity, seed storage, gene regulation, and response to abiotic and biotic stresses. Little is known about the functions, evolutionary history, and expression patterns of basic region-leucine zipper TF family genes in pear, despite the release of the genome of Chinese white pears (“Dangshansuli”). Results Overall, 92 bZIP genes were identified in the pear genome (Pyrus breschneideri). Of these, 83 were randomly distributed on all 17 chromosomes except chromosome 4, and the other 9 genes were located on loose scaffolding. The genes were divided into 14 subgroups. Whole-genome duplications, dispersed duplication, and purifying selection for whole-genome duplications are the main reasons for the expansion of the PbrbZIP gene family. The analysis of functional annotation enrichment indicated that most of the functions of PbrbZIP genes were enriched in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways involved in the abiotic stress response. Next, expression analysis and virus-induced gene silencing results indicated that PbrbZIP genes might play critical roles in response to drought and cold stresses, especially for the genes from subgroups A, C, G, I, and S. Conclusions Ninety-two PbrbZIP genes were identified from the pear genome and classified into 14 subgroups. PbrbZIP genes were mainly expanded from whole-genome duplications and dispersed duplications and retained by purifying selection. PbrbZIP genes were induced by cold and drought stresses and played important roles in drought and cold tolerance. These results provided useful information for further increasing the tolerance of pears to stresses and a foundation to study the cold and drought tolerance mechanism of PbrbZIP genes.

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Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica

PLoS ONE ◽

10.1371/journal.pone.0252647 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0252647

Author(s):

N. S. Kron ◽

L. A. Fieber

Keyword(s):

Sensory Neuron ◽

Expression Analysis ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Aplysia Californica ◽

Orthologous Genes ◽

Viral Response ◽

Gene Correlation ◽

Neuro Inflammation

Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.

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A Systematic Comparison of Differential Analysis Methods for CyTOF Data

10.1101/2021.08.09.455609 ◽

2021 ◽

Author(s):

Lis Arend ◽

Judith Bernett ◽

Quirin Manz ◽

Melissa Klug ◽

Olga Lazareva ◽

...

Keyword(s):

Differential Expression ◽

Expression Analysis ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Differential Analysis ◽

Web Interface ◽

Analysis Methods ◽

Shiny App ◽

R Shiny ◽

User Friendly

Cytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell abundance. For differential expression analysis of markers between conditions, only few tools exist. These tools either reduce the data distribution to medians, discarding valuable information, or have underlying assumptions that may not hold for all expression patterns. Here, we systematically evaluated existing and novel approaches for differential expression analysis on real and simulated CyTOF data. We found that methods using median marker expressions compute fast and reliable results when the data is not strongly zero-inflated. Methods using all data detect changes in strongly zero-inflated markers, but partially suffer from overprediction or cannot handle big datasets. We present a new method, CyEMD, based on calculating the Earth Mover's Distance between expression distributions that can handle strong zero-inflation without being too sensitive. Additionally, we developed CYANUS, a user-friendly R Shiny App allowing the user to analyze cytometry data with state-of-the-art tools, including well-performing methods from our comparison. A public web interface is available at https://exbio.wzw.tum.de/cyanus/.

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Identification of sheep lncRNAs related to the immune response to vaccines and aluminium adjuvants

BMC Genomics ◽

10.1186/s12864-021-08086-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Martin Bilbao-Arribas ◽

Endika Varela-Martínez ◽

Naiara Abendaño ◽

Damián de Andrés ◽

Lluís Luján ◽

...

Keyword(s):

Immune Response ◽

Expression Analysis ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Rna Seq ◽

Protein Coding ◽

Protein Coding Genes ◽

Livestock Species ◽

Non Coding Rnas ◽

Aluminium Adjuvant

Abstract Background Long non-coding RNAs (lncRNAs) are involved in several immune processes, including the immune response to vaccination, but most of them remain uncharacterised in livestock species. The mechanism of action of aluminium adjuvants as vaccine components is neither not fully understood. Results We built a transcriptome from sheep PBMCs RNA-seq data in order to identify unannotated lncRNAs and analysed their expression patterns along protein coding genes. We found 2284 novel lncRNAs and assessed their conservation in terms of sequence and synteny. Differential expression analysis performed between animals inoculated with commercial vaccines or aluminium adjuvant alone and the co-expression analysis revealed lncRNAs related to the immune response to vaccines and adjuvants. A group of co-expressed genes enriched in cytokine signalling and production highlighted the differences between different treatments. A number of differentially expressed lncRNAs were correlated with a divergently located protein-coding gene, such as the OSM cytokine. Other lncRNAs were predicted to act as sponges of miRNAs involved in immune response regulation. Conclusions This work enlarges the lncRNA catalogue in sheep and puts an accent on their involvement in the immune response to repetitive vaccination, providing a basis for further characterisation of the non-coding sheep transcriptome within different immune cells.

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De novo Transcriptome Sequencing Coupled With Co-expression Analysis Reveal the Transcriptional Regulation of Key Genes Involved in the Formation of Active Ingredients in Peucedanum praeruptorum Dunn Under Bolting Period

Frontiers in Genetics ◽

10.3389/fgene.2021.683037 ◽

2021 ◽

Vol 12 ◽

Author(s):

Cheng Song ◽

Xiaoli Li ◽

Bin Jia ◽

Li Liu ◽

Jinmei Ou ◽

...

Keyword(s):

Circadian Rhythm ◽

Expression Analysis ◽

Transcriptome Sequencing ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Phenylpropanoid Pathway ◽

Mapk Signaling ◽

Flowering Plant ◽

Regulation Mechanism ◽

Key Genes

Peucedanum praeruptorum Dunn is a perennial and one-off flowering plant of the Peucedanum genus in Umbelliferae. The cultivated P. praeruptorum Dunn usually grows nutritionally in the first year and then moves into the reproductive growth in the second year. The lignification of the roots caused by bolting leads to the quality decline of crude materials. Since most of the previous studies have dealt with coumarin biosynthesis and identification of functional genes in P. praeruptorum, the scientific connotation of the inability that the bolted P. praeruptorum cannot be used medically is still unclear. Here, we employed a transcriptome sequencing combined with coexpression analysis to unearth the regulation mechanism of key genes related to coumarin synthesis in pre- and postbolting period, and to explore the mechanisms underlying the effects of bolting on the formation and transport of coumarins between the annual and biennial plants. Six cDNA libraries were constructed, and the transcripts were sequenced and assembled by Illumina Hiseq platform. A total of 336,505 unigenes were obtained from 824,129 non-redundant spliced transcripts. Unigenes (114,488) were annotated to the NCBI nr database, 119,017 and 10,475 unigenes were aligned to Gene Ontology (GO) functional groups and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Differential expression analysis screened out a series of upregulated and downregulated genes related to the phenylpropanoid pathway. The heatmap clustering showed that the similar expression patterns were both observed in groups C vs. D and groups C vs. F. The WGCNA-based coexpression was performed to elucidate the module and trait relationship to unearth important genes related to the bolting process. Seven pivotal modules on the KEGG functional annotations suggested these genes were mainly enriched in the process of plant–pathogen interaction, plant hormone signal transduction, MAPK signaling pathway, α-linolenic acid metabolism, circadian rhythm, and phenylpropanoid pathway. Further analysis provided clues that the key genes of the phenylpropanoid pathway, the ABC transporters, the apoptosis-related and circadian rhythm regulatory genes may play pivotal roles in regulating bolting signaling, biosynthesis, and transportation of coumarins.

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Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon

Genes ◽

10.3390/genes11091059 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1059

Author(s):

Alice Shwe ◽

Tone-Kari Knutsdatter Østbye ◽

Aleksei Krasnov ◽

Sigmund Ramberg ◽

Rune Andreassen

Keyword(s):

Gene Expression ◽

Atlantic Salmon ◽

Target Genes ◽

Sea Water ◽

Expression Patterns ◽

Regulation Of Gene Expression ◽

Head Kidney ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Small Rna Sequencing

Smoltification and early seawater phase are critical developmental periods with physiological and biochemical changes in Atlantic salmon that facilitates survival in saltwater. MicroRNAs (miRNAs) are known to have important roles in development, but whether any miRNAs are involved in regulation of gene expression during smoltification and the adaption to seawater is largely unknown. Here, small RNA sequencing of materials from head kidney before, during smoltification and post seawater transfer were used to study expression dynamics of miRNAs, while microarray analysis was applied to study mRNA expression dynamics. Comparing all timepoints, 71 miRNAs and 2709 mRNAs were identified as differentially expressed (DE). Hierarchical clustering analysis of the DE miRNAs showed three major clusters with characteristic expression changes. Eighty-one DE mRNAs revealed negatively correlated expression patterns to DE miRNAs in Cluster I and III. Furthermore, 42 of these mRNAs were predicted as DE miRNA targets. Gene enrichment analysis of negatively correlated target genes showed they were enriched in gene ontology groups hormone biosynthesis, stress management, immune response, and ion transport. The results strongly indicate that post-transcriptional regulation of gene expression by miRNAs is important in smoltification and sea water adaption, and this study identifies several putative miRNA-target pairs for further functional studies.

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