scholarly journals Systematic Analysis of Monoallelic Gene Expression and Chromatin Accessibility Across Multiple Tissues in Hybrid Mice

2021 ◽  
Vol 9 ◽  
Author(s):  
Weizheng Liang ◽  
Xudong Zou ◽  
Guipeng Li ◽  
Shaojie Zhou ◽  
Chi Tian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Autosomal Gene ◽  
Monoallelic Expression ◽  
Specific Gene ◽  
Imprinted Genes ◽  
Mus Spretus ◽  
Genetic Origin ◽  
Systematic Analysis ◽  
Specific Regulation

In diploid eukaryotic organisms, both alleles of each autosomal gene are usually assumed to be simultaneously expressed at similar levels. However, some genes can be expressed preferentially or strictly from a single allele, a process known as monoallelic expression. Classic monoallelic expression of X-chromosome-linked genes, olfactory receptor genes and developmentally imprinted genes is the result of epigenetic modifications. Genetic-origin-dependent monoallelic expression, however, is caused by cis-regulatory differences between the alleles. There is a paucity of systematic study to investigate these phenomena across multiple tissues, and the mechanisms underlying such monoallelic expression are not yet fully understood. Here we provide a detailed portrait of monoallelic gene expression across multiple tissues/cell lines in a hybrid mouse cross between the Mus musculus strain C57BL/6J and the Mus spretus strain SPRET/EiJ. We observed pervasive tissue-dependent allele-specific gene expression: in total, 1,839 genes exhibited monoallelic expression in at least one tissue, and 410 genes in at least two tissues. Among these 88 are monoallelic genes with different active alleles between tissues, probably representing genetic-origin-dependent monoallelic expression. We also identified six autosomal monoallelic genes with the active allele being identical in all eight tissues, which are likely novel candidates of imprinted genes. To depict the underlying regulatory mechanisms at the chromatin layer, we performed ATAC-seq in two different cell lines derived from the F1 mouse. Consistent with the global expression pattern, cell-type dependent monoallelic peaks were found, and a higher proportion of C57BL/6J-active peaks were observed in both cell types, implying possible species-specific regulation. Finally, only a small part of monoallelic gene expression could be explained by allelic differences in chromatin organization in promoter regions, suggesting that other distal elements may play important roles in shaping the patterns of allelic gene expression across tissues.

scholarly journals Methylation of the Cyclin A1 Promoter Correlates with Gene Silencing in Somatic Cell Lines, while Tissue-Specific Expression of Cyclin A1 Is Methylation Independent

2000 ◽  
Vol 20 (9) ◽  
pp. 3316-3329 ◽  
Author(s):  
Carsten Müller ◽  
Carol Readhead ◽  
Sven Diederichs ◽  
Gregory Idos ◽  
Rong Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Promoter Methylation ◽  
Cpg Island ◽  
Trichostatin A ◽  
Specific Gene ◽  
Cyclin A1 ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

ABSTRACT Gene expression in mammalian organisms is regulated at multiple levels, including DNA accessibility for transcription factors and chromatin structure. Methylation of CpG dinucleotides is thought to be involved in imprinting and in the pathogenesis of cancer. However, the relevance of methylation for directing tissue-specific gene expression is highly controversial. The cyclin A1 gene is expressed in very few tissues, with high levels restricted to spermatogenesis and leukemic blasts. Here, we show that methylation of the CpG island of the human cyclin A1 promoter was correlated with nonexpression in cell lines, and the methyl-CpG binding protein MeCP2 suppressed transcription from the methylated cyclin A1 promoter. Repression could be relieved by trichostatin A. Silencing of a cyclin A1 promoter-enhanced green fluorescent protein (EGFP) transgene in stable transfected MG63 osteosarcoma cells was also closely associated with de novo promoter methylation. Cyclin A1 could be strongly induced in nonexpressing cell lines by trichostatin A but not by 5-aza-cytidine. The cyclin A1 promoter-EGFP construct directed tissue-specific expression in male germ cells of transgenic mice. Expression in the testes of these mice was independent of promoter methylation, and even strong promoter methylation did not suppress promoter activity. MeCP2 expression was notably absent in EGFP-expressing cells. Transcription from the transgenic cyclin A1 promoter was repressed in most organs outside the testis, even when the promoter was not methylated. These data show the association of methylation with silencing of the cyclin A1 gene in cancer cell lines. However, appropriate tissue-specific repression of the cyclin A1 promoter occurs independently of CpG methylation.

scholarly journals High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta

BMC Genetics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 25 ◽  
Author(s):  
Caroline Daelemans ◽  
Matthew E Ritchie ◽  
Guillaume Smits ◽  
Sayeda Abu-Amero ◽  
Ian M Sudbery ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Specific Gene ◽  
Imprinted Genes ◽  
High Throughput Analysis ◽  
Human Term Placenta ◽  
Throughput Analysis ◽  
Term Placenta ◽  
Specific Gene Expression ◽  
Allele Specific

scholarly journals Growth-Rate Dependent And Nutrient-Specific Gene Expression Resource Allocation In Fission Yeast

2021 ◽  
Author(s):  
Istvan T. Kleijn ◽  
Amalia Martínez-Segura ◽  
François Bertaux ◽  
Malika Saint ◽  
Holger Kramer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Rate ◽  
Resource Allocation ◽  
Fission Yeast ◽  
Metabolic Enzymes ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Rate Dependent ◽  
Specific Regulation ◽  
Yeast Genes

Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining relative protein abundances. Here, we used the simple eukaryote Schizosaccharomyces pombe to determine the importance of growth rate in explaining relative changes in protein and mRNA levels during growth on a series of non-limiting nitrogen sources. Although half of fission yeast genes were significantly correlated with the growth rate, this came alongside wide-spread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production with the notable exception of RNA polymerase II, whereas those negatively correlated mainly belonged to the environmental stress response programme. Critically, metabolic enzymes, which represent ~55-70% of the proteome by mass, showed mainly condition-specific regulation. Specifically, many enzymes involved in glycolysis and NAD-dependent metabolism as well as the fermentative and respiratory pathways were condition-dependent and not consistently correlated with growth. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate dependent and nutrient-specific gene expression.

scholarly journals Arachidonic acid drives adaptive responses to chemotherapy-induced stress in malignant mesothelioma

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Mario Cioce ◽  
Claudia Canino ◽  
Harvey Pass ◽  
Giovanni Blandino ◽  
Sabrina Strano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arachidonic Acid ◽  
Cell Lines ◽  
Adaptive Response ◽  
Response To Therapy ◽  
Specific Gene ◽  
Induced Stress ◽  
Cell Subpopulations ◽  
Transformed Cell Lines

Abstract Background High resistance to therapy and poor prognosis characterizes malignant pleural mesothelioma (MPM). In fact, the current lines of treatment, based on platinum and pemetrexed, have limited impact on the survival of MPM patients. Adaptive response to therapy-induced stress involves complex rearrangements of the MPM secretome, mediated by the acquisition of a senescence-associated-secretory-phenotype (SASP). This fuels the emergence of chemoresistant cell subpopulations, with specific gene expression traits and protumorigenic features. The SASP-driven rearrangement of MPM secretome takes days to weeks to occur. Thus, we have searched for early mediators of such adaptive process and focused on metabolites differentially released in mesothelioma vs mesothelial cell culture media, after treatment with pemetrexed. Methods Mass spectrometry-based (LC/MS and GC/MS) identification of extracellular metabolites and unbiased statistical analysis were performed on the spent media of mesothelial and mesothelioma cell lines, at steady state and after a pulse with pharmacologically relevant doses of the drug. ELISA based evaluation of arachidonic acid (AA) levels and enzyme inhibition assays were used to explore the role of cPLA2 in AA release and that of LOX/COX-mediated processing of AA. QRT-PCR, flow cytometry analysis of ALDH expressing cells and 3D spheroid growth assays were employed to assess the role of AA at mediating chemoresistance features of MPM. ELISA based detection of p65 and IkBalpha were used to interrogate the NFkB pathway activation in AA-treated cells. Results We first validated what is known or expected from the mechanism of action of the antifolate. Further, we found increased levels of PUFAs and, more specifically, arachidonic acid (AA), in the transformed cell lines treated with pemetrexed. We showed that pharmacologically relevant doses of AA tightly recapitulated the rearrangement of cell subpopulations and the gene expression changes happening in pemetrexed -treated cultures and related to chemoresistance. Further, we showed that release of AA following pemetrexed treatment was due to cPLA2 and that AA signaling impinged on NFkB activation and largely affected anchorage-independent, 3D growth and the resistance of the MPM 3D cultures to the drug. Conclusions AA is an early mediator of the adaptive response to pem in chemoresistant MPM and, possibly, other malignancies.

scholarly journals Tramtrack acts during late pupal development to direct ant caste identity

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009801
Author(s):  
Karl M. Glastad ◽  
Linyang Ju ◽  
Shelley L. Berger
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Behavioral Plasticity ◽  
Regulation Of Gene Expression ◽  
Pupal Stage ◽  
Specific Gene ◽  
Pupal Development ◽  
Camponotus Floridanus ◽  
Hormonal Function ◽  
Specific Regulation

A key question in the rising field of neuroepigenetics is how behavioral plasticity is established and maintained in the developing CNS of multicellular organisms. Behavior is controlled through systemic changes in hormonal signaling, cell-specific regulation of gene expression, and changes in neuronal connections in the nervous system, however the link between these pathways is unclear. In the ant Camponotus floridanus, the epigenetic corepressor CoREST is a central player in experimentally-induced reprogramming of caste-specific behavior, from soldier (Major worker) to forager (Minor worker). Here, we show this pathway is engaged naturally on a large genomic scale during late pupal development targeting multiple genes differentially expressed between castes, and central to this mechanism is the protein tramtrack (ttk), a DNA binding partner of CoREST. Caste-specific differences in DNA binding of ttk co-binding with CoREST correlate with caste-biased gene expression both in the late pupal stage and immediately after eclosion. However, we find a unique set of exclusive Minor-bound genes that show ttk pre-binding in the late pupal stage preceding CoREST binding, followed by caste-specific gene repression on the first day of eclosion. In addition, we show that ttk binding correlates with neurogenic Notch signaling, and that specific ttk binding between castes is enriched for regulatory sites associated with hormonal function. Overall our findings elucidate a pathway of transcription factor binding leading to a repressive epigenetic axis that lies at the crux of development and hormonal signaling to define worker caste identity in C. floridanus.

scholarly journals SUMO Paralog Specific Functions Revealed through Systematic Analysis of Human Knockout Cell Lines and Gene Expression Data

2021 ◽  
pp. mbc.E21-01-0031
Author(s):  
Danielle Bouchard ◽  
Wei Wang ◽  
Wei-Chih Yang ◽  
Shuying He ◽  
Anthony Garcia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Lines ◽  
Genotoxic Stress ◽  
Nuclear Body ◽  
Human Tissues ◽  
Cellular Functions ◽  
Systematic Analysis ◽  
Control Of Gene Expression ◽  
Knock Out ◽  
Sequence Homologies

The small ubiquitin-related modifiers (SUMOs) regulate nearly every aspect of cellular function, from gene expression in the nucleus to ion transport at the plasma membrane. In humans, the SUMO pathway has five SUMO paralogs with sequence homologies that range from 45% to 97%. SUMO1 and SUMO2 are the most distantly related paralogs, and also the best studied. To what extent SUMO1, SUMO2 and the other paralogs impart unique and non-redundant effects on cellular functions, however, has not been systematically examined and is therefore not fully understood. For instance, knockout studies in mice have revealed conflicting requirements for the paralogs during development and studies in cell culture have relied largely on transient paralog overexpression or knockdown. To address the existing gap in understanding, we first analyzed SUMO paralog gene expression levels in normal human tissues and found unique patterns of SUMO1-3 expression across 30 tissue types, suggesting paralog-specific functions in adult human tissues. To systematically identify and characterize unique and non-redundant functions of the SUMO paralogs in human cells, we next used CRISPR-Cas9 to knock out SUMO1 and SUMO2 expression in osteosarcoma (U2OS) cells. Analysis of these knockout cell lines revealed essential functions for SUMO1 and SUMO2 in regulating cellular morphology, PML nuclear body structure, responses to proteotoxic and genotoxic stress, and control of gene expression. Collectively, our findings reveal non-redundant regulatory roles for SUMO1 and SUMO2 in controlling essential cellular processes and provide a basis for more precise SUMO-targeting therapies.

An Enriched Multigen Low-Density Array To Predict Outcome in Advanced Hodgkin Lymphoma Paraffin-Embedded Samples.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 383-383
Author(s):  
Beatriz Sanchez-Espiridion ◽  
Abel Sanchez-Aguilera ◽  
Carlos Montalban ◽  
Monica Garcia-Cosio ◽  
Carmen Bellas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hodgkin Lymphoma ◽  
Cell Lines ◽  
Mapk Pathway ◽  
Unfavorable Outcome ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Low Density ◽  
Tissue Samples ◽  
Increased Risk

Abstract Despite the major advances in the treatment of classical Hodgkin Lymphoma (cHL) patients, around 30% to 40% of cases in advanced stages may relapse or die as result of the disease, and current markers to predict prognosis are rather unreliable. The identification of molecular events and biological processes associated with treatment failure are essential to develop new predictive tools. We used gene expression data from 29 samples of advanced cHL patients and HL-derived cell lines in order to identify transcriptional patterns from both tumoral cells and cell microenvironment. Student t-test was used to detect genes differentially overexpressed in cell lines and in tumor samples, thus creating two databases that report for genes expressed by the tumor HRS cells and genes expressed by the microenvironment. Using Gene Set Enrichment analysis (GSEA) we identified specific gene sets enriched in both databases in patients with favorable and unfavorable outcome, respectively. To validate these pathways we designed a novel Taqman low-density array (LDA) to examine the expression of the most relevant genes in 60 formalin-fixed, paraffin embedded (FFPE) tissue samples, and correlated the results with treatment outcome. Functional pathways related to unfavorable outcome significantly enriched in the HRS cells included the regulation of the G2/M checkpoint of the cell cycle, S phase and G1/S transition, chaperons, histone modification and other signaling pathways with an important representation of the MAPK pathway. On the other hand, genes reporting for specific T-cell populations (T-cytotoxic and T-regulatory cells) and macrophage activation were found to be overexpressed in the microenvironment. The final model presents a balanced representation of these genes, including also genes encoding factors implicated in drug resistance (RRM2, TYMS and TOP2A). RNA extracted from FFPE sections yielded analyzable data for 80% of samples. LDA analysis of the genes included in the model confirmed the feasibility of this approach, and the capacity for identifying cases with increased risk of failure.LDA provides an effective technique for analyzing gene expression in FFPE tissues, and it can be used for clinical prediction in diagnostic samples, using a selection of genes identified after GSEA analysis of the initial molecular signatures. This novel Taqman LDA will be used to develop a new molecular predictor of the outcome of patients with advanced cHL.

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