Salt-Responsive Genes are Differentially Regulated at the Chromatin Levels Between Seedlings and Roots in Rice

2019 ◽  
Vol 60 (8) ◽  
pp. 1790-1803 ◽  
Author(s):  
Dongyang Zheng ◽  
Lei Wang ◽  
Lifen Chen ◽  
Xiucai Pan ◽  
Kande Lin ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Differential Expression ◽  
Mutual Exclusion ◽  
Positive Association ◽  
Specific Gene ◽  
Epigenetic Mechanisms ◽  
Chromatin Modifications ◽  
Tissue Specific ◽  
Underlying Mechanisms

Abstract The elucidation of epigenetic responses of salt-responsive genes facilitates understanding of the underlying mechanisms that confer salt tolerance in rice. However, it is still largely unknown how epigenetic mechanisms are associated with the expression of salt-responsive genes in rice and other crops. In this study, we reported tissue-specific gene expression and tissue-specific changes in chromatin modifications or signatures between seedlings and roots in response to salt treatment. Our study indicated that among six of individual mark examined (H3K4me3, H3K27me3, H4K12ac, H3K9ac, H3K27ac and H3K36me3), a positive association between salt-related changes in histone marks and the expression of differentially expressed genes (DEGs) was observed only for H3K9ac and H4K12ac in seedlings and H3K36me3 in roots. In contrast, chromatin states (CSs) with combinations of six histone modification marks played crucial roles in the differential expression of salt-responsive genes between seedlings and roots. Most importantly, CS7 containing the bivalent marks H3K4me3 and H3K27me3, with a mutual exclusion of functions with each other, displayed distinct functions in the expression of DEGs in both tissues. Specifically, H3K27me3 in CS7 mainly suppressed the expression of DEGs in roots, while H3K4me3 affected the expression of down- and up-regulated genes, possibly by antagonizing the repressive role of H3K27me3 in seedlings. Our findings indicate distinct impacts of the CSs on the differential expression of salt-responsive genes between seedlings and roots in rice, which provides an important background for understanding chromatin-based epigenetic mechanisms that might confer salt tolerance in plants.

Mother Phubbing and Adolescent Cyberbullying: The Mediating Role of Perceived Mother Acceptance and the Moderating Role of Emotional Stability

2020 ◽  
pp. 088626052098390
Author(s):  
Jiahui Qu ◽  
Li Lei ◽  
Xingchao Wang ◽  
Xiaochun Xie ◽  
Pengcheng Wang
Keyword(s):  
High School Students ◽  
Positive Association ◽  
Emotional Stability ◽  
School Students ◽  
Mediation Analyses ◽  
Mediating Role ◽  
Indirect Path ◽  
Underlying Mechanisms ◽  
The Relationship

Previous studies have found some risk factors of cyberbullying. However, little is known about how mother phubbing may influence adolescent cyberbullying, and the mediating and moderating mechanisms underlying this relationship. “Phubbing,” which is a portmanteau of “phone” and “subbing,” refers to snubbing other people and focus on smartphones in social interactions. This study examined whether mother phubbing, which refers to being phubbed by one’s mother, would be positively related to adolescent cyberbullying, whether perceived mother acceptance would mediate the relationship between mother phubbing and adolescent cyberbullying, and whether emotional stability would moderate the pathways between mother phubbing and adolescent cyberbullying. The sample consisted of 4,213 Chinese senior high school students (mean age 16.41 years, SD = 0.77, 53% were female). Participants completed measurements regarding mother phubbing, cyberbullying, perceived mother acceptance, and emotional stability. The results indicated that mother phubbing was positively related to cyberbullying, which was mediated by perceived mother acceptance. Further, moderated mediation analyses showed that emotional stability moderated the direct path between mother phubbing and cyberbullying and the indirect path between mother phubbing and perceived mother acceptance. This study highlighted the harmful impact of mother phubbing on adolescents by showing a positive association between mother phubbing and adolescent cyberbullying, as well as the underlying mechanisms between mother phubbing and adolescent cyberbullying.

Role of the extracellular matrix in tissue-specific gene expression in the sea urchin embryo

1991 ◽  
Vol 29 (3) ◽  
pp. 220-226 ◽  
Author(s):  
Steve Benson ◽  
Robert Rawson ◽  
Christopher Killian ◽  
Fred Wilt
Keyword(s):  
Gene Expression ◽  
Extracellular Matrix ◽  
Sea Urchin ◽  
Specific Gene ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression ◽  
Sea Urchin Embryo

scholarly journals Elucidation of new vitamin K function aiming at application to cardiovascular disease prevention and treatment

Impact ◽  
2021 ◽  
Vol 2021 (5) ◽  
pp. 37-39
Author(s):  
Kimie Nakagawa
Keyword(s):  
Cardiovascular Disease ◽  
Disease Prevention ◽  
Vitamin K ◽  
Human Body ◽  
Physiological Function ◽  
Specific Gene ◽  
Tissue Specific ◽  
Prevention And Treatment

Although Vitamin K is known to be required by the human body for blood clotting and bone metabolism, there remain many unknowns about this group of vitamins and there is a lack of biochemical research on vitamin K. Limitations in knowledge about vitamin k may mean that decisions about the vitamin's uptake and bone health may not be optimal. Professor Kimie Nakagawa Laboratory of Hygienic Sciences, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Japan, is performing detailed investigations on vitamin K to shed light on its specific functions in the human body and contribute to advancements in disease prevention and treatment, including cardiovascular disease. Her studies centre on UBIAD1 (UbiA prenyltransferase domain containing protein 1) and MK-4 (menaquinone-4). She is seeking to elucidate the role of MK-4 in the human body and reveal the unknown functions of UBIAD1. Nakagawa and the teams are doing so using UBIAD1 tissue-specific gene-deficient mice, which they are analysing in order to clarify the significance of biosynthesis of MK-4 in vivo and unravel the role of UBIAD1 and MK-4 in each tissue. Specific research goals for Nakagawa are to elucidate vitamin K conversion mechanisms, establish improved understanding of the physiological function of the vitamin, identify vitamin K converting enzymes and learn and explain more about the physiological function of this enzyme. The team made an important discovery in that UBIAD1 is the enzyme responsible for the conversion of vitamin k to MK-4 and the researchers will continue to build on this groundbreaking finding.

scholarly journals A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiao-Long Cui ◽  
Ji Nie ◽  
Jeremy Ku ◽  
Urszula Dougherty ◽  
Diana C. West-Szymanski ◽  
...  
Keyword(s):  
Human Tissue ◽  
Tissue Specificity ◽  
Dna Demethylation ◽  
Tissue Type ◽  
Specific Gene ◽  
Mammalian Development ◽  
Tissue Specific ◽  
Genome Wide ◽  
Organ Systems

AbstractDNA 5-hydroxymethylcytosine (5hmC) modification is known to be associated with gene transcription and frequently used as a mark to investigate dynamic DNA methylation conversion during mammalian development and in human diseases. However, the lack of genome-wide 5hmC profiles in different human tissue types impedes drawing generalized conclusions about how 5hmC is implicated in transcription activity and tissue specificity. To meet this need, we describe the development of a 5hmC tissue map by characterizing the genomic distributions of 5hmC in 19 human tissues derived from ten organ systems. Subsequent sequencing results enabled the identification of genome-wide 5hmC distributions that uniquely separates samples by tissue type. Further comparison of the 5hmC profiles with transcriptomes and histone modifications revealed that 5hmC is preferentially enriched on tissue-specific gene bodies and enhancers. Taken together, the results provide an extensive 5hmC map across diverse human tissue types that suggests a potential role of 5hmC in tissue-specific development; as well as a resource to facilitate future studies of DNA demethylation in pathogenesis and the development of 5hmC as biomarkers.

scholarly journals TBC1D3 promotes neural progenitor proliferation by suppressing the histone methyltransferase G9a

2021 ◽  
Vol 7 (3) ◽  
pp. eaba8053
Author(s):  
Qiong-Qiong Hou ◽  
Qi Xiao ◽  
Xin-Yao Sun ◽  
Xiang-Chun Ju ◽  
Zhen-Ge Luo
Keyword(s):  
Histone Methyltransferase ◽  
Neural Progenitors ◽  
Specific Gene ◽  
Thought Processes ◽  
Methyltransferase Activity ◽  
Genomic Changes ◽  
Histone 3 ◽  
Histone Lysine ◽  
Underlying Mechanisms

Genomic changes during human linage evolution contribute to the expansion of the cerebral cortex to allow more advanced thought processes. The hominoid-specific gene TBC1D3 displays robust capacity of promoting the generation and proliferation of neural progenitors (NPs), which are thought to contribute to cortical expansion. However, the underlying mechanisms remain unclear. Here, we found that TBC1D3 interacts with G9a, a euchromatic histone lysine N-methyltransferase, which mediates dimethylation of histone 3 in lysine 9 (H3K9me2), a suppressive mark for gene expression. TBC1D3 displayed an inhibitory role in G9a’s histone methyltransferase activity. Treatment with G9a inhibitor markedly increased NP proliferation and promoted human cerebral organoid expansion, mimicking the effects caused by TBC1D3 up-regulation. By contrast, blockade of TBC1D3/G9a interaction to disinhibit G9a caused up-regulation of H3K9me2, suppressed NP proliferation, and impaired organoid development. Together, this study has demonstrated a mechanism underlying the role of a hominoid-specific gene in promoting cortical expansion.

Differential expression of miR-20a and miR-145 in colorectal tumors as potential location-specific miRNAs.

MicroRNA ◽  
2020 ◽  
Vol 09 ◽  
Author(s):  
Sara Eslamizadeh ◽  
Ali-Akbar Zare ◽  
Atefeh Talebi ◽  
Seidamir Pasha Tabaeian ◽  
Zahra Shokati Eshkiki ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Rectal Cancer ◽  
Differential Expression ◽  
Potential Role ◽  
Colorectal Tumors ◽  
Tissue Specific ◽  
Normal Tissues ◽  
Qrt Pcr ◽  
Auc Value

Background: MicroRNAs (miRNAs), as tissue specific regulators of gene transcription, may be served as biomarkers for colorectal cancer (CRC). Objective: This study aimed to investigate the potential role of the cancer-related hsa-miRNAs as biomarkers in colon cancer (CC) and rectal cancer (RC). Methods: A total of 148 CRC samples (74 rectum and 74 colon) and 74 adjacent normal tissues were collected to examine the differential expression of selected ten hsa-miRNAs using quantitative reverse transcriptase PCR (qRT-PCR). Results: The significantly elevated levels of miR-21, miR-133b, miR-18a, miR-20a, miR-135b, and decreased levels of miR-34a, miR-200c, miR-145, and let-7g were detected in colorectal tumors compared to the healthy tissues (P<0.05). HsamiR-20a was significantly overexpressed in rectum compared to colon (p =0.028) from a cut-off value of 3.15 with a sensitivity of 66% and a specificity of 60% and an AUC value of 0.962. Also, hsa-miR-145 was significantly overexpressed in colon compared to rectum (p =0.02) from a cut-off value of 3.9 with a sensitivity of 55% and a specificity of 61% and an AUC value of 0.91. Conclusion: In conclusion, hsa-miR-20a and hsa-miR-145 as potential tissue-specific biomarkers for distinguishing RC and CC, improve realizing the molecular differences between these local tumors.

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