scholarly journals Polymorphism and Divergence of Novel Gene Expression Patterns in Drosophila melanogaster

Genetics ◽  
2020 ◽  
Vol 216 (1) ◽  
pp. 79-93
Author(s):  
Julie M. Cridland ◽  
Alex C. Majane ◽  
Hayley K. Sheehy ◽  
David J. Begun
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Transcript Abundance ◽  
Instar Larva ◽  
Accessory Gland ◽  
Male Reproduction ◽  
Specific Expression ◽  
Quantitative Expression ◽  
Female Head ◽  
Larval Salivary Gland

Transcriptomes may evolve by multiple mechanisms, including the evolution of novel genes, the evolution of transcript abundance, and the evolution of cell, tissue, or organ expression patterns. Here, we focus on the last of these mechanisms in an investigation of tissue and organ shifts in gene expression in Drosophila melanogaster. In contrast to most investigations of expression evolution, we seek to provide a framework for understanding the mechanisms of novel expression patterns on a short population genetic timescale. To do so, we generated population samples of D. melanogaster transcriptomes from five tissues: accessory gland, testis, larval salivary gland, female head, and first-instar larva. We combined these data with comparable data from two outgroups to characterize gains and losses of expression, both polymorphic and fixed, in D. melanogaster. We observed a large number of gain- or loss-of-expression phenotypes, most of which were polymorphic within D. melanogaster. Several polymorphic, novel expression phenotypes were strongly influenced by segregating cis-acting variants. In support of previous literature on the evolution of novelties functioning in male reproduction, we observed many more novel expression phenotypes in the testis and accessory gland than in other tissues. Additionally, genes showing novel expression phenotypes tend to exhibit greater tissue-specific expression. Finally, in addition to qualitatively novel expression phenotypes, we identified genes exhibiting major quantitative expression divergence in the D. melanogaster lineage.

scholarly journals Cell-type Specific Expression Quantitative Trait Loci Associated with Alzheimer Disease in Blood and Brain Tissue

2020 ◽  
Author(s):  
Devanshi Patel ◽  
Xiaoling Zhang ◽  
John J. Farrell ◽  
Jaeyoon Chung ◽  
Thor D. Stein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Eqtl Analysis ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

ABSTRACTBecause regulation of gene expression is heritable and context-dependent, we investigated AD-related gene expression patterns in cell-types in blood and brain. Cis-expression quantitative trait locus (eQTL) mapping was performed genome-wide in blood from 5,257 Framingham Heart Study (FHS) participants and in brain donated by 475 Religious Orders Study/Memory & Aging Project (ROSMAP) participants. The association of gene expression with genotypes for all cis SNPs within 1Mb of genes was evaluated using linear regression models for unrelated subjects and linear mixed models for related subjects. Cell type-specific eQTL (ct-eQTL) models included an interaction term for expression of “proxy” genes that discriminate particular cell type. Ct-eQTL analysis identified 11,649 and 2,533 additional significant gene-SNP eQTL pairs in brain and blood, respectively, that were not detected in generic eQTL analysis. Of note, 386 unique target eGenes of significant eQTLs shared between blood and brain were enriched in apoptosis and Wnt signaling pathways. Five of these shared genes are established AD loci. The potential importance and relevance to AD of significant results in myeloid cell-types is supported by the observation that a large portion of GWS ct-eQTLs map within 1Mb of established AD loci and 58% (23/40) of the most significant eGenes in these eQTLs have previously been implicated in AD. This study identified cell-type specific expression patterns for established and potentially novel AD genes, found additional evidence for the role of myeloid cells in AD risk, and discovered potential novel blood and brain AD biomarkers that highlight the importance of cell-type specific analysis.

scholarly journals Development of cDNA normalization system and preliminary transcription analysis of KCS genes in apple tissues

2011 ◽  
Vol 59 (3) ◽  
pp. 9-12 ◽  
Author(s):  
Zsolt Albert ◽  
Cs. Deák ◽  
A. Miskó ◽  
M. Tóth ◽  
I. Papp
Keyword(s):  
Gene Expression ◽  
Expression System ◽  
Expression Patterns ◽  
Housekeeping Genes ◽  
Apple Fruit ◽  
Rt Pcr ◽  
Specific Primers ◽  
Specific Expression ◽  
Transcription Analysis ◽  
Tissue Specific

Wax production is an important aspect of apple (Malus domestica Borkh.) fruit development from both theoretical and practical point of views. The complex molecular mechanism that controls wax biosynthesis is still widely unknown but many studies focused on this topic. We aimed to develop further the experimental framework of these efforts with a description of an improved reference genes expression system. Results in the literature show that similarities exist among the expression of some housekeeping genes of different plant species. Based on these considerations and on gene expression data from Arabidopsis thaliana, some genes in apple were assigned for analysis. EST sequences of apple were used to design specific primers for RT-PCR experiments. Isolation of intact RNA from different apple tissues and performing RT-PCR reaction were also key point in obtaining expression patterns. To monitor DNA contamination of the RNA samples, specific primers were used that amplify intron-containing sequences from the cDNA. We found that actin primers can be used for the detection of intron containing genomic DNA, and tubulin primers are good internal controls in RT-PCR experiments. We were able to make a difference between tissue-specific and tissue-independent gene-expression, furthermore we found tissue specific differences between the expression patterns of candidate genes, that are potentially involved in wax-biosynthesis. Our results show that KCS1 and KCS4 are overexpressed in the skin tissue, this could mean that these genes have skin-specific expression in apple fruit.

Acute Myeloid Leukemia with Translocation t(8;16) Demonstrates Specific Cytomorphological, Cytogenetic, and Gene Expression Characteristics and Can Clearly Be Discriminated from Other AML with Balanced Translocations.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2897-2897
Author(s):  
Torsten Haferlach ◽  
Helmut Loeffler ◽  
Alexander Kohlmann ◽  
Martin Dugas ◽  
Wolfgang Hiddemann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Who Classification ◽  
De Novo ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Support Vector ◽  
Gene Expression Patterns ◽  
Down Regulation ◽  
Specific Expression ◽  
Balanced Translocations

Abstract Balanced chromosomal rearrangements leading to fusion genes on the molecular level define distinct biological subsets in AML. The four balanced rearrangements (t(15;17), t(8;21), inv(16), and 11q23/MLL) show a close correlation to cytomorphology and gene expression patterns. We here focused on seven AML with t(8;16)(p11;p13). This translocation is rare (7/3515 cases in own cohort). It is more frequently found in therapy-related AML than in de novo AML (3/258 t-AML, and 4/3287 de novo, p=0.0003). Cytomorphologically, AML with t(8;16) is characterized by striking features: In all 7 cases the positivity for myeloperoxidase on bone marrow smears was >70% and intriguingly, in parallel >80% of blast cells stained strongly positive for non-specific esterase (NSE) in all cases. Thus, these cases can not be classified according to FAB categories. These data suggest that AML-t(8;16) arise from a very early stem cell with both myeloid and monoblastic potential. Furthermore, we detected erythrophagocytosis in 6/7 cases that was described as specific feature in AML with t(8;16). Four pts. had chromosomal aberrations in addition to t(8;16), 3 of these were t-AML all showing aberrations of 7q. Survival was poor with 0, 1, 1, 2, 20 and 18+ (after alloBMT) mo., one lost to follow-up, respectively. We then analyzed gene expression patterns in 4 cases (Affymetrix U133A+B). First we compared t(8;16) AML with 46 AML FAB M1, 41 M4, 9 M5a, and 16 M5b, all with normal karyotype. Hierachical clustering and principal component analyses (PCA) revealed that t(8;16) AML were intercalating with FAB M4 and M5b and did not cluster near to M1. Thus, monocytic characteristics influence the gene expression pattern stronger than myeloid. Next we compared the t(8;16) AML with the 4 other balanced subtypes according to the WHO classification (t(15;17): 43; t(8;21): 40; inv(16): 49; 11q23/MLL-rearrangements: 50). Using support vector machines the overall accuracy for correct subgroup assignment was 97.3% (10-fold CV), and 96.8% (2/3 training and 1/3 test set, 100 runs). In PCA and hierarchical cluster analysis the t(8;16) were grouped in the vicinity of the 11q23 cases. However, in a pairwise comparison these two subgroups could be discriminated with an accuracy of 94.4% (10-fold CV). Genes with a specific expression in AML-t(8;16) were further investigated in pathway analyses (Ingenuity). 15 of the top 100 genes associated with AML-t(8;16) were involved in the CMYC-pathway with up regulation of BCOR, COXB5, CDK10, FLI1, HNRPA2B1, NSEP1, PDIP38, RAD50, SUPT5H, TLR2 and USP33, and down regulation of ERG, GATA2, NCOR2 and RPS20. CEBP beta, known to play a role in myelomonocytic differentiation, was also up-regulated in t(8;16)-AML. Ten additional genes out of the 100 top differentially expressed genes were also involved in this pathway with up-regulation of DDB2, HIST1H3D, NSAP1, PTPNS1, RAN, USP4, TRIM8, ZNF278 and down regulation of KIT and MBD2. In conclusion, AML with t(8;16) is a specific subtype of AML with unique characteristics in morphology and gene expression patterns. It is more frequently found in t-AML, outcome is inferior in comparison to other AML with balanced translocations. Due to its unique features, it is a candidate for inclusion into the WHO classification as a specific entity.

scholarly journals Signals from the notochord and floor plate regulate the region-specific expression of two Pax genes in the developing spinal cord

Development ◽  
1993 ◽  
Vol 117 (3) ◽  
pp. 1001-1016 ◽  
Author(s):  
M.D. Goulding ◽  
A. Lumsden ◽  
P. Gruss
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Neural Tube ◽  
Neural Progenitor Cells ◽  
Expression Patterns ◽  
Primitive Streak ◽  
Floor Plate ◽  
Neural Patterning ◽  
Specific Expression ◽  
Early Effect

Members of the paired box (Pax) gene family are expressed in discrete regions of the developing central nervous system, suggesting a role in neural patterning. In this study, we describe the isolation of the chicken homologues of Pax-3 and Pax-6. Both genes are very highly conserved and share extensive homology with the mouse Pax-3 and Pax-6 genes. Pax-3 is expressed in the primitive streak and in two bands of cells at the lateral extremity of the neural plate. In the spinal cord, Pax-6 is expressed later than Pax-3 with the first detectable expression preceding closure of the neural tube. When the neural tube closes, transcripts of both genes become dorsoventrally restricted in the undifferentiated mitotic neuroepithelium. We show that the removal of the notochord, or implantation of an additional notochord, dramatically alter the dorsoventral (DV) expression patterns of Pax-3 and Pax-6. These manipulations suggest that signals from the notochord and floor plate regulate the establishment of the dorsoventrally restricted expression domains of Pax-3 and Pax-6 in the spinal cord. The rapid changes to Pax gene expression that occur in neural progenitor cells following the grafting of an ectopic notochord suggest that changes to Pax gene expression are an early effect of the notochord on spinal cord patterning.

scholarly journals A genomic analysis and transcriptomic atlas of gene expression inPsoroptes ovisreveals feeding- and stage-specific patterns of allergen expression

2019 ◽  
Author(s):  
Stewart TG Burgess ◽  
Edward J Marr ◽  
Kathryn Bartley ◽  
Francesca G Nunn ◽  
Rachel E Down ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Specific Gene ◽  
Multigene Families ◽  
Psoroptes Ovis ◽  
Specific Expression ◽  
Development Of Resistance

ABSTRACTPsoroptic mange, caused by infestation with the ectoparasitic mite,Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack ofP. ovistranscriptomic and genomic resources. Building on the recent publication of theP. ovisdraft genome, here we present a genomic analysis and transcriptomic atlas of gene expression inP. ovisrevealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3,075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis ofP. ovisallergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novelP. ovismultigene families including known allergens and novel genes with high levels of stage-specific expression. The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draftP. ovisgenome.

scholarly journals Can Forest Trees Cope with Climate Change?—Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change

2021 ◽  
Vol 22 (24) ◽  
pp. 13524
Author(s):  
Ewelina A. Klupczyńska ◽  
Ewelina Ratajczak
Keyword(s):  
Climate Change ◽  
Gene Expression ◽  
Dna Methylation ◽  
Global Climate ◽  
Regional Climate ◽  
Expression Patterns ◽  
Forest Tree ◽  
Epigenetic Modifications ◽  
Specific Expression ◽  
Epigenome Editing

Epigenetic modifications, including chromatin modifications and DNA methylation, play key roles in regulating gene expression in both plants and animals. Transmission of epigenetic markers is important for some genes to maintain specific expression patterns and preserve the status quo of the cell. This article provides a review of existing research and the current state of knowledge about DNA methylation in trees in the context of global climate change, along with references to the potential of epigenome editing tools and the possibility of their use for forest tree research. Epigenetic modifications, including DNA methylation, are involved in evolutionary processes, developmental processes, and environmental interactions. Thus, the implications of epigenetics are important for adaptation and phenotypic plasticity because they provide the potential for tree conservation in forest ecosystems exposed to adverse conditions resulting from global warming and regional climate fluctuations.

Expression profiling of purified male germ cells: stage-specific expression patterns related to meiosis and postmeiotic development

2006 ◽  
Vol 24 (2) ◽  
pp. 75-85 ◽  
Author(s):  
Alan L. Y. Pang ◽  
Warren Johnson ◽  
Neelakanta Ravindranath ◽  
Martin Dym ◽  
Owen M. Rennert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Germ Cells ◽  
Expression Profiling ◽  
Intracellular Transport ◽  
Expression Patterns ◽  
Male Gamete ◽  
Specific Expression ◽  
Differential Expression Pattern ◽  
Pachytene Spermatocytes ◽  
Cycle Regulation

Gene expression profiling was performed using the National Institute on Aging 15,000-cDNA microarray to reveal the differential expression pattern of 160 genes between meiotic pachytene spermatocytes and postmeiotic round spermatids of the mouse. Our results indicate that more genes are expressed in spermatids than in spermatocytes. Genes participating in cell cycle regulation and chromatin structure and dynamics are preferentially expressed in spermatocytes, while genes for protein turnover, signal transduction, energy metabolism, and intracellular transport are prevalent in spermatids. This suggests that a switch of functional requirement occurs when meiotic germ cells differentiate into haploid spermatids. Concordant expression patterns were obtained when quantitative real-time polymerase chain reaction was performed to verify the microarray data. Interestingly, the majority of the differentially expressed genes were underrepresented in mitotic type A spermatogonia, and they were preferentially expressed in the testis. Our results suggest that an even higher proportion of the mouse genome is devoted to male gamete development from meiosis than was previously estimated. We also provide evidence that underscores the advantage of using purified germ cells over whole testes in profiling spermatogenic gene expression to identify transcripts that demonstrate stage-specific expression patterns.

scholarly journals Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba)

Polar Biology ◽  
2019 ◽  
Vol 42 (12) ◽  
pp. 2205-2217
Author(s):  
Leonie Suter ◽  
Andrea Maree Polanowski ◽  
Robert King ◽  
Chiara Romualdi ◽  
Gabriele Sales ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sex Determination ◽  
Antarctic Krill ◽  
Sex Differentiation ◽  
Expression Patterns ◽  
Keystone Species ◽  
Euphausia Superba ◽  
Specific Expression ◽  
Large Gene ◽  
Juvenile Stages

Abstract Antarctic krill (Euphausia superba) is a highly abundant keystone species of the Southern Ocean ecosystem, directly connecting primary producers to high-trophic level predators. Sex ratios of krill vary remarkably between swarms and this phenomenon is poorly understood, as identification of krill sex relies on external morphological differences that appear late during development. Sex determination mechanisms in krill are unknown, but could include genetic, environmental or parasitic mechanisms. Similarly, virtually nothing is known about molecular sex differentiation. The krill genome has to date not been sequenced, and due to its enormous size and large amount of repetitive elements, it is currently not feasible to develop sex-specific DNA markers. To produce a reliable molecular marker for sex in krill and to investigate molecular sex differentiation we therefore focused on identifying sex-specific transcriptomic differences. Through transcriptomic analysis, we found large gene expression differences between testes and ovaries and identified three genes exclusively expressed in female whole krill from early juvenile stages onwards. The sex-specific expression of these three genes persisted through sexual regression, although our regressed samples originated from a krill aquarium and may differ from wild-regressed krill. Two slightly male-biased genes did not display sufficient expression differences to clearly differentiate sexes. Based on the expression of the three female-specific genes we developed a molecular test that for the first time allows the unambiguous sex determination of krill samples lacking external sex-specific features from juvenile stages onwards, including the sexually regressed krill we examined.

Epigenetic Remodeling in Innate Immunity and Inflammation

2021 ◽  
Vol 39 (1) ◽  
Author(s):  
Qian Zhang ◽  
Xuetao Cao
Keyword(s):  
Gene Expression ◽  
Innate Immunity ◽  
Regulatory Element ◽  
Expression Patterns ◽  
Innate Immune ◽  
Annual Review ◽  
Specific Gene ◽  
Publication Date ◽  
Specific Expression ◽  
Epigenetic Remodeling

The innate immune response is a rapid response to pathogens or danger signals. It is precisely activated not only to efficiently eliminate pathogens but also to avoid excessive inflammation and tissue damage. cis-Regulatory element–associated chromatin architecture shaped by epigenetic factors, which we define as the epiregulome, endows innate immune cells with specialized phenotypes and unique functions by establishing cell-specific gene expression patterns, and it also contributes to resolution of the inflammatory response. In this review, we focus on two aspects: ( a) how niche signals during lineage commitment or following infection and pathogenic stress program epiregulomes by regulating gene expression levels, enzymatic activities, or gene-specific targeting of chromatin modifiers and ( b) how the programed epiregulomes in turn mediate regulation of gene-specific expression, which contributes to controlling the development of innate cells, or the response to infection and inflammation, in a timely manner. We also discuss the effects of innate immunometabolic rewiring on epiregulomes and speculate on several future challenges to be encountered during the exploration of the master regulators of epiregulomes in innate immunity and inflammation. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Role of CEBPA-Mutations in AML with Prognostically Intermediate Cytogenetics: Data of the AMLCG Study Group and Gene Expression Analyses.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 571-571 ◽  
Author(s):  
Susanne Schnittger ◽  
Viola Conrad ◽  
Alexander Kohlmann ◽  
Martin Dugas ◽  
Sylvia Merk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Prognostic Significance ◽  
Normal Karyotype ◽  
Prognostic Impact ◽  
Reciprocal Translocations ◽  
Specific Expression ◽  
Cebpa Mutations ◽  
Cluster 2

Abstract Approximately 50% of acute myeloid leukemia (AML) have no karyotype changes or those with yet unknown prognostic significance. They are usually pooled together into the prognostically intermediate group. Here we approached the role of CEBPA mutations within this AML subgroup. In total, 255 AML, 237 with normal and 18 with “other” intermediate risk group karyotypes were screened for CEBPA mutations by sequencing. The total incidence of CEBPA mutations was 51/255 (20%) (48/237 (20.3%) in the normal and 3/18 (16.7%) in the “other” karyotypes). Most of the patients showed an M1 (n=16), or M2 (n=25) morphology, but there were also some with FAB M0 (n=1), M4 (n=4), M5 (n=3), and M6 (n=2). CEBPA+ cases were younger as compared to the CEBPA- cases (54.7 vs. 60.0, p=0.023). Leukocyte und platelet counts were similar. Clinical follow up data were available for 191 (37 mutated, 154 unmutated) patients. OS and EFS were significantly better in the patients with compared to those without CEBPA mutations (median 1092 vs. 259 days, p=0.0072; 375 vs. 218 days, p=0.0102, respectively). In addition, 18/42 (42.9%) of CEBPA+ cases had an FLT3-LM, 4/40 (10%) an FLT3-TKD, 4/41 (9.8%) an MLL-PTD, 3/34 (8.8%) an NRAS, 2/40 (5%) a KITD816 mutation. In four cases 2 additional mutations were detected: 1 x FLT3-LM+KITD816, 1 x FLT3-LM+FLT3-TKD, and 2 x MLL-PTD+FLT3-LM. The favorable prognostic impact of CEBPA mutations was not affected by additional mutations. Furthermore, 22 of the CEBPA+ case were analyzed by microarray analysis using the U133A+B array set (Affymetrix) and compared to the expression profile of 131 CEBPA- normal karyotype AML, as well as to 204 AML characterized by the reciprocal translocations t(15;17) (n=43), t(8;21) (n=36), inv(16) (n=48), t(11q23) (n=50), inv(3) (n=27). The discrimination of CEBPA+ cases and reciprocal translocations revealed a classification accuracy of 94.7% with 75% sensitivity and 98.5% specificity. However, the CEPBA+ cases did not show a specific expression pattern within the total group with normal karyotype and could not be discriminated from CEBPA- cases. By use of PCA and hierachical cluster analysis it was obvious that the CEBPA+ cases separated into two domains. One subcluster (cluster 1) was distributed among the cases with CEBPA- normal karyotype AML. A second cluster (cluster 2) was very close to the t(8;21) cases. Accordingly, cases of cluster 2 similar to t(8;21) and in contrast to cluster 1 highly expressed MPO and had low expression of HOXA3, HOXA7, HOXA9, HOXB4, HOXB6, and PBX3. Using the top 100 differentially expressed genes and applying 100 runs of SVM with 2/3 of samples being randomly selected as training set and 1/3 as test set samples, groups A and B could be classified with an overall accuracy of 100% (sensitivity 100% and specificity 100%). A detailed analysis of the two subclusters showed that all 8 cases of cluster 1 revealed mutations in the TAD2 domain of CEBPA and 6 of these had an FLT3-LM in addition. In contrast, 12/14 cases of cluster 2 had mutations that lead to an N-terminal stop and only 2 had an FLT3-LM. Thus these two subclusters have biological differences that may explain the different gene expression patterns. Despite the different functional consequences of the mutations in the two CEBPA-clusters no differences with respect to FAB type and prognosis were found between cluster 1 and 2.

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