Melatonin and chromatin

2019 ◽  
Vol 2 (1) ◽  
pp. 67-93 ◽  
Author(s):  
Ruediger Hardeland
Keyword(s):  
Gene Expression ◽  
Chromatin Remodeling ◽  
Cpg Islands ◽  
Noncoding Rnas ◽  
Sirtuin 1 ◽  
Light At Night ◽  
Control Of Gene Expression ◽  
Super Enhancer ◽  
Toxin Exposure

Melatonin affects chromatin remodeling, thereby activating or silencing specific genes and, presumably, also by modulating circadian-mediated changes in chromatin structure. Melatonin has been shown to exert effects on chromatin under conditions of toxin exposure, treatment with other hormones such as glucocorticoids or leptin, in cancer, and during developmental processes. Most of the documented actions concern histone modifications or their reversal that facilitate or prevent nucleosome eviction. Less information is available on DNA methylation or demethylation at regulatory CpG islands. To date, this has been mainly studied under conditions of early development, occasionally concerning seasonality or shiftwork with light at night. Another emerging field, which is still insufficiently studied, concerns regulation via DNA-interacting noncoding RNAs, in particular, super-enhancer lncRNAs. Although the direct information on actions by melatonin is widely missing, this field promises to become important, as numerous RNAs of this type have been shown to be rhythmically expressed. The circadian aspect of melatonin’s role in chromatin remodeling and control of gene expression deserves future attention. This includes the role of sirtuin 1, which participates in the circadian machinery and apparently mediates several effects of melatonin that are suppressed by sirtuin inhibitors or sirtuin 1 knockdown. 

The Role of Long Noncoding RNAs in the Epigenetic Control of Gene Expression

ChemMedChem ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. 505-510 ◽  
Author(s):  
Mariangela Morlando ◽  
Monica Ballarino ◽  
Alessandro Fatica ◽  
Irene Bozzoni
Keyword(s):  
Gene Expression ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Control Of Gene Expression ◽  
Epigenetic Control

scholarly journals Indole Acts as an Extracellular Cue Regulating Gene Expression in Vibrio cholerae

2009 ◽  
Vol 191 (11) ◽  
pp. 3504-3516 ◽  
Author(s):  
Ryan S. Mueller ◽  
Sinem Beyhan ◽  
Simran G. Saini ◽  
Fitnat H. Yildiz ◽  
Douglas H. Bartlett
Keyword(s):  
Gene Expression ◽  
Vibrio Cholerae ◽  
Biofilm Formation ◽  
Signal Molecule ◽  
Control Of Gene Expression ◽  
Protozoan Grazing ◽  
Extracellular Signal ◽  
Grazing Resistance ◽  
Indole Signaling

ABSTRACT Indole has been proposed to act as an extracellular signal molecule influencing biofilm formation in a range of bacteria. For this study, the role of indole in Vibrio cholerae biofilm formation was examined. It was shown that indole activates genes involved in vibrio polysaccharide (VPS) production, which is essential for V. cholerae biofilm formation. In addition to activating these genes, it was determined using microarrays that indole influences the expression of many other genes, including those involved in motility, protozoan grazing resistance, iron utilization, and ion transport. A transposon mutagenesis screen revealed additional components of the indole-VPS regulatory circuitry. The indole signaling cascade includes the DksA protein along with known regulators of VPS production, VpsR and CdgA. A working model is presented in which global control of gene expression by indole is coordinated through σ54 and associated transcriptional regulators.

scholarly journals Cryptic Transcription and Early Termination in the Control of Gene Expression

2011 ◽  
Vol 2011 ◽  
pp. 1-10 ◽  
Author(s):  
Jessie Colin ◽  
Domenico Libri ◽  
Odil Porrua
Keyword(s):  
Gene Expression ◽  
Rna Polymerase Ii ◽  
Regulatory Function ◽  
Large Set ◽  
Control Of Gene Expression ◽  
Alternative Transcription ◽  
Cryptic Transcription ◽  
Nuclear Exosome ◽  
The Impact

Recent studies on yeast transcriptome have revealed the presence of a large set of RNA polymerase II transcripts mapping to intergenic and antisense regions or overlapping canonical genes. Most of these ncRNAs (ncRNAs) are subject to termination by the Nrd1-dependent pathway and rapid degradation by the nuclear exosome and have been dubbed cryptic unstable transcripts (CUTs). CUTs are often considered as by-products of transcriptional noise, but in an increasing number of cases they play a central role in the control of gene expression. Regulatory mechanisms involving expression of a CUT are diverse and include attenuation, transcriptional interference, and alternative transcription start site choice. This review focuses on the impact of cryptic transcription on gene expression, describes the role of the Nrd1-complex as the main actor in preventing nonfunctional and potentially harmful transcription, and details a few systems where expression of a CUT has an essential regulatory function. We also summarize the most recent studies concerning other types of ncRNAs and their possible role in regulation.

scholarly journals The emerging role of super enhancer-derived noncoding RNAs in human cancer

Theranostics ◽  
2020 ◽  
Vol 10 (24) ◽  
pp. 11049-11062 ◽  
Author(s):  
Yutong Wang ◽  
Hui Nie ◽  
Xiaoyun He ◽  
Zhiming Liao ◽  
Yangying Zhou ◽  
...  
Keyword(s):  
Human Cancer ◽  
Noncoding Rnas ◽  
Super Enhancer

scholarly journals The Mycobacterium tuberculosis sRNA F6 regulates expression of groEL/S

2020 ◽  
Author(s):  
Joanna Houghton ◽  
Angela Rodgers ◽  
Graham Rose ◽  
Kristine B. Arnvig
Keyword(s):  
Gene Expression ◽  
Mycobacterium Tuberculosis ◽  
Small Rnas ◽  
Transcriptional Control ◽  
Cold Shock ◽  
Control Of Gene Expression ◽  
Rna Biology ◽  
Mouse Model Of Infection

ABSTRACTAlmost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of post-transcriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA, F6, and show it to be dependent on SigF for expression and significantly induced during in vitro starvation and in a mouse model of infection. However, we found no evidence of attenuation of a ΔF6 strain within the first 20 weeks of infection. A further exploration of F6 using in vitro models of infection suggests a role for F6 as a highly specific regulator of the heat shock repressor, HrcA. Our results point towards a role for F6 during periods of low metabolic activity similar to cold shock and associated with nutrient starvation such as that found in human granulomas in later stages of infection.

scholarly journals The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer

Cancers ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2701
Author(s):  
Naiade Calanca ◽  
Cecilie Abildgaard ◽  
Cláudia Aparecida Rainho ◽  
Silvia Regina Rogatto
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Noncoding Rnas ◽  
Response To Therapy ◽  
Long Noncoding Rnas ◽  
Cancer Type ◽  
Aberrant Expression ◽  
Term Survival ◽  
Control Of Gene Expression ◽  
Epigenetic Machinery

Comprehensive large-scale sequencing and bioinformatics analyses have uncovered a myriad of cancer-associated long noncoding RNAs (lncRNAs). Aberrant expression of lncRNAs is associated with epigenetic reprogramming during tumor development and progression, mainly due to their ability to interact with DNA, RNA, or proteins to regulate gene expression. LncRNAs participate in the control of gene expression patterns during development and cell differentiation and can be cell and cancer type specific. In this review, we described the potential of lncRNAs for clinical applications in ovarian cancer (OC). OC is a complex and heterogeneous disease characterized by relapse, chemoresistance, and high mortality rates. Despite advances in diagnosis and treatment, no significant improvements in long-term survival were observed in OC patients. A set of lncRNAs was associated with survival and response to therapy in this malignancy. We manually curated databases and used bioinformatics tools to identify lncRNAs implicated in the epigenetic regulation, along with examples of direct interactions between the lncRNAs and proteins of the epigenetic machinery in OC. The resources and mechanisms presented herein can improve the understanding of OC biology and provide the basis for further investigations regarding the selection of novel biomarkers and therapeutic targets.

scholarly journals Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis

2019 ◽  
Vol 20 (12) ◽  
pp. 3073 ◽  
Author(s):  
Ana Dienstbier ◽  
Fabian Amman ◽  
Daniel Štipl ◽  
Denisa Petráčková ◽  
Branislav Večerek
Keyword(s):  
Gene Expression ◽  
Bordetella Pertussis ◽  
Transcriptional Control ◽  
Whooping Cough ◽  
Expression Profiles ◽  
Bacterial Pathogen ◽  
Gene Expression Profiles ◽  
Control Of Gene Expression ◽  
Proteomic Data

Bordetella pertussis is a Gram-negative strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Previously, we have shown that RNA chaperone Hfq is required for virulence of B. pertussis. Furthermore, microarray analysis revealed that a large number of genes are affected by the lack of Hfq. This study represents the first attempt to characterize the Hfq regulon in bacterial pathogen using an integrative omics approach. Gene expression profiles were analyzed by RNA-seq and protein amounts in cell-associated and cell-free fractions were determined by LC-MS/MS technique. Comparative analysis of transcriptomic and proteomic data revealed solid correlation (r2 = 0.4) considering the role of Hfq in post-transcriptional control of gene expression. Importantly, our study confirms and further enlightens the role of Hfq in pathogenicity of B. pertussis as it shows that Δhfq strain displays strongly impaired secretion of substrates of Type III secretion system (T3SS) and substantially reduced resistance to serum killing. On the other hand, significantly increased production of proteins implicated in transport of important metabolites and essential nutrients observed in the mutant seems to compensate for the physiological defect introduced by the deletion of the hfq gene.

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