scholarly journals Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function

2007 ◽  
Vol 3 (4) ◽  
pp. e63 ◽  
Author(s):  
Yili Chen ◽  
Thomas W Blackwell ◽  
Ji Chen ◽  
Jing Gao ◽  
Angel W Lee ◽  
...  
2020 ◽  
Vol 32 (11) ◽  
pp. 709-717 ◽  
Author(s):  
Lukas Amann ◽  
Marco Prinz

Abstract The field of macrophage biology has made enormous progress over recent years. This was triggered by the advent of several new techniques such as the establishment of Cre/loxP-based transgenic mouse models that allowed for the first time delineation of the ontogeny and function of specific macrophage populations across many tissues. In addition, the introduction of new high-throughput technologies like bulk RNA sequencing and later single-cell RNA sequencing as well as advances in epigenetic analysis have helped to establish gene expression profiles, enhancer landscapes and local signaling cues that define and shape the identity of diverse macrophage populations. Nonetheless, some macrophage populations, like the ones residing in the peripheral nervous system (PNS), have not been studied in such detail yet. Here, we discuss recent studies that shed new light on the ontogeny, heterogeneity and gene expression profiles of resident macrophages in peripheral nerves and described differential activation of macrophage subsets during and after acute sciatic nerve injury.


Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1982
Author(s):  
Guillaume Bordet ◽  
Niraj Lodhi ◽  
Andrew Kossenkov ◽  
Alexei Tulin

An individual’s gene expression profile changes throughout their life. This change in gene expression is shaped by differences in physiological needs and functions between the younger and older organism. Despite intensive studies, the aging process is not fully understood, and several genes involved in this process may remain to be identified. Here we report a transcriptomic analysis of Drosophila melanogaster using microarrays. We compared the expression profiles of two-day-old female adult flies with those of 45-day-old flies. We identified 1184 genes with pronounced differences in expression level between young and old age groups. Most genes involved in muscle development/maintenance that display different levels of expression with age were downregulated in older flies. Many of these genes contributed to sarcomere formation and function. Several of these genes were functionally related to direct and indirect flight muscles; some of them were exclusively expressed in these muscles. Conversely, several genes involved in apoptosis processes were upregulated in aging flies. In addition, several genes involved in resistance to toxic chemicals were upregulated in aging flies, which is consistent with a global upregulation of the defense response system in aging flies. Finally, we randomly selected 12 genes among 232 genes with unknown function and generated transgenic flies expressing recombinant proteins fused with GFP protein to determine their subcellular expression. We also found that the knockdown of some of those 12 genes can affect the lifespan of flies.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 668-668
Author(s):  
Manoj M. Pillai ◽  
Mineo Iwata ◽  
Debra D. Dahlen ◽  
Beverly Torok-Storb

Abstract CXCL7 is a 14.0 Kd chemokine produced by megakaryocytes. There are 4 different peptides derived from the pro-peptide by cleavage of the amino terminal, each with distinctive functions: The longest form, LDGF (Leukocyte Derived Growth Factor) is mitogenic for fibroblasts while the smallest, Neutrophil Activating Peptide-2 (NAP-2) inhibits megakaryocytopoiesis. Therefore both forms have, in theory, the potential to influence the composition of the marrow microenvironment. We report here that an additional source of CXCL7 is the monocyte, which upregulates CXCL7 mRNA several fold when stimulated by stromal cells. Briefly, flow sorted CD 14+ monocytes were cultured alone and in co-culture with stromal cell lines HS-5 and HS-27a. Between group comparisons of gene expression profiles were made to identify genes up or down regulated in co-cultures. Expression of CXCL7 was found to be upregulated 25 fold when monocytes were co-cultured with HS-5 and 13 fold with HS-27a as compared to monocytes cultured alone. The array data was confirmed by RT-PCR. Using transwell cultures it was possible to demonstrate that the monocytes and not the stromal cells were responsible for CXCL7 gene expression, which peaked at 6 days. ELISA-based assays detected CXCL7 peptides in the supernatants of monocyte/stroma co-cultures after day 2 of culture. Levels detected ranged from 10 to 50 ng/ml, which are physiologically relevant concentrations. Western Blot analysis showed the 3 day cultures had predominantly LDGF; by day 6 the smaller form, NAP-2 was also present. Since peptide cleavage involves Cathepsin and related proteinases, this delayed appearance of NAP-2 may suggest that the required concentrations of proteinases accumulate with time. The presence of both mRNA and secreted protein in primary long-term cultures of human bone marrow, (peptide levels peaking at 125 ng/ml on day 22) suggest that normal, non-immortalized stroma also induces expression of the CXCL7 gene in the monocytes. Stroma-derived molecules known to stimulate monocytes (IL-1beta, IL-6, GM-CSF and G-CSF) were evaluated for their ability to induce CXCL7 gene expression. Of those tested, only GM-CSF was shown to induce the expression of CXCL7, but at levels far lower than induced by HS-5. As reported previously addition of NAP-2 to CFU-Meg cultures decreased the CFU-Megs by up to 40% despite maximal TPO and the CFU-Megs that did grow were smaller than those in control cultures. Also, addition of flow-sorted monocytes to cultures of primary marrow stroma, not only resulted in CXCL7 gene expression, but significantly increased fibroblast growth in these cultures. In summary our data show that a stroma-derived signal induces the expression of CXCL7 gene products in monocytes. Given that the monocyte is a critical component of the marrow microenvironment we postulate that induction of CXCL7 by stromal signals can affect both structure and function of the marrow microenvironment by increasing fibrosis and decreasing platelet production. Preliminary data from monocytes of 5 patients with Myelodysplastic Syndrome (MDS) suggests that MDS derived monocytes have abnormal patterns of CXCL7 expression. Whether this contributes to the pathophysiology of MDS remains to be determined.


2014 ◽  
Vol 306 (8) ◽  
pp. E854-E868 ◽  
Author(s):  
Mohit Jain ◽  
Soeun Ngoy ◽  
Sunil A. Sheth ◽  
Raymond A. Swanson ◽  
Eugene P. Rhee ◽  
...  

Lipids are a diverse collection of macromolecules essential for normal physiology, but the tissue distribution and function for many individual lipid species remain unclear. Here, we report a mass spectrometry survey of lipid abundance across 18 mouse tissues, detecting ∼1,000 mass spectrometry features, of which we identify 179 lipids from the glycerolipids, glycerophospholipids, lysophospholipids, acylcarnitines, sphingolipids, and cholesteryl ester classes. Our data reveal tissue-specific organization of lipids and can be used to generate testable hypotheses. For example, our data indicate that circulating triglycerides positively and negatively associated with future diabetes in humans are enriched in mouse adipose tissue and liver, respectively, raising hypotheses regarding the tissue origins of these diabetes-associated lipids. We also integrate our tissue lipid data with gene expression profiles to predict a number of substrates of lipid-metabolizing enzymes, highlighting choline phosphotransferases and sterol O-acyltransferases. Finally, we identify several tissue-specific lipids not present in plasma under normal conditions that may be of interest as biomarkers of tissue injury, and we show that two of these lipids are released into blood following ischemic brain injury in mice. This resource complements existing compendia of tissue gene expression and may be useful for integrative physiology and lipid biology.


Author(s):  
Yuki Fujita ◽  
Toshihide Yamashita

Microglia are resident immune cells in the central nervous system (CNS). Microglia exhibit diversity in their morphology, density, electrophysiological properties, and gene expression profiles, and play various roles in neural development and adulthood in both physiological and pathological conditions. Recent transcriptomic analysis using bulk and single-cell RNA-seq has revealed that microglia can shift their gene expression profiles in various contexts, such as developmental stages, aging, and disease progression in the CNS, suggesting that the heterogeneity of microglia may be associated with their distinct functions. Epigenetic changes, including histone modifications and DNA methylation, coordinate gene expression, thereby contributing to the regulation of cellular state. In this review, we summarize the current knowledge regarding the epigenetic mechanisms underlying spatiotemporal and functional diversity of microglia that are altered in response to developmental stages and disease conditions. We also discuss how this knowledge may lead to advances in therapeutic approaches for diseases.


2016 ◽  
Author(s):  
KM Handley ◽  
YM Piceno ◽  
P Hu ◽  
LM Tom ◽  
OU Mason ◽  
...  

AbstractThe release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Previous 4 studies have examined the phylogeny and function of these changes, but until now a 5 fundamental examination of the extant hydrocarbon metabolisms that supported these 6 changes had not been performed. Here, we reconstructed the genomes of 57 widespread 7 uncultivated bacteria from post spill sediments, and recovered their gene expression 8 pattern across the seafloor. These genomes comprised a common collection of bacteria 9 that were highly enriched in heavily affected sediments around the wellhead. While rare in distal sediments, some members were still detectable at sites up to 60 km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Observed alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, while just 3 harbored elaborate gene inventories for the degradation of alkanes and (poly)aromatic hydrocarbons. Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene up-regulation associated with polyaromatic hydrocarbon degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. The resulting analysis suggests a broad metabolic capacity to respond to oil exists across a large array of usually rare bacteria.


2007 ◽  
Vol 31 (3) ◽  
pp. 429-440 ◽  
Author(s):  
Vikas Misra ◽  
Hannah Lee ◽  
Anju Singh ◽  
Kewu Huang ◽  
Rajesh K. Thimmulappa ◽  
...  

This study identified gene expression profiles that provided evidence for genomic mechanisms underlying the pathophysiology of aging lung. Aging lungs from C57BL/6 (B6) and DBA/2 (D2) mouse strains differ in physiology and morphometry. Lungs were harvested from B6 mice at 2, 18, and 26 mo and from D2 mice at 2 and 18 mo of age. Purified RNA was subjected to oligonucleotide microarray analyses, and differential expression analyses were performed for comparison of various data sets. A significant majority of differentially expressed genes were upregulated with aging in both strains. Aging D2 lungs uniquely exhibited upregulation in stress-response genes including xenobiotic detoxification cascades. In contrast, aging B6 lungs showed downregulation of heat shock-response genes. Age-dependent downregulation of genes common to both B6 and D2 strains included several collagen genes (e.g., Col1a1 and Col3a1). There was a greater elastin gene ( Eln) expression in D2 mice at 2 mo, and Eln was uniquely downregulated with age in this strain. The matrix metalloproteinase 14 gene ( Mmp14), critical to alveolar structural integrity, was also downregulated with aging in D2 mice only. Several polymorphisms in the regulatory and untranslated regions of Mmp14 were identified between strains, suggesting that variation in Mmp14 gene regulation contributes to accelerated aging of lungs in D2 mice. In summary, lungs of B6 and D2 mice age with variable rates at the gene expression level, and these quantifiable genomic differences provide a template for understanding the variability in age-dependent changes in lung structure and function.


2010 ◽  
Vol 298 (5) ◽  
pp. G582-G589 ◽  
Author(s):  
Robert S. Chapkin ◽  
Chen Zhao ◽  
Ivan Ivanov ◽  
Laurie A. Davidson ◽  
Jennifer S. Goldsby ◽  
...  

We have developed a novel molecular methodology that utilizes stool samples containing intact sloughed epithelial cells to quantify intestinal gene expression profiles in the developing human neonate. Since nutrition exerts a major role in regulating neonatal intestinal development and function, our goal was to identify gene sets (combinations) that are differentially regulated in response to infant feeding. For this purpose, fecal mRNA was isolated from exclusively breast-fed ( n = 12) and formula-fed ( n = 10) infants at 3 mo of age. Linear discriminant analysis was successfully used to identify the single genes and the two- to three-gene combinations that best distinguish the feeding groups. In addition, putative “master” regulatory genes were identified using coefficient of determination analysis. These results support our premise that mRNA isolated from stool has value in terms of characterizing the epigenetic mechanisms underlying the developmentally regulated transcriptional activation/repression of genes known to modulate gastrointestinal function. As larger data sets become available, this methodology can be extended to validation and, ultimately, identification of the main nutritional components that modulate intestinal maturation and function.


2020 ◽  
Author(s):  
Lucía Gutiérrez-Chamorro ◽  
Eva Riveira-Muñoz ◽  
Clara Barrios ◽  
Vanesa Palau ◽  
Marta Massanella ◽  
...  

AbstractThere is an urgent need to elucidate the molecular mechanisms underlying the transmissibility and pathogenesis of SARS-CoV-2. ACE2 is a host ectopeptidase with well-described anti-inflammatory and tissue protective functions and the receptor for the virus. Understanding SARS-CoV-2-ACE2 interaction and the expression of antiviral host genes in early infection phase is crucial for fighting the pandemic. We tested the significance of soluble ACE2 enzymatic activity longitudinally in positive nasopharyngeal swabs at two time points after symptom consultation, along with gene expression profiles of ACE2, its proteases, ADAM17 and TMPRRS2, and interferon-stimulated genes (ISGs), DDX58, CXCL10 and IL-6. Soluble ACE2 activity decreased during infection course, in parallel to ACE2 gene expression. On the contrary, SARS-CoV-2 infection induced expression of the ISG genes in positive SARS-CoV-2 samples at baseline compared to negative control subjects, although this increase wanes with time. These changes positively correlated with viral load. Our results demonstrate the existence of mechanisms by which SARS-CoV-2 suppress ACE2 expression and function casting doubt on the IFN-induced upregulation of the receptor. Moreover, we show that initial intracellular viral sensing and subsequent ISG induction is also rapidly downregulated. Overall, our results offer new insights into ACE2 dynamics and inflammatory response in the human upper respiratory tract that may contribute to understand the early antiviral host response to SARS-CoV-2 infection.


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