scholarly journals Interrogating the Interplay between Cardiac Transcription Factors and Non-Coding RNAs in Atrial Fibrillation

2018 ◽  
Author(s):  
Alexander T. Mikhailov ◽  
Mario Torrado
Keyword(s):  
Atrial Fibrillation ◽  
Transcription Factors ◽  
Non Coding Rnas ◽  
Cardiac Transcription Factors

scholarly journals Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

2021 ◽  
Author(s):  
Xiaoping Huang ◽  
Hongyu Zhang ◽  
Qiang Wang ◽  
Rong Guo ◽  
Lingxia Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Flag Leaf ◽  
Reduction Process ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

Cardiac Transcription Factors Driven Lineage-Specification of Adult Stem Cells

2009 ◽  
Vol 3 (1) ◽  
pp. 61-65 ◽  
Author(s):  
Ana Armiñán ◽  
Carolina Gandía ◽  
José Manuel García-Verdugo ◽  
Elisa Lledó ◽  
José Luis Mullor ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Adult Stem Cells ◽  
Lineage Specification ◽  
Cardiac Transcription Factors

Abstract P493: Histone Reader PHF7 Cooperates With The SWI/SNF Complex At Cardiac Super Enhancers To Promote Direct Reprogramming

2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Glynnis A Garry ◽  
Svetlana Bezprozvannaya ◽  
Huanyu Zhou ◽  
Hisayuki Hashimoto ◽  
Kenian Chen ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cardiac Fibroblasts ◽  
Human Fibroblasts ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Direct Reprogramming ◽  
Ischemic Disease ◽  
Treat Heart Failure ◽  
Cardiac Transcription Factors ◽  
Adult Fibroblasts

Ischemic heart disease is the leading cause of death worldwide. Direct reprogramming of resident cardiac fibroblasts (CFs) to induced cardiomyocytes (iCLMs) has emerged as a potential therapeutic approach to treat heart failure and ischemic disease. Cardiac reprogramming was first achieved through forced expression of the transcription factors Gata4, Mef2c, and Tbx5 (GMT); our laboratory found that Hand2 (GHMT) and Akt1 (AGHMT) markedly enhanced reprogramming efficiency in embryonic and postnatal cell types. However, adult mouse and human fibroblasts are resistant to reprogramming due to staunch epigenetic barriers. We undertook a screen of mammalian gene regulatory factors to discover novel regulators of cardiac reprogramming in adult fibroblasts and identified the epigenetic reader PHF7 as the most potent activating factor. We validated the findings of this screen and found that PHF7 augmented reprogramming of adult fibroblasts ten-fold. Mechanistically, PHF7 localized to cardiac super enhancers in fibroblasts by reading H3K4me2 marks, and through cooperation with the SWI/SNF complex, increased chromatin accessibility and transcription factor binding at these multivalent enhancers. Further, PHF7 recruited cardiac transcription factors to activate a positive transcriptional autoregulatory circuit in reprogramming. Importantly, PHF7 achieved efficient reprogramming through these mechanisms in the absence of Gata4. Collectively, these studies highlight the underexplored necessity of cardiac epigenetic readers, such as PHF7, in harnessing chromatin remodeling and transcriptional complexes to overcome critical barriers to direct cardiac reprogramming.

Abstract 33: Unlocking Reprogramming Capability: Silencing Antiplasticity Gene p63 Enhances the Reprogramming of Fibroblasts into Induced Cardiomyocytes

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Vivekkumar Patel ◽  
Austin Cooney ◽  
Elsa Flores ◽  
Vivek Singh ◽  
Megumi Mathison ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Troponin T ◽  
Cardiac Fibroblasts ◽  
Fold Increase ◽  
Cellular Reprogramming ◽  
Embryonic Fibroblasts ◽  
Reprogramming Efficiency ◽  
Cardiac Transcription Factors

Objective: In situ cellular reprogramming of cardiac fibroblasts into (induced) cardiomyocytes (iCMs) represents a promising new potential intervention for the treatment of heart failure. Despite encouraging in vivo data in rodent myocardial infarction models, the relative resistance of human cells to reprogramming may be a significant barrier to the clinical application of this new therapy. We hypothesized that knockdown of the anti-plasticity gene p63 could therefore be used to enhance cellular reprogramming efficiency. Methods: p63 knockout (KO) murine embryonic fibroblasts (MEFs) and MEFs treated with p63 silencing shRNA were assessed for expression of the cardiomyocyte marker Cardiac Troponin T (cTnT) and pro-cardiogenic genes, with or without the treatment with known cardiac transcription factors Hand2 and Myocardin (HM). Results: After 3 wks in culture, expression of the cardiomyocyte marker cTnT (FACS) was significantly greater in p63 KO MEFs than in wild-type (WT) MEFs or WT MEFs treated with transcription factors Hand2 and Myocardin (39% ± 8%, 2.0% ± 1% and 2.7 ± 0.3%, respectively, p < 0.05). Treatment of p63 KO MEFs with Hand2 and Myocardin further increased cTnT expression up to 74% ± 3%. Treatment of WT MEFs with p63 shRNA likewise yielded a 20-fold increase in cTnT expression (qPCR) without HM and a 600-fold increase with HM when compared to non-silencing shRNA treated MEFs. Consistent with these findings, p63 KO or p63 shRNA-treated MEFs demonstrated increased expression (qPCR) of pro-cardiogenic genes Gata4, Mef2c and Tbx5 compared to naïve or non-silencing shRNA treated MEFs. After treatment with p63 shRNA, adult human epidermal cells also demonstrated increased expression of cTnT, myosin heavy chain and pro-cardiogenic genes when analyzed by qPCR. Conclusions: Downregulation of the anti-plasticity gene p63 enhances cellular reprogramming efficiency and iCM generation, as reflected in the increased expression of the cardiomyocyte marker cTnT and pro-cardiogenic genes Gata4, Mef2c and Tbx5. Use of such cellular plasticity enhancing strategies may be a useful strategy to overcome barriers to cellular reprogramming in the clinical arena.

Molecular and biochemical analyses of avocado (Persea americana) reveal differences in the oil accumulation pattern between the mesocarp and seed during the fruit developmental period

2020 ◽  
Author(s):  
Yu Ge ◽  
Xiangshu Dong ◽  
Yuanzheng Liu ◽  
Ying Yang ◽  
Rulin Zhan
Keyword(s):  
Transcription Factors ◽  
Fatty Acid ◽  
Single Molecule ◽  
Oil Production ◽  
Developmental Period ◽  
Persea Americana ◽  
Oil Accumulation ◽  
Accumulation Pattern ◽  
Tissue Specific ◽  
Non Coding Rnas

Abstract Background: The avocado (Persea americana) mesocarp and seed contain high-value oil with broad industrial applications. The oil contents in these two tissues vary considerably at maturity. Additionally, the molecular mechanism underlying the tissue-specific oil accumulation in the developing avocado mesocarp and seed remains unclear, which has hampered the exploration of the utility of avocado for oil production.Results: To clarify the mechanisms mediating the differences in oil contents and fatty acid compositions, the transcriptomes and oil bodies were compared between the oil-storing tissues during the fruit developmental period. The results revealed the increasing and fluctuating trends in the oil accumulation in the developing avocado mesocarp and seed, respectively. Additionally, striking differences in the lipid droplets between the mature mesocarp and seed were revealed in confocal microscopy images. Subsequently, the gene transcription profiles of the developing mesocarp and seed were characterized via a comprehensive transcriptome analysis involving second-generation sequencing and single-molecule real-time sequencing techniques. The tissue-specific transcription of lipid-related genes contributing to fatty acid synthesis, triacylglycerol assembly, and triacylglycerol storage was examined, with most of the lipid-related genes expressed at higher levels in the developing mesocarp than in the developing seed. A weighted gene co-expression network analysis uncovered 291 transcription factors that were commonly or uniquely correlated with the oil contents in the avocado mesocarp and seed. Moreover, 11 trans-acting and 79 cis-acting long non-coding RNAs were identified as common or unique to the developing avocado mesocarp and seed. These long non-coding RNAs may regulate the expression of 43 lipid-related genes. Finally, a network of genes associated with oil accumulation in the developing avocado mesocarp and seed was established.Conclusions: The results of this study further elucidate the tissue-specific oil biosynthesis and related regulatory network in the avocado mesocarp and seed. Furthermore, tissue-specific lipid-related genes, putative transcription factors, and putativelong non-coding RNAs affecting oil accumulation were identified. Our data may also be useful for characterizing tissue-specific oil accumulation at the transcriptomic level, thereby identifying candidate genes for improving the oil production of related plant species.

scholarly journals The PARP Inhibitor Olaparib Modulates the Transcriptional Regulatory Networks of Long Non-Coding RNAs during Vasculogenic Mimicry

Cells ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 2690
Author(s):  
Mónica Fernández-Cortés ◽  
Eduardo Andrés-León ◽  
Francisco Javier Oliver
Keyword(s):  
Transcription Factors ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Target Genes ◽  
Parp Inhibitor ◽  
Vasculogenic Mimicry ◽  
Transcriptome Profiling ◽  
Key Species ◽  
Non Coding Rnas ◽  
The Impact

In highly metastatic tumors, vasculogenic mimicry (VM) involves the acquisition by tumor cells of endothelial-like traits. Poly-(ADP-ribose) polymerase (PARP) inhibitors are currently used against tumors displaying BRCA1/2-dependent deficient homologous recombination, and they may have antimetastatic activity. Long non-coding RNAs (lncRNAs) are emerging as key species-specific regulators of cellular and disease processes. To evaluate the impact of olaparib treatment in the context of non-coding RNA, we have analyzed the expression of lncRNA after performing unbiased whole-transcriptome profiling of human uveal melanoma cells cultured to form VM. RNAseq revealed that the non-coding transcriptomic landscape differed between olaparib-treated and non-treated cells: olaparib significantly modulated the expression of 20 lncRNAs, 11 lncRNAs being upregulated, and 9 downregulated. We subjected the data to different bioinformatics tools and analysis in public databases. We found that copy-number variation alterations in some olaparib-modulated lncRNAs had a statistically significant correlation with alterations in some key tumor suppressor genes. Furthermore, the lncRNAs that were modulated by olaparib appeared to be regulated by common transcription factors: ETS1 had high-score binding sites in the promoters of all olaparib upregulated lncRNAs, while MZF1, RHOXF1 and NR2C2 had high-score binding sites in the promoters of all olaparib downregulated lncRNAs. Finally, we predicted that olaparib-modulated lncRNAs could further regulate several transcription factors and their subsequent target genes in melanoma, suggesting that olaparib may trigger a major shift in gene expression mediated by the regulation lncRNA. Globally, olaparib changed the lncRNA expression landscape during VM affecting angiogenesis-related genes.

Transcriptome Analysis of Canine Cardiac Fat Pads: Involvement of Two Novel Long Non-Coding RNAs in Atrial Fibrillation Neural Remodeling

2015 ◽  
Vol 116 (5) ◽  
pp. 809-821 ◽  
Author(s):  
Weizong Wang ◽  
Ximin Wang ◽  
Yujiao Zhang ◽  
Zhan Li ◽  
Xinxing Xie ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Transcriptome Analysis ◽  
Non Coding Rnas ◽  
Neural Remodeling ◽  
Fat Pads
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