scholarly journals Landscape and regulation of m6A and m6Am methylome across human and mouse tissues

2019 ◽  
Author(s):  
Jun’e Liu ◽  
Kai Li ◽  
Jiabin Cai ◽  
Mingchang Zhang ◽  
Xiaoting Zhang ◽  
...  
Keyword(s):  
Distribution Patterns ◽  
Mouse Tissue ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
Tissue Samples ◽  
Mouse Tissues ◽  
Mammalian Tissues ◽  
Primary Determinant ◽  
Human And Mouse ◽  
Brain Tissues

SUMMARYN6-methyladenosine (m6A), the most abundant internal mRNA modification, and N6,2’-O-dimethyladenosine (m6Am), found at the first-transcribed nucleotide, are two examples of dynamic and reversible epitranscriptomic marks. However, the profiles and distribution patterns of m6A and m6Am across different human and mouse tissues are poorly characterized. Here we report the m6A and m6Am methylome through an extensive profiling of 42 human tissues and 16 mouse tissue samples. Globally, the m6A and m6Am peaks in non-brain tissues demonstrates mild tissue-specificity but are correlated in general, whereas the m6A and m6Am methylomes of brain tissues are clearly resolved from the non-brain tissues. Nevertheless, we identified a small subset of tissue-specific m6A peaks that can readily classify the tissue types. The number of m6A and m6Am peaks are partially correlated with the expression levels of their writers and erasers. In addition, the m6A- and m6Am-containing regions are enriched for single nucleotide polymorphisms. Furthermore, cross-species analysis of m6A and m6Am methylomes revealed that species, rather than tissue types, is the primary determinant of methylation. Collectively, our study provides an in-depth resource for dissecting the landscape and regulation of the m6A and m6Am epitranscriptomic marks across mammalian tissues.

scholarly journals Rapid and Sensitive Quantification ofBorrelia burgdorferi-Infected Mouse Tissues by Continuous Fluorescent Monitoring of PCR

1999 ◽  
Vol 37 (4) ◽  
pp. 987-992 ◽  
Author(s):  
Tom B. Morrison ◽  
Ying Ma ◽  
John H. Weis ◽  
Janis J. Weis
Keyword(s):  
Absolute Quantification ◽  
Product Formation ◽  
Mouse Tissue ◽  
Pcr Analysis ◽  
Tissue Samples ◽  
Bacterial Dna ◽  
Double Stranded Dna ◽  
Mouse Tissues ◽  
External Standard ◽  
Pcr Method

The quantity of Borrelia burgdorferi organisms in tissue samples is an important determinant for infection studies in the mouse model of Lyme disease. This report presents the development of a rapid and sensitive external-standard-based PCR assay for the absolute quantification of B. burgdorferi in mouse tissue samples. The assay uses a double-stranded DNA dye to continuously monitor product formation and in less than an hour was able to quantify samples ranging up to 6 log units in concentration. The PCR efficiencies of the sample and the standard were matched by using a standard composed of purified B. burgdorferi chromosome mixed with tissue-matched mouse genome lacking bacterial DNA. Normalization ofB. burgdorferi quantities to the mouse nidogengene allowed comparison of B. burgdorferi numbers in samples isolated from different tissues and strains. PCR analysis of the chromosomal gene recA in cultured B. burgdorferi was consistent with a single recA per bacterium. The parameters defined in this assay should be applicable to quantification of other organisms, even infectious agents for which no ready source of DNA standard is available. In summary, this report presents a rapid external-standard-based PCR method for the quantification of B. burgdorferi in mouse DNA samples.

scholarly journals A mouse tissue atlas of small non-coding RNA

2018 ◽  
Author(s):  
Alina Isakova ◽  
Tobias Fehlmann ◽  
Andreas Keller ◽  
Stephen R. Quake
Keyword(s):  
Distribution Patterns ◽  
Cell Types ◽  
Vital Role ◽  
The Body ◽  
Mouse Tissue ◽  
List Type ◽  
Tissue Specific ◽  
Small Ncrnas ◽  
Mouse Tissues ◽  
Specific Manner

SUMMARYSmall non-coding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (miRNA, snoRNA, snRNA, scaRNA and tRNA fragments) across eleven mouse tissues by deep sequencing. Using fourteen biological replicates spanning both sexes, we identified that ~ 30% of small ncRNAs are distributed across the body in a tissue-specific manner with some are also being sexually dimorphic. We found that miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of eleven profiled tissues we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified for the first time in this study. Furthermore, by combining these findings with single-cell ATAC-seq data, we were able to connect identified brain-specific ncRNA with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that this data will be a resource for the further identification of ncRNAs involved in tissue-function in health and dysfunction in disease.HIGHLIGHTS-An atlas of tissue levels of multiple small ncRNA classes generated from 14 biological replicates of both sexes across 11 tissues-Distinct distribution patterns of miRNA arms and tRNA fragments across tissues suggest the existence of tissue-specific mechanisms of ncRNA cleavage and retention-miRNA expression is sex specific in healthy tissues-Small RNA-seq and scATAC-seq data integration produce a detailed map of cell-type specific ncRNA profiles in the mouse brain

scholarly journals Human and mouse bones physiologically integrate in a humanized mouse model while maintaining species-specific ultrastructure

2020 ◽  
Vol 6 (44) ◽  
pp. eabb9265
Author(s):  
I. Moreno-Jiménez ◽  
A. Cipitria ◽  
A. Sánchez-Herrero ◽  
A. F. van Tol ◽  
A. Roschger ◽  
...  
Keyword(s):  
Materials Science ◽  
Multiple Scales ◽  
Original Method ◽  
Mouse Tissue ◽  
Humanized Mouse ◽  
Humanized Mouse Model ◽  
Mouse Tissues ◽  
Human Collagen ◽  
Species Specific ◽  
Human And Mouse

Humanized mouse models are increasingly studied to recapitulate human-like bone physiology. While human and mouse bone architectures differ in multiple scales, the extent to which chimeric human-mouse bone physiologically interacts and structurally integrates remains unknown. Here, we identify that humanized bone is formed by a mosaic of human and mouse collagen, structurally integrated within the same bone organ, as shown by immunohistochemistry. Combining this with materials science techniques, we investigate the extracellular matrix of specific human and mouse collagen regions. We show that human-like osteocyte lacunar-canalicular network is retained within human collagen regions and is distinct to that of mouse tissue. This multiscale analysis shows that human and mouse tissues physiologically integrate into a single, functional bone tissue while maintaining their species-specific ultrastructural differences. These results offer an original method to validate and advance tissue-engineered human-like bone in chimeric animal models, which grow to be eloquent tools in biomedical research.

Discovery of intracellular 2,8 dihydroxyadenine crystals in bovine lymphatic and hepatic cells

1987 ◽  
Vol 45 ◽  
pp. 906-907
Author(s):  
W. E. Rigsby ◽  
D. M. Hinton ◽  
V. J. Hurst ◽  
P. C. McCaskey
Keyword(s):  
Polarized Light ◽  
Paraffin Sections ◽  
Tissue Samples ◽  
Whole Cells ◽  
Tissue Sections ◽  
Hepatic Cells ◽  
Slaughter House ◽  
Mammalian Tissues ◽  
Carbon Coated ◽  
Cellular Components

Crystalline intracellular inclusions are rarely seen in mammalian tissues and are often difficult to positively identify. Lymph node and liver tissue samples were obtained from two cows which had been rejected at the slaughter house due to the abnormal appearance of these organs in the animals. The samples were fixed in formaldehyde and some of the fixed material was embedded in paraffin. Examination of the paraffin sections with polarized light microscopy revealed the presence of numerous crystals in both hepatic and lymph tissue sections. Tissue sections were then deparaffinized in xylene, mounted, carbon coated, and examined in a Phillips 505T SEM equipped with a Tracor Northern X-ray Energy Dispersive Spectroscopy (EDS) system. Crystals were obscured by cellular components and membranes so that EDS spectra were only obtainable from whole cells. Tissue samples which had been fixed but not paraffin-embedded were dehydrated, embedded in Spurrs plastic, and sectioned.

Activation of Factor X by Factor VIIa Complexed with Human-mouse Tissue Factor Chimeras Requires Human Exon 3

1996 ◽  
Vol 76 (03) ◽  
pp. 361-368 ◽  
Author(s):  
Carrie H Fang ◽  
T-C Lin ◽  
Arabinda Guha ◽  
Yale Nemerson ◽  
William H Konigsberg
Keyword(s):  
Tissue Factor ◽  
Human Factor ◽  
Factor Viia ◽  
Mouse Tissue ◽  
Factor X ◽  
Lower Affinity ◽  
E Coli ◽  
Sequence Elements ◽  
Specific Activities ◽  
Human And Mouse

SummaryIn an attempt to define sequence elements in human and mouse tissue factor (TF) that are responsible for the species specificity observed in their interaction with human factor VIIa (HVIIa), we constructed human-mouse chimeric TF cDNAs, inserted them into plasmid vectors, and induced their expression in E.coli. Assays for procoagulant activity were carried out with the resulting E. coli lysates using (HVIIa) human and mouse (MVIIa). The ratio of the procoagulant activities, HVIIa/MVIIa, revealed that human TF exon 3 was essential for activity when the TF:VIIa complex was formed with HVIIa. By ligating the maltose binding protein (MBP) gene to TF cDNAs it was possible to construct, express and purify MBP-TF chimeras as well as to estimate their specific activities. With selected MBP-TF chimeras and HVIIa we determined kinetic parameters for the activation of human factor X. Replacement of exon 3 in human TF cDNA with the corresponding exon from mouse TF cDNA resulted in both lower affinity for HVIIa and failure to convert bound HVIIa into a potent protease

Immunodetection of UCP1, UCP2, and UCP3 in human and mouse tissues

2000 ◽  
Vol 28 (5) ◽  
pp. A187-A187
Author(s):  
P. Brauner ◽  
P. Flachs ◽  
J. Kopecký
Keyword(s):  
Mouse Tissues ◽  
Human And Mouse

scholarly journals Type 2 Diabetes (T2D) Associated Polymorphisms Regulate Expression of Adjacent Transcripts in Transformed Lymphocytes, Adipose, and Muscle from Caucasian and African-American Subjects

2011 ◽  
Vol 96 (2) ◽  
pp. E394-E403 ◽  
Author(s):  
Neeraj K. Sharma ◽  
Kurt A. Langberg ◽  
Ashis K. Mondal ◽  
Steven C. Elbein ◽  
Swapan K. Das
Keyword(s):  
Genome Wide Association ◽  
Small Subset ◽  
Nucleotide Polymorphisms ◽  
Healthy Individuals ◽  
Allelic Expression Imbalance ◽  
Single Nucleotide ◽  
Metabolic Traits ◽  
Genome Wide

abstract Context: Genome-wide association scans (GWAS) have identified novel single nucleotide polymorphisms (SNPs) that increase T2D susceptibility and indicated the role of nearby genes in T2D pathogenesis. Objective: We hypothesized that T2D-associated SNPs act as cis-regulators of nearby genes in human tissues and that expression of these transcripts may correlate with metabolic traits, including insulin sensitivity (SI). Design, Settings, and Patients: Association of SNPs with the expression of their nearest transcripts was tested in adipose and muscle from 168 healthy individuals who spanned a broad range of SI and body mass index (BMI) and in transformed lymphocytes (TLs). We tested correlations between the expression of these transcripts in adipose and muscle with metabolic traits. Utilizing allelic expression imbalance (AEI) analysis we examined the presence of other cis-regulators for those transcripts in TLs. Results: SNP rs9472138 was significantly (P = 0.037) associated with the expression of VEGFA in TLs while rs6698181 was detected as a cis-regulator for the PKN2 in muscle (P = 0.00027) and adipose (P = 0.018). Significant association was also observed for rs17036101 (P = 0.001) with expression of SYN2 in adipose of Caucasians. Among 19 GWAS-implicated transcripts, expression of VEGFA in adipose was correlated with BMI (r = −0.305) and SI (r = 0.230). Although only a minority of the T2D-associated SNPs were validated as cis-eQTLs for nearby transcripts, AEI analysis indicated presence of other cis-regulatory polymorphisms in 54% of these transcripts. Conclusions: Our study suggests that a small subset of GWAS-identified SNPs may increase T2D susceptibility by modulating expression of nearby transcripts in adipose or muscle.

224 Expression of presenilin 1 and 2 in human and mouse tissues

1996 ◽  
Vol 17 (4) ◽  
pp. S56
Author(s):  
M.K. Lee ◽  
H.H. Slunt ◽  
G. Thinakaran ◽  
D.L. Price ◽  
S. Sisodia
Keyword(s):  
Presenilin 1 ◽  
Mouse Tissues ◽  
Human And Mouse

scholarly journals Comparison of human and mouse tissues with focus on genes with no 1-to-1 homology

2021 ◽  
Author(s):  
Jieun Jeong ◽  
Manolis Kellis
Keyword(s):  
Immune Response ◽  
Target Genes ◽  
Expression Patterns ◽  
Adaptive Immune Response ◽  
Mouse Skin ◽  
Rna Seq ◽  
Therapy Targets ◽  
Mouse Tissues ◽  
Tissues Expression ◽  
Human And Mouse

We assembled a panel of 28 tissue pairs of human and mouse with RNA-Seq data on gene expression. We focused on genes with no 1-to-1 homology, because they pose special challenges. In this way, we identified expression patterns that identify and explain differences between the two species and suggest target genes for therapeutic applications. Here we mention three examples. One pattern is observed by defining the aggregate expression of immunoglobulin genes (which have no homology) as a measure of different levels of an immune response. In Lung, we used this statistic to find genes that have significantly higher expression in low/moderate response, and thus they may be therapy targets: increasing their expression or mimicking their function with medications may help in recovery from inflammation in the lungs. Some of the observed associations are common to human and mouse; other associations involve genes involved in cell-to-cell signaling or in regeneration but were not known to be important in Lung. Second pattern is that in the Small Intestine, mouse expresses much less antimicrobial defensins, while it has much higher expression of enzymes that are found to improve adaptive immune response. Such enzymes may be tested if they improve probiotic supplements that help in gut inflammation and other diseases. Another pattern involves a many-to-many homology group of defensins that did not have a described function. In human tissues, expression of its genes was found only in a study of a disease of hair covered skin, but several of its genes are highly expressed in two tissues of our panel: mouse Skin and to a lesser degree mouse Vagina. This suggests that those genes or their homologs in other species may provide non-antibiotic medications for hair covered skin and other tissues with microbiome that includes fungi.

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