Reprogramming of H3K9bhb at Regulatory Elements is an Epigenetic Feature of Fasting in the Small Intestine

2020 ◽  
Author(s):  
Christopher Terranova ◽  
Kristina M. Stemler ◽  
Praveen Barrodia ◽  
Sabrina L. Jeter-Jones ◽  
Zhongqi Ge ◽  
...  
Keyword(s):  
Small Intestine ◽  
Regulatory Elements ◽  
Epigenetic Feature

Tissue Factor Expression in Vital Organs during Murine Traumatic Shock 

1999 ◽  
Vol 91 (6) ◽  
pp. 1844-1844 ◽  
Author(s):  
Valerie E. Armstead ◽  
Irina L. Opentanova ◽  
Alexander G. Minchenko ◽  
Allan M. Lefer
Keyword(s):  
Small Intestine ◽  
Mrna Expression ◽  
Tissue Factor ◽  
Messenger Rna ◽  
Mrna Level ◽  
Regulatory Elements ◽  
Traumatic Shock ◽  
Surface Glycoprotein ◽  
Cell Surface Glycoprotein ◽  
Nf Kappab

Background Tissue factor (TF) is a cell-surface glycoprotein responsible for initiating the extrinsic pathway of coagulation that has been shown to have a role in the pathophysiology of sepsis and reperfusion injury. The purpose of this study was to investigate TF expression in vital organs and to determine possible regulatory mechanisms of TF expression in the lung during traumatic shock in rats. Methods Noble-Collip drum trauma was induced in anesthetized Sprague-Dawley rats. Anesthetized rats without trauma served as controls. TF activity was measured in plasma and lung tissue. TF messenger RNA (mRNA) was measured in the lung, liver, and small intestine using ribonuclease protection assays. Electromobility shift assays were used to quantify binding of nuclear extracts from lung to TF-specific consensus domains for transcription factors NF-kappaB and AP-1. Results TF activity in plasma increased up to 14-fold and +232% in the lung (P < 0.001 for plasma and lung) 2 h after trauma. TF mRNA level was significantly increased in the lungs (P < 0.01), small intestine (P < 0.01), and liver (P < 0.05) 1 h after trauma compared to sham-operated control rats. TF mRNA expression continued to increase in the lungs and the liver (both, P < 0.001) 2 h after trauma TF sequence-specific complex binding to AP-1 and NF-kappaB domains was enhanced in the lungs of trauma rats (+395%, P < 0.001 and +168%, P < 0.001, respectively). Conclusions These results suggest that TF may play an important role in the pathophysiology of severe trauma and that regulatory elements AP-1 and NF-kappaB may be involved in the regulation of TF mRNA expression in traumatic shock.

scholarly journals Identification and characterization of the hypoxia response regulatory elements in the accessible genome

2020 ◽  
Author(s):  
Xi Lu ◽  
Xingqi Chen
Keyword(s):  
Solid Tumor ◽  
Regulatory Elements ◽  
Hypoxia Response ◽  
Genomic Features ◽  
Structure Response ◽  
Precision Therapy ◽  
Identification And Characterization ◽  
Epigenetic Feature ◽  
Hypoxia Treatment

AbstractHypoxia is commonly observed in the solid tumor and contributes to the drug resistance in cancer therapy. Deciphering the epigenetic feature under the hypoxia condition in the solid tumor is critical for us to understand the tumorigenesis and design the precision therapy. Using the time series of ATAC-seq data under the hypoxia treatment from the epithelia cells, we identified the hypoxia response regulatory elements (HRREs) in the accessible genome. We found that these different HRREs have unique genomic features and are enriched with different transcriptional factors (TFs). Our study provides insights into the chromatin structure response to the hypoxia treatment and identifies useful genomic features for a better understanding of the hypoxia biology in the solid tumor.

An Information Gain-based Method for Evaluating the Classification Power of Features Towards Identifying Enhancers

2020 ◽  
Vol 15 (6) ◽  
pp. 574-580
Author(s):  
Tianjiao Zhang ◽  
Rongjie Wang ◽  
Qinghua Jiang ◽  
Yadong Wang
Keyword(s):  
Dna Sequences ◽  
Evaluation Method ◽  
Information Gain ◽  
Predictive Performance ◽  
Entropy Change ◽  
Regulatory Elements ◽  
Sequence Feature ◽  
Transcription Start Sites ◽  
Enhance Gene Expression ◽  
Epigenetic Feature

Background: Enhancers are cis-regulatory elements that enhance gene expression on DNA sequences. Since most of enhancers are located far from transcription start sites, it is difficult to identify them. As other regulatory elements, the regions around enhancers contain a variety of features, which can help in enhancer recognition. Objective: The classification power of features differs significantly, the performances of existing methods that use one or a few features for identifying enhancer vary greatly. Therefore, evaluating the classification power of each feature can improve the predictive performance of enhancers. Methods: We present an evaluation method based on Information Gain (IG) that captures the entropy change of enhancer recognition according to features. To validate the performance of our method, experiments using the Single Feature Prediction Accuracy (SFPA) were conducted on each feature. Results: The average IG values of the sequence feature, transcriptional feature and epigenetic feature are 0.068, 0.213, and 0.299, respectively. Through SFPA, the average AUC values of the sequence feature, transcriptional feature and epigenetic feature are 0.534, 0.605, and 0.647, respectively. The verification results are consistent with our evaluation results. Conclusion: This IG-based method can effectively evaluate the classification power of features for identifying enhancers. Compared with sequence features, epigenetic features are more effective for recognizing enhancers.

scholarly journals Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

eLife ◽  
2013 ◽  
Vol 2 ◽  
Author(s):  
Hannah K Long ◽  
David Sims ◽  
Andreas Heger ◽  
Neil P Blackledge ◽  
Claudia Kutter ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Cpg Islands ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Central Feature ◽  
Gene Promoters ◽  
Methylated Dna ◽  
Promoter Architecture ◽  
Gene Regulatory Elements ◽  
Epigenetic Feature

Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation on chromatin. In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution.

scholarly journals Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine

Cell Reports ◽  
2021 ◽  
Vol 37 (8) ◽  
pp. 110044
Author(s):  
Christopher J. Terranova ◽  
Kristina M. Stemler ◽  
Praveen Barrodia ◽  
Sabrina L. Jeter-Jones ◽  
Zhongqi Ge ◽  
...  
Keyword(s):  
Small Intestine ◽  
Regulatory Elements

The human sucrase-isomaltase gene directs complex patterns of gene expression in transgenic mice

1993 ◽  
Vol 265 (3) ◽  
pp. G526-G539 ◽  
Author(s):  
A. J. Markowitz ◽  
G. D. Wu ◽  
E. H. Birkenmeier ◽  
P. G. Traber
Keyword(s):  
Gene Expression ◽  
Small Intestine ◽  
Transgenic Mice ◽  
Spatial Patterns ◽  
Cell Lineage ◽  
Human Growth ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Aberrant Expression ◽  
Intestinal Crypt

Sucrase-isomaltase (SI) is an enterocyte-specific gene that is expressed in complex developmental and spatial patterns. In this study, we examine the ability of regulatory elements within the human SI (hSI) gene to direct appropriate cell lineage and spatial patterns of expression in transgenic mice. Transgenic mouse lines were established using a construct containing bases -3424 to +54 of the hSI gene linked to the human growth hormone (hGH) structural gene. In each transgenic line, hGH mRNA and protein were expressed only in the small intestine and colon. In contrast to the endogenous mouse SI (mSI) gene, which was expressed along the entire length of the small intestine, hGH mRNA expression was predominantly found in the distal jejunum and ileum, with very low levels in more proximal portions of the small intestine. However, the pattern of transgene expression along the small intestinal crypt-villus axis was identical to the pattern of the endogenous mSI gene. These results suggest that regulatory elements necessary for intestine-specific transcription and differential expression along the intestinal crypt-villus axis are included in the 5'-flanking region of the hSI gene. Furthermore, these data suggest that different DNA regulatory regions regulate transcription along the horizontal intestinal axis. In the colon, there was aberrant expression of hGH in a subpopulation of enteroendocrine cells that contained peptide tyrosine tyrosine (PYY). This suggests that there are DNA regulatory elements, missing in the transgene construct, which normally suppress expression of the endogenous mSI gene in these cells. Taken together, these findings define the SI gene as a useful model for studies of differentiation, cell lineage determination, and mechanisms of complex spatial gene expression in the intestine.

Electron probe x-ray microanalysis and electron microscopy of amino acid absorption and transport by the small intestine: inhibition by chemical poisons and correlation to the elemental composition of the epithelial cells

1986 ◽  
Vol 44 ◽  
pp. 134-135
Author(s):  
A. J. Tousimis
Keyword(s):  
Small Intestine ◽  
Amino Acid ◽  
Epithelial Cells ◽  
Elemental Composition ◽  
Isotope Labeling ◽  
Structural Components ◽  
X Ray ◽  
Human Small Intestine ◽  
Transport Studies

The elemental composition of amino acids is similar to that of the major structural components of the epithelial cells of the small intestine and other tissues. Therefore, their subcellular localization and concentration measurements are not possible by x-ray microanalysis. Radioactive isotope labeling: I131-tyrosine, Se75-methionine and S35-methionine have been successfully employed in numerous absorption and transport studies. The latter two have been utilized both in vitro and vivo, with similar results in the hamster and human small intestine. Non-radioactive Selenomethionine, since its absorption/transport behavior is assumed to be the same as that of Se75- methionine and S75-methionine could serve as a compound tracer for this amino acid.

The protease phenotype and crystalline nature of the granules of intraepithelial mast cells in Trichinella spiralis-infected mice

1995 ◽  
Vol 53 ◽  
pp. 818-819
Author(s):  
D.S. Friend ◽  
N. Ghildyal ◽  
M.F. Gurish ◽  
K.F. Austen ◽  
R.L. Stevens
Keyword(s):  
Small Intestine ◽  
Mast Cells ◽  
Epithelial Cells ◽  
Lamina Propria ◽  
Trichinella Spiralis ◽  
Intestinal Epithelial ◽  
Carboxypeptidase A ◽  
C3h Mice ◽  
Granule Morphology ◽  
Crystalline Nature

Trichinella spiralis induces a profound mastocytosis and eosinophilia in the small intestine of the infected mouse. Mouse mast cells (MC) store in their granules various combinations of at least five chymotryptic chymases [designated mouse MC protease (mMCP) 1 to 5], two tryptic proteases designated mMCP-6 and mMCP-7 and an exopeptidase, carboxypeptidase A (mMC-CPA). Using antipeptide, protease -specific antibodies to these MC granule proteases, immunohistochemistry was done to determine the distribution, number and protease phenotype of the MCs in the small intestine and spleen 10 to >60 days after Trichinella infection of BALB/c and C3H mice. TEM was performed to evaluate the granule morphology of the MCs between intestinal epithelial cells and in the lamina propria (mucosal MCs) and in the submucosa, muscle and serosa of the intestine (submucosal MCs).As noted in the table below, the number of submucosal MCs remained constant throughout the study. In contrast, on day 14, the number of MCs in the mucosa increased ~25 fold. Increased numbers of MCs were observed between epithelial cells in the mucosal crypts, in the lamina propria and to a lesser extent, between epithelial cells of the intestinal villi.

Immunochemical visualization of cyclic AMP in myenteric neurons of guinea-pig small intestine+

2001 ◽  
Vol 120 (5) ◽  
pp. A683-A683
Author(s):  
J GUZMAN ◽  
S SHARP ◽  
J YU ◽  
F MCMORRIS ◽  
A WIEMELT ◽  
...  
Keyword(s):  
Small Intestine ◽  
Cyclic Amp ◽  
Guinea Pig ◽  
Myenteric Neurons

In situ demonstration of migration of dendritic cells released from rat small intestine to mesenteric lymph nodes

2001 ◽  
Vol 120 (5) ◽  
pp. A183-A183
Author(s):  
H KOBAYASHI ◽  
H NAGATA ◽  
S MIURA ◽  
T AZUMA ◽  
H SUZUKI ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Small Intestine ◽  
Lymph Nodes ◽  
Rat Small Intestine ◽  
Mesenteric Lymph Nodes ◽  
Mesenteric Lymph
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