scholarly journals A Comparative Analysis of Super-Enhancers and Broad H3K4me3 Domains in Pig, Human, and Mouse Tissues

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanling Peng ◽  
Huifang Kang ◽  
Jing Luo ◽  
Yubo Zhang
Keyword(s):  
Comparative Analysis ◽  
Tissue Specificity ◽  
Sequence Conservation ◽  
Transcriptomic Data ◽  
Sequence Features ◽  
Mouse Tissues ◽  
Gene Regulatory ◽  
Computational Analyses ◽  
Human And Mouse

Super-enhancers (SEs) and broad H3K4me3 domains (BDs) are crucial regulators in the control of tissue identity in human and mouse. However, their features in pig remain largely unknown. In this study, by integrative computational analyses of epigenomic and transcriptomic data, we have characterized SEs and BDs in six pig tissues and analyzed their conservation in comparison with human and mouse tissues. Similar to human and mouse, pig SEs and BDs display higher tissue specificity than their typical counterparts. Genes proximal to SEs and BDs are associated with tissue identity in most tissues. About 55–182 SEs (5–17% in total) and 99–309 BDs (8–16% in total) across pig tissues are considered as functionally conserved elements because they have orthologous SEs and BDs in human and mouse. However, these elements do not necessarily exhibit sequence conservation. The functionally conserved SEs are correlated to tissue identity in majority of pig tissues, while those conserved BDs are linked to tissue identity in a few tissues. Our study provides resources for future gene regulatory studies in pig. It highlights that SEs are more effective in defining tissue identity than BDs, which is contrasting to a previous study. It also provides novel insights on understanding the sequence features of functionally conserved elements.

scholarly journals Learning a genome-wide score of human–mouse conservation at the functional genomics level

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Soo Bin Kwon ◽  
Jason Ernst
Keyword(s):  
Mouse Model ◽  
Functional Genomics ◽  
Functional Genomic ◽  
Transcriptomic Data ◽  
Model Studies ◽  
Genome Wide ◽  
A Genome ◽  
Important Challenge ◽  
Genomic Regions ◽  
Human And Mouse

AbstractIdentifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.

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

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 Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin

2021 ◽  
Author(s):  
Xiran Wang ◽  
Zhihua Ou ◽  
Peiwen Ding ◽  
Chengcheng Sun ◽  
Daxi Wang ◽  
...  
Keyword(s):  
Immune System ◽  
Comparative Analysis ◽  
Single Cell ◽  
Animal Species ◽  
Respiratory Viruses ◽  
Virus Infections ◽  
Species Comparison ◽  
Transcriptomic Data ◽  
Horseshoe Bat ◽  
Horseshoe Bats

Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as SARS-CoV and SARS-CoV-2. It has long been suggested that bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the COVID-19 pandemic, multiple animal species were diseased by SARS-CoV-2 infection, especially in the respiratory system. Herein, single-cell transcriptomic data of the lungs of a horseshoe bat, a cat, a tiger, and a pangolin were generated. The receptor distribution of twenty-eight respiratory viruses belonging to fourteen viral families were characterized for the four species. Comparison on the immune-related transcripts further revealed limited cytokine activations in bats, which might explain the reason why bats experienced only mild diseases or even no symptoms upon virus infection. Our findings might increase our understanding of the immune background of horseshoe bats and their insensitivity to virus infections.

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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