Genome-wide profiling of transcribed enhancers during macrophage activation

AbstractMacrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well-known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in mouse macrophages, their time kinetics and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers and find that genes associated to many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli-specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue to further elucidate enhancer regulation in macrophages.

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H3 K79 dimethylation marks developmental activation of the β-globin gene but is reduced upon LCR-mediated high-level transcription

Blood ◽

10.1182/blood-2007-12-128983 ◽

2008 ◽

Vol 112 (2) ◽

pp. 406-414 ◽

Cited By ~ 11

Author(s):

Tomoyuki Sawado ◽

Jessica Halow ◽

Hogune Im ◽

Tobias Ragoczy ◽

Emery H. Bresnick ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Activation ◽

Globin Gene ◽

Erythroid Differentiation ◽

Genome Wide ◽

Activation Of Transcription ◽

High Level ◽

The Relationship ◽

Mutant Genes ◽

Gene Expression Levels

Abstract Genome-wide analyses of the relationship between H3 K79 dimethylation and transcription have revealed contradictory results. To clarify this relationship at a single locus, we analyzed expression and H3 K79 modification levels of wild-type (WT) and transcriptionally impaired β-globin mutant genes during erythroid differentiation. Analysis of fractionated erythroid cells derived from WT/Δ locus control region (LCR) heterozygous mice reveals no significant H3 K79 dimethylation of the β-globin gene on either allele prior to activation of transcription. Upon transcriptional activation, H3 K79 di-methylation is observed along both WT and ΔLCR alleles, and both alleles are located in proximity to H3 K79 dimethylation nuclear foci. However, H3 K79 di-methylation is significantly increased along the ΔLCR allele compared with the WT allele. In addition, analysis of a partial LCR deletion mutant reveals that H3 K79 dimethylation is inversely correlated with β-globin gene expression levels. Thus, while our results support a link between H3 K79 dimethylation and gene expression, high levels of this mark are not essential for high level β-globin gene transcription. We propose that H3 K79 dimethylation is destabilized on a highly transcribed template.

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Tri-methylation of Histone H3 Lysine 4 Facilitates Gene Expression in Ageing Cells

10.1101/238048 ◽

2017 ◽

Cited By ~ 1

Author(s):

Cristina Cruz ◽

Monica Della Rosa ◽

Christel Krueger ◽

Qian Gao ◽

Lucy Field ◽

...

Keyword(s):

Gene Expression ◽

Budding Yeast ◽

Histone H3 ◽

Specific Factor ◽

Protein Coding ◽

Replicative Lifespan ◽

Protein Coding Genes ◽

Genome Wide ◽

Normal Expression ◽

Transcriptional Induction

AbstractTranscription of protein coding genes is accompanied by recruitment of COMPASS to promoter-proximal chromatin, which deposits di- and tri-methylation on histone H3 lysine 4 (H3K4) to form H3K4me2 and H3K4me3. Here we determine the importance of COMPASS in maintaining gene expression across lifespan in budding yeast. We find that COMPASS mutations dramatically reduce replicative lifespan and cause widespread gene expression defects. Known repressive functions of H3K4me2 are progressively lost with age, while hundreds of genes become dependent on H3K4me3 for full expression. Induction of these H3K4me3 dependent genes is also impacted in young cells lacking COMPASS components including the H3K4me3-specific factor Spp1. Remarkably, the genome-wide occurrence of H3K4me3 is progressively reduced with age despite widespread transcriptional induction, minimising the normal positive correlation between promoter H3K4me3 and gene expression. Our results provide clear evidence that H3K4me3 is required to attain normal expression levels of many genes across organismal lifespan.

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Riboregulators in plant development

Biochemical Society Transactions ◽

10.1042/bst0351638 ◽

2007 ◽

Vol 35 (6) ◽

pp. 1638-1642 ◽

Cited By ~ 18

Author(s):

P. Laporte ◽

F. Merchan ◽

B.B. Amor ◽

S. Wirth ◽

M. Crespi

Keyword(s):

Large Scale ◽

Transcriptional Control ◽

Rna Binding ◽

Bioinformatic Analysis ◽

Nodule Development ◽

Small Interfering Rnas ◽

Cortical Cells ◽

Protein Coding ◽

Early Nodulin ◽

Model Plant Arabidopsis Thaliana

npcRNA (non-protein-coding RNAs) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small RNAs [miRNAs (microRNAs)/siRNAs (small interfering RNAs)] that are involved in various developmental processes in plants and animals. In addition, several other npcRNAs encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. Much less is known about the mechanism of action of these other classes of riboregulators also present in the cell. The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells that express the npcRNA MtENOD40 (Medicago truncatula early nodulin 40). We have identified a novel RBP (RNA-binding protein), MtRBP1 (M. truncatula RBP 1), which interacts with the MtENOD40 RNA, and is exported into the cytoplasm during legume nodule development in the region expressing MtENOD40. A direct involvement of the MtENOD40 RNA in the relocalization of this RBP into cytoplasmic granules could be demonstrated, revealing a new RNA function in the cell. To extend these results, we searched for npcRNAs in the model plant Arabidopsis thaliana whose genome is completely known. We have identified 86 novel npcRNAs from which 27 corresponded to antisense RNAs of known coding regions. Using a dedicated ‘macroarray’ containing these npcRNAs and a collection of RBPs, we characterized their regulation in different tissues and plants subjected to environmental stresses. Most of the npcRNAs showed high variations in gene expression in contrast with the RBP genes. Recent large-scale analysis of the sRNA component of the transcriptome revealed an enormous diversity of siRNAs/miRNAs in the Arabidopsis genome. Bioinformatic analysis revealed that 34 large npcRNAs are precursors of siRNAs/miRNAs. npcRNAs, which are a sensitive component of the transcriptome, may reveal novel riboregulatory mechanisms involved in post-transcriptional control of differentiation or environmental responses.

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Sex differences in viral entry protein expression and host transcript responses to SARS-CoV-2

10.21203/rs.3.rs-100914/v2 ◽

2020 ◽

Author(s):

Mengying Sun ◽

Rama Shankar ◽

Meehyun Ko ◽

Christopher Daniel Chang ◽

Shan-Ju Yeh ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Viral Entry ◽

Large Scale ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Scale Analysis ◽

Transcriptional Responses ◽

Deconvolution Analysis ◽

Large Scale Analysis

Abstract Epidemiological studies suggest that men exhibit a higher mortality rate to COVID-19 than women, yet the underlying biology is largely unknown. Here, we seek to delineate sex differences in the gene expression of viral entry proteins ACE2 and TMPRSS2, and host transcriptional responses to SARS-CoV-2 through large-scale analysis of genomic and clinical data. We first compiled 220,000 human gene expression profiles from three databases and completed the meta-information through machine learning and manual annotation. Large scale analysis of these profiles indicated that male samples show higher expression levels of ACE2 and TMPRSS2 than female samples, especially in the older group (>60 years) and in the kidney. Subsequent analysis of 6,031 COVID-19 patients at Mount Sinai Health System revealed that men have significantly higher creatinine levels, an indicator of impaired kidney function. Further analysis of 782 COVID-19 patient gene expression profiles taken from upper airway and blood suggested men and women present distinct expression changes. Computational deconvolution analysis of these profiles revealed male COVID-19 patients have enriched kidney-specific mesangial cells in blood compared to healthy patients. Together, this study suggests biological differences in the kidney between sexes may contribute to sex disparity in COVID-19.

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Listeria monocytogenes σB Modulates PrfA-Mediated Virulence Factor Expression

Infection and Immunity ◽

10.1128/iai.01205-08 ◽

2009 ◽

Vol 77 (5) ◽

pp. 2113-2124 ◽

Cited By ~ 66

Author(s):

Juliane Ollinger ◽

Barbara Bowen ◽

Martin Wiedmann ◽

Kathryn J. Boor ◽

Teresa M. Bergholz

Keyword(s):

Gene Expression ◽

Listeria Monocytogenes ◽

Transcriptional Activation ◽

Virulence Gene ◽

Transcript Profiling ◽

Virulence Gene Expression ◽

Qrt Pcr ◽

Genome Wide

ABSTRACT Listeria monocytogenes σB and positive regulatory factor A (PrfA) are pleiotropic transcriptional regulators that coregulate a subset of virulence genes. A positive regulatory role for σB in prfA transcription has been well established; therefore, observations of increased virulence gene expression and hemolytic activity in a ΔsigB strain initially appeared paradoxical. To test the hypothesis that L. monocytogenes σB contributes to a regulatory network critical for appropriate repression as well as induction of virulence gene expression, genome-wide transcript profiling and follow-up quantitative reverse transcriptase PCR (qRT-PCR), reporter fusion, and phenotypic experiments were conducted using L. monocytogenes prfA*, prfA* ΔsigB, ΔprfA, and ΔprfA ΔsigB strains. Genome-wide transcript profiling and qRT-PCR showed that in the presence of active PrfA (PrfA*), σB is responsible for reduced expression of the PrfA regulon. σB-dependent modulation of PrfA regulon expression reduced the cytotoxic effects of a PrfA* strain in HepG2 cells, highlighting the functional importance of regulatory interactions between PrfA and σB. The emerging model of the role of σB in regulating overall PrfA activity includes a switch from transcriptional activation at the P2 prfA promoter (e.g., in extracellular bacteria when PrfA activity is low) to posttranscriptional downregulation of PrfA regulon expression (e.g., in intracellular bacteria when PrfA activity is high).

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The nutritionally responsive transcriptome of the polyphenic beetle Onthophagus taurus and the importance of sexual dimorphism and body region

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2014.2084 ◽

2014 ◽

Vol 281 (1797) ◽

pp. 20142084 ◽

Cited By ~ 21

Author(s):

Teiya Kijimoto ◽

Emilie C. Snell-Rood ◽

Melissa H. Pespeni ◽

Guilherme Rocha ◽

Karen Kafadar ◽

...

Keyword(s):

Gene Expression ◽

Sexual Dimorphism ◽

Functional Enrichment ◽

Adaptive Plasticity ◽

Body Region ◽

Transcriptional Responses ◽

Onthophagus Taurus ◽

Body Regions ◽

Genome Wide ◽

Evolutionary Consequences

Developmental responses to nutritional variation represent one of the ecologically most important classes of adaptive plasticity. However, knowledge of genome-wide patterns of nutrition-responsive gene expression is limited. Here, we studied genome-wide transcriptional responses to nutritional variation and their dependency on trait and sex in the beetle Onthophagus taurus. We find that averaged across the transcriptome, nutrition contributes less to overall variation in gene expression than do sex or body region, but that for a modest subset of genes nutrition is by far the most important determinant of expression variation. Furthermore, our results reject the hypothesis that a common machinery may underlie nutrition-sensitive development across body regions. Instead, we find that magnitude (measured by number of differentially expressed contigs), composition (measured by functional enrichment) and evolutionary consequences (measured by patterns of sequence variation) are heavily dependent on exactly which body region is considered and the degree of sexual dimorphism observed on a morphological level. More generally, our findings illustrate that studies into the developmental mechanisms and evolutionary consequences of nutrition-biased gene expression must take into account the dynamics and complexities imposed by other sources of variation in gene expression such as sexual dimorphism and trait type.

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Gene Expression in Trypanosomatid Parasites

Journal of Biomedicine and Biotechnology ◽

10.1155/2010/525241 ◽

2010 ◽

Vol 2010 ◽

pp. 1-15 ◽

Cited By ~ 91

Author(s):

Santiago Martínez-Calvillo ◽

Juan C. Vizuet-de-Rueda ◽

Luis E. Florencio-Martínez ◽

Rebeca G. Manning-Cela ◽

Elisa E. Figueroa-Angulo

Keyword(s):

Gene Expression ◽

Dna Sequences ◽

Transcription Initiation ◽

Histone Variants ◽

Protein Coding ◽

Functional Studies ◽

Polycistronic Transcription ◽

General Transcription Factors ◽

Genome Wide ◽

Trypanosomatid Parasites

The parasitesLeishmaniaspp.,Trypanosoma brucei,andTrypanosoma cruziare the trypanosomatid protozoa that cause the deadly human diseases leishmaniasis, African sleeping sickness, and Chagas disease, respectively. These organisms possess unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes and trans-splicing. Little is known about either the DNA sequences or the proteins that are involved in the initiation and termination of transcription in trypanosomatids.In silicoanalyses of the genome databases of these parasites led to the identification of a small number of proteins involved in gene expression. However, functional studies have revealed that trypanosomatids have more general transcription factors than originally estimated. Many posttranslational histone modifications, histone variants, and chromatin modifying enzymes have been identified in trypanosomatids, and recent genome-wide studies showed that epigenetic regulation might play a very important role in gene expression in this group of parasites. Here, we review and comment on the most recent findings related to transcription initiation and termination in trypanosomatid protozoa.

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Leishmania major Abrogates Gamma Interferon-Induced Gene Expression in Human Macrophages from a Global Perspective

Infection and Immunity ◽

10.1128/iai.00277-07 ◽

2007 ◽

Vol 75 (7) ◽

pp. 3506-3515 ◽

Cited By ~ 29

Author(s):

Nisha Dogra ◽

Corinna Warburton ◽

W. Robert McMaster

Keyword(s):

Gene Expression ◽

Host Cell ◽

Large Scale ◽

Leishmania Major ◽

Gamma Interferon ◽

Receptor Expression ◽

Global Perspective ◽

Monocytic Cell ◽

Monocytic Cell Line ◽

Ifn Γ

ABSTRACT Infection with Leishmania major triggers several pathways in the host cell that are crucial to initial infection as well as those that are used by Leishmania to enhance its replication and virulence. To identify the molecular events of the host cell in response to Leishmania, the global gene expression of the human monocytic cell line THP-1 either infected with Leishmania major in the presence and absence of gamma interferon (IFN-γ) or in the presence of IFN-γ alone was analyzed using high-density human oligonucleotide microarrays, followed by statistical analysis. The persistence of the parasite despite an extensive response to IFN-γ, added 24 h after infection with L. major, suggests that L. major can survive in an IFN-γ-enriched environment in vitro. Results demonstrate that L. major counteracts the IFN-γ response in macrophages on a large scale. Expression of genes involved in the innate immune response, cell adhesion, proteasomal degradation, Toll-like receptor expression, a variety of signaling molecules, and matrix metalloproteinases was significantly modulated.

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Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

10.1101/072470 ◽

2016 ◽

Cited By ~ 21

Author(s):

Morgan N. Price ◽

Kelly M. Wetmore ◽

R. Jordan Waters ◽

Mark Callaghan ◽

Jayashree Ray ◽

...

Keyword(s):

Protein Function ◽

Large Scale ◽

Hypothetical Proteins ◽

Data Set ◽

Protein Coding ◽

Bacterial Proteins ◽

Genome Wide ◽

Protein Functions ◽

Mutant Phenotypes ◽

Related Proteins

SummaryThe function of nearly half of all protein-coding genes identified in bacterial genomes remains unknown. To systematically explore the functions of these proteins, we generated saturated transposon mutant libraries from 25 diverse bacteria and we assayed mutant phenotypes across hundreds of distinct conditions. From 3,903 genome-wide mutant fitness assays, we obtained 14.9 million gene phenotype measurements and we identified a mutant phenotype for 8,487 proteins with previously unknown functions. The majority of these hypothetical proteins (57%) had phenotypes that were either specific to a few conditions or were similar to that of another gene, thus enabling us to make informed predictions of protein function. For 1,914 of these hypothetical proteins, the functional associations are conserved across related proteins from different bacteria, which confirms that these associations are genuine. This comprehensive catalogue of experimentally-annotated protein functions also enables the targeted exploration of specific biological processes. For example, sensitivity to a DNA-damaging agent revealed 28 known families of DNA repair proteins and 11 putative novel families. Across all sequenced bacteria, 14% of proteins that lack detailed annotations have an ortholog with a functional association in our data set. Our study demonstrates the utility and scalability of high-throughput genetics for large-scale annotation of bacterial proteins and provides a vast compendium of experimentally-determined protein functions across diverse bacteria.

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DksA-dependent regulation of RpoS contributes to Borrelia burgdorferi tick-borne transmission and mammalian infectivity

PLoS Pathogens ◽

10.1371/journal.ppat.1009072 ◽

2021 ◽

Vol 17 (2) ◽

pp. e1009072

Author(s):

William K. Boyle ◽

Crystal L. Richards ◽

Daniel P. Dulebohn ◽

Amanda K. Zalud ◽

Jeff A. Shaw ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Rna Polymerase ◽

Nutrient Limitation ◽

Pathogenic Bacteria ◽

Transcriptional Control ◽

Ixodes Scapularis ◽

Stringent Response ◽

Transcriptional Responses

Throughout its enzootic cycle, the Lyme disease spirochete Borreliella (Borrelia) burgdorferi, senses and responds to changes in its environment using a small repertoire of transcription factors that coordinate the expression of genes required for infection of Ixodes ticks and various mammalian hosts. Among these transcription factors, the DnaK suppressor protein (DksA) plays a pivotal role in regulating gene expression in B. burgdorferi during periods of nutrient limitation and is required for mammalian infectivity. In many pathogenic bacteria, the gene regulatory activity of DksA, along with the alarmone guanosine penta- and tetra-phosphate ((p)ppGpp), coordinate the stringent response to various environmental stresses, including nutrient limitation. In this study, we sought to characterize the role of DksA in regulating the transcriptional activity of RNA polymerase and its role in the regulation of RpoS-dependent gene expression required for B. burgdorferi infectivity. Using in vitro transcription assays, we observed recombinant DksA inhibits RpoD-dependent transcription by B. burgdorferi RNA polymerase independent of ppGpp. Additionally, we determined the pH-inducible expression of RpoS-dependent genes relies on DksA, but this relationship is independent of (p)ppGpp produced by Relbbu. Subsequent transcriptomic and western blot assays indicate DksA regulates the expression of BBD18, a protein previously implicated in the post-transcriptional regulation of RpoS. Moreover, we observed DksA was required for infection of mice following intraperitoneal inoculation or for transmission of B. burgdorferi by Ixodes scapularis nymphs. Together, these data suggest DksA plays a central role in coordinating transcriptional responses in B. burgdorferi required for infectivity through DksA’s interactions with RNA polymerase and post-transcriptional control of RpoS.

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