scholarly journals Analysis of pir gene expression across the Plasmodium life cycle

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Timothy S. Little ◽  
Deirdre A. Cunningham ◽  
Audrey Vandomme ◽  
Carlos Talavera Lopez ◽  
Sarah Amis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Antigenic Variation ◽  
Expression Patterns ◽  
Data Sets ◽  
Life Cycle Stages ◽  
Determine Function ◽  
Repetitive Nature ◽  
Gene Expression Studies ◽  
Functional Investigation

Abstract Background Plasmodium interspersed repeat (pir) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. Methods Here pir gene expression was examined across the life cycle of Plasmodium berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from Plasmodium chabaudi. Results Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. Conclusions The identification of distinct expression patterns for different pir genes and subfamilies is likely to provide a basis for the design of future experiments to uncover their function.

scholarly journals Analysis of Pir Gene Expression Across the Plasmodium Life Cycle

2021 ◽  
Author(s):  
Timothy S. Little ◽  
Deirdre A. Cunningham ◽  
Audrey Vandomme ◽  
Carlos Talavera Lopez ◽  
Sarah I. Amis ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Antigenic Variation ◽  
Expression Patterns ◽  
Plasmodium Species ◽  
Data Sets ◽  
Life Cycle Stages ◽  
Determine Function ◽  
Gene Expression Studies ◽  
Functional Investigation

Abstract Background Plasmodium interspersed repeat ( pir ) is the largest multigene family in the genomes of most Plasmodium species. A variety of functions for the PIR proteins which they encode have been proposed, including antigenic variation, immune evasion, sequestration and rosetting. However, direct evidence for these is lacking. The repetitive nature of the family has made it difficult to determine function experimentally. However, there has been some success in using gene expression studies to suggest roles for some members in virulence and chronic infection. Methods Here we examined pir gene expression across the life cycle of P. berghei using publicly available RNAseq data-sets, and at high resolution in the intraerythrocytic development cycle using new data from P. chabaudi . Results Expression of pir genes is greatest in stages of the parasite which invade and reside in red blood cells. The marked exception is that liver merozoites and male gametocytes produce a very large number of pir gene transcripts, notably compared to female gametocytes, which produce relatively few. Within the asexual blood stages different subfamilies peak at different times, suggesting further functional distinctions. Representing a subfamily of its own, the highly conserved ancestral pir gene warrants further investigation due to its potential tractability for functional investigation. It is highly transcribed in multiple life cycle stages and across most studied Plasmodium species and thus is likely to play an important role in parasite biology. Conclusions By identifying distinct expression patterns for different pir genes and subfamilies we hope to provide a basis for the design of future experiments to uncover their function.

scholarly journals Rapid Turnover of Life-Cycle-Related Genes in the Brown Algae

2018 ◽  
Author(s):  
A.P. Lipinska ◽  
M.L. Serrano-Serrano ◽  
Akira F. Peters ◽  
K. Kogame ◽  
J Mark Cock ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Brown Algae ◽  
Phenotypic Diversity ◽  
Expression Patterns ◽  
Life Cycles ◽  
Sexual Life ◽  
High Turnover ◽  
Life Cycle Stages ◽  
Eukaryotic Group

ABSTRACTBackgroundSexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free living, and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures in each of the life cycle generations. Here, we have analysed the nature and extent of genome-wide generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations, in order to assess the potential role of generation-specific selection in shaping patterns of gene expression and divergence.ResultsWe show that the proportion of the transcriptome that is generation-biased is associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also a key role for newly emerged, lineage-specific genes in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes exhibit changes in their patterns of expression.ConclusionOur analysis uncovers the characteristics, expression patterns and evolution of generation-biased genes and underline the selective forces that shape this previously underappreciated source of phenotypic diversity.

scholarly journals The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites

2019 ◽  
Vol 18 (5) ◽  
pp. 302-313 ◽  
Author(s):  
Steven Abel ◽  
Karine G Le Roch
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Chromatin Structure ◽  
Expression Patterns ◽  
Large Body ◽  
Gene Families ◽  
Dimensional Structure ◽  
Parasite Life Cycle ◽  
Life Cycle Stages ◽  
Parasite Plasmodium Falciparum

AbstractDue to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Thus, the factors involved in the maintenance and regulation of chromatin and epigenetic features represent potential targets for antimalarial drugs. In this review, we discuss the mechanisms in P. falciparum that regulate chromatin structure, nucleosome landscape, the 3-dimensional structure of the genome and additional distinctive features created by parasite-specific genes and gene families. We review conserved traits of chromatin in eukaryotes in order to highlight what is unique in the parasite.

A Global Vista of the Epigenomic State of the Mouse Submandibular Gland

2021 ◽  
pp. 002203452110120
Author(s):  
C. Gluck ◽  
S. Min ◽  
A. Oyelakin ◽  
M. Che ◽  
E. Horeth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Submandibular Salivary Gland ◽  
Data Sets ◽  
Control Mechanisms ◽  
Chromatin Immunoprecipitation Sequencing

The parotid, submandibular, and sublingual glands represent a trio of oral secretory glands whose primary function is to produce saliva, facilitate digestion of food, provide protection against microbes, and maintain oral health. While recent studies have begun to shed light on the global gene expression patterns and profiles of salivary glands, particularly those of mice, relatively little is known about the location and identity of transcriptional control elements. Here we have established the epigenomic landscape of the mouse submandibular salivary gland (SMG) by performing chromatin immunoprecipitation sequencing experiments for 4 key histone marks. Our analysis of the comprehensive SMG data sets and comparisons with those from other adult organs have identified critical enhancers and super-enhancers of the mouse SMG. By further integrating these findings with complementary RNA-sequencing based gene expression data, we have unearthed a number of molecular regulators such as members of the Fox family of transcription factors that are enriched and likely to be functionally relevant for SMG biology. Overall, our studies provide a powerful atlas of cis-regulatory elements that can be leveraged for better understanding the transcriptional control mechanisms of the mouse SMG, discovery of novel genetic switches, and modulating tissue-specific gene expression in a targeted fashion.

SYSTEMATIC VARIATION NORMALIZATION IN MICROARRAY DATA TO GET GENE EXPRESSION COMPARISON UNBIASED

2005 ◽  
Vol 03 (02) ◽  
pp. 225-241 ◽  
Author(s):  
JEFF W. CHOU ◽  
RICHARD S. PAULES ◽  
PIERRE R. BUSHEL
Keyword(s):  
Gene Expression ◽  
Linear Regression ◽  
Microarray Data ◽  
Expression Patterns ◽  
Microarray Gene Expression Data ◽  
Systematic Variation ◽  
Data Sets ◽  
Microarray Gene Expression ◽  
Pixel Intensity ◽  
Non Linear

Normalization removes or minimizes the biases of systematic variation that exists in experimental data sets. This study presents a systematic variation normalization (SVN) procedure for removing systematic variation in two channel microarray gene expression data. Based on an analysis of how systematic variation contributes to variability in microarray data sets, our normalization procedure includes background subtraction determined from the distribution of pixel intensity values from each data acquisition channel and log conversion, linear or non-linear regression, restoration or transformation, and multiarray normalization. In the case when a non-linear regression is required, an empirical polynomial approximation approach is used. Either the high terminated points or their averaged values in the distributions of the pixel intensity values observed in control channels may be used for rescaling multiarray datasets. These pre-processing steps remove systematic variation in the data attributable to variability in microarray slides, assay-batches, the array process, or experimenters. Biologically meaningful comparisons of gene expression patterns between control and test channels or among multiple arrays are therefore unbiased using normalized but not unnormalized datasets.

scholarly journals Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gilbert O. Silveira ◽  
Murilo S. Amaral ◽  
Helena S. Coelho ◽  
Lucas F. Maciel ◽  
Adriana S. A. Pereira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Schistosoma Mansoni ◽  
Reference Genes ◽  
Large Scale ◽  
Developmental Stages ◽  
Adult Males ◽  
Histone H4 ◽  
Expression Levels ◽  
Life Cycle Stages

AbstractReverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is the most used, fast, and reproducible method to confirm large-scale gene expression data. The use of stable reference genes for the normalization of RT-qPCR assays is recognized worldwide. No systematic study for selecting appropriate reference genes for usage in RT-qPCR experiments comparing gene expression levels at different Schistosoma mansoni life-cycle stages has been performed. Most studies rely on genes commonly used in other organisms, such as actin, tubulin, and GAPDH. Therefore, the present study focused on identifying reference genes suitable for RT-qPCR assays across six S. mansoni developmental stages. The expression levels of 25 novel candidates that we selected based on the analysis of public RNA-Seq datasets, along with eight commonly used reference genes, were systematically tested by RT-qPCR across six developmental stages of S. mansoni (eggs, miracidia, cercariae, schistosomula, adult males and adult females). The stability of genes was evaluated with geNorm, NormFinder and RefFinder algorithms. The least stable candidate reference genes tested were actin, tubulin and GAPDH. The two most stable reference genes suitable for RT-qPCR normalization were Smp_101310 (Histone H4 transcription factor) and Smp_196510 (Ubiquitin recognition factor in ER-associated degradation protein 1). Performance of these two genes as normalizers was successfully evaluated with females maintained unpaired or paired to males in culture for 8 days, or with worm pairs exposed for 16 days to double-stranded RNAs to silence a protein-coding gene. This study provides reliable reference genes for RT-qPCR analysis using samples from six different S. mansoni life-cycle stages.

scholarly journals What functional genomics has taught us about transcriptional regulation in malaria parasites

2019 ◽  
Vol 18 (5) ◽  
pp. 290-301 ◽  
Author(s):  
Christa G Toenhake ◽  
Richárd Bártfai
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Life Cycle ◽  
Functional Genomics ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Complex Life Cycle ◽  
Malaria Parasites ◽  
Gene Regulatory

Abstract Malaria parasites are characterized by a complex life cycle that is accompanied by dynamic gene expression patterns. The factors and mechanisms that regulate gene expression in these parasites have been searched for even before the advent of next generation sequencing technologies. Functional genomics approaches have substantially boosted this area of research and have yielded significant insights into the interplay between epigenetic, transcriptional and post-transcriptional mechanisms. Recently, considerable progress has been made in identifying sequence-specific transcription factors and DNA-encoded regulatory elements. Here, we review the insights obtained from these efforts including the characterization of core promoters, the involvement of sequence-specific transcription factors in life cycle progression and the mapping of gene regulatory elements. Furthermore, we discuss recent developments in the field of functional genomics and how they might contribute to further characterization of this complex gene regulatory network.

Gene Expression Patterns and Life Cycle Responses of Toxicant-Exposed Chironomids

2012 ◽  
Vol 46 (22) ◽  
pp. 12679-12686 ◽  
Author(s):  
Marino Marinković ◽  
Wim C. de Leeuw ◽  
Wim A. Ensink ◽  
Mark de Jong ◽  
Timo M. Breit ◽  
...  
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Expression Patterns ◽  
Gene Expression Patterns

scholarly journals How long does the mRNA remains stable in untreated whole bovine blood?

2021 ◽  
Author(s):  
Rodrigo Giglioti ◽  
Bianca Tainá Azevedo ◽  
Henrique Nunes de Oliveira ◽  
Luciana Morita Katiki ◽  
Anibal Eugênio Vercesi Filho ◽  
...  
Keyword(s):  
Gene Expression ◽  
Messenger Rna ◽  
Expression Patterns ◽  
Rna Extraction ◽  
Bovine Blood ◽  
Rna Integrity ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Altered Gene ◽  
The Stability

Abstract Background: High quality and quantity of messenger RNA (mRNA) are required for accuracy of gene expression studies and other RNA-based downstream applications. Since RNA is considered a labile macromolecular prone to degradation, which may result in falsely altered gene expression patterns, several commercial stabilizing reagents have been developed aiming to keep RNA stable for long period. However, for studies involving large number of experimental samples, the high costs related to these specific reagents may constitute a barrier. Methods and Results: In this context the present study was designed aiming to evaluate the stability of mRNA in whole bovine blood collected in EDTA tubes during storage at common fridge (4°C). Whole blood samples were collected from six Holstein calves and submitted to RNA extraction in each different interval: immediately after blood sampling (< 2 h), at 1-day post-sampling (dps), 2 dps, 3 dps, 7 dps and 14dps intervals. RNA integrity and purity were evaluated, and RT-qPCR assays were run using seven different genes (B2M, ACTB, PPIA, GAPDH, YWHAZ, CD4 and IFN-γ) aiming to evaluate the presence of altered gene transcription during storage. All extracted RNA samples presented high purity, while optimal integrity and unaltered gene expression were observed in whole experimental group up to 3 days of storage.Conclusion: Bovine blood RNA remained stable in K3EDTA tubes for 3 days stored at common fridge and can be successfully and accurately used for gene expression studies.

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