Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiaeThis paper is one of a selection of papers published in this Special Issue, entitled 30th Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

2009 ◽  
Vol 87 (5) ◽  
pp. 767-779 ◽  
Author(s):  
Benjamin R. Harrison ◽  
Oya Yazgan ◽  
Jocelyn E. Krebs
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Messenger Rna ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Small Interfering Rnas ◽  
Ideal System

There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.

scholarly journals Dynamical Mechanisms for Gene Regulation Mediated by Two Noncoding RNAs in Long-Term Memory Formation

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Lijie Hao ◽  
Zhuoqin Yang
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Regulation Of Gene Expression ◽  
Network Motif ◽  
Noncoding Rnas ◽  
Memory Formation ◽  
Long Term Memory ◽  
Term Memory ◽  
Motif Model

Noncoding RNAs such as miRNAs and piRNAs have long-lasting effects on the regulation of gene expression involved in long-term synaptic changes. To characterize gene regulation mediated by small noncoding RNAs associated with long-term memory in Aplysia, we consider two noncoding RNAs stimulated by 5-HT into a gene regulatory network motif model, including miR-124 that binds to and inhibits the mRNA of CREB1 and piR-F that facilitates serotonin-dependent DNA methylation to lead to repression of CREB2. Codimension-1 and -2 bifurcation analyses of 5-HT regulating both miR-124 and piR-F and a negative feedback strength for oscillation reveal rich dynamical properties of bistability and oscillations robust to variations in all other parameters. More importantly, we verify three stimulus protocols of 5-HT in experiments by our model and find that application of five pulses of 5-HT leads to a transient decrease of miR-124 but increase of piR-F concentrations, which matters sustained high level of CREB1 concentration associated with long-term memory. Furthermore, we perform bifurcation analyses for the concentrations of miR-124 and piR-F as two parameters to explore dynamical mechanisms underlying the epigenetic regulation in long-term memory formation. This study provides insights into revealing regulatory roles of epigenetic changes in gene expression involving noncoding RNAs associated with synaptic plasticity.

Factors regulating lactoferrin gene expressionThis paper is one of a selection of papers published in this Special Issue, entitled 7th International Conference on Lactoferrin: Structure, Function, and Applications, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (3) ◽  
pp. 263-267 ◽  
Author(s):  
Christina T. Teng
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Nuclear Receptors ◽  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Limited Information ◽  
Lactoferrin Gene

Regulation of gene expression by nuclear receptors and transcription factors involves the concerted action of multiple proteins. The process of transcriptional activation involves chromatin modification, nuclear receptor or transcription factor binding to the response element of the promoter, and coregulator recruitment. Despite advances in knowledge pertaining to the molecular mechanisms of gene regulation overall, there is very limited information available on the molecular mechanism of lactoferrin gene regulation. This review will outline novel information relating to general gene regulation and will discuss the current understanding of the regulation of lactoferrin gene expression by nuclear receptors and transcription factors.

scholarly journals Regulatory microRNAs in Brown, Brite and White Adipose Tissue

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2489
Author(s):  
Seley Gharanei ◽  
Kiran Shabir ◽  
James E. Brown ◽  
Martin O. Weickert ◽  
Thomas M. Barber ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Messenger Rna ◽  
Regulation Of Gene Expression ◽  
Rna Degradation ◽  
Comprehensive Overview ◽  
Brown Adipocytes ◽  
White Adipocytes ◽  
Different Types ◽  
Brown Adipogenesis

MicroRNAs (miRNAs) constitute a class of short noncoding RNAs which regulate gene expression by targeting messenger RNA, inducing translational repression and messenger RNA degradation. This regulation of gene expression by miRNAs in adipose tissue (AT) can impact on the regulation of metabolism and energy homeostasis, particularly considering the different types of adipocytes which exist in mammals, i.e., white adipocytes (white AT; WAT), brown adipocytes (brown AT; BAT), and inducible brown adipocytes in WAT (beige or brite or brown-in-white adipocytes). Indeed, an increasing number of miRNAs has been identified to regulate key signaling pathways of adipogenesis in BAT, brite AT, and WAT by acting on transcription factors that promote or inhibit adipocyte differentiation. For example, MiR-328, MiR-378, MiR-30b/c, MiR-455, MiR-32, and MiR-193b-365 activate brown adipogenesis, whereas MiR-34a, MiR-133, MiR-155, and MiR-27b are brown adipogenesis inhibitors. Given that WAT mainly stores energy as lipids, whilst BAT mainly dissipates energy as heat, clarifying the effects of miRNAs in different types of AT has recently attracted significant research interest, aiming to also develop novel miRNA-based therapies against obesity, diabetes, and other obesity-related diseases. Therefore, this review presents an up-to-date comprehensive overview of the role of key regulatory miRNAs in BAT, brite AT, and WAT.

The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme

2008 ◽  
Vol 389 (4) ◽  
pp. 323-331 ◽  
Author(s):  
David Umlauf ◽  
Peter Fraser ◽  
Takashi Nagano
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Chromatin Structure ◽  
Genome Architecture ◽  
Paradoxical Situation ◽  
Intergenic Regions ◽  
Non Coding Rnas ◽  
Variations On A Theme

Abstract Transcriptome studies have uncovered a plethora of non-coding RNAs (ncRNA) in mammals. Most originate within intergenic regions of the genome and recent evidence indicates that some are involved in many different pathways that ultimately act on genome architecture and gene expression. In this review, we discuss the role of well-characterized long ncRNAs in gene regulation pointing to their similarities, but also their differences. We will attempt to highlight a paradoxical situation in which transcription is needed to repress entire chromosomal domains possibly through the action of ncRNAs that create nuclear environments refractory to transcription.

scholarly journals Computational modelling unravels the precise clockwork of cyanobacteria

2018 ◽  
Vol 8 (6) ◽  
pp. 20180038 ◽  
Author(s):  
Nicolas M. Schmelling ◽  
Ilka M. Axmann
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Circadian Clock ◽  
Environmental Changes ◽  
Regulation Of Gene Expression ◽  
Computational Modelling ◽  
Circadian Clocks ◽  
Fitness Advantage ◽  
Fundamental Part ◽  
Global Gene Regulation

Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock. Here, we summarize the findings and insights into various parts of the cyanobacterial circadian clock made by mathematical modelling. These findings have implications for eukaryotic circadian research as well as synthetic biology harnessing the power and efficiency of global gene regulation.

scholarly journals Integration of Long-Term-Memory-Related Synaptic Plasticity Involves Bidirectional Regulation of Gene Expression and Chromatin Structure

Cell ◽  
2002 ◽  
Vol 111 (4) ◽  
pp. 483-493 ◽  
Author(s):  
Zhonghui Guan ◽  
Maurizio Giustetto ◽  
Stavros Lomvardas ◽  
Joung-Hun Kim ◽  
Maria Concetta Miniaci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Synaptic Plasticity ◽  
Chromatin Structure ◽  
Regulation Of Gene Expression ◽  
Long Term Memory ◽  
Term Memory ◽  
Bidirectional Regulation

scholarly journals Long Noncoding RNA Plays a Key Role in Metastasis and Prognosis of Hepatocellular Carcinoma

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Guangbing Li ◽  
Haohai Zhang ◽  
Xueshuai Wan ◽  
Xiaobo Yang ◽  
Chengpei Zhu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Regulation Of Gene Expression ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Comprehensive Review ◽  
Cellular Processes

Long noncoding RNAs (lncRNAs) have been attracting immense research interests. However, only a handful of lncRNAs had been thoroughly characterized. They were involved in fundamental cellular processes including regulation of gene expression at epigenetics as well as tumorogenesis. In this paper, we give a systematic and comprehensive review of existing literature about lncRNA involvement in hepatocellular carcinoma. This review exhibited that lncRNAs played important roles in tumorigenesis and subsequent prognosis and metastasis of hepatocellular carcinoma and elucidated the role of some specific lncRNAs such as MALAT1 and HOTAIR in the pathophysiology of hepatocellular carcinoma and their potential of being therapeutic targets.

scholarly journals Changes of DNA methylation and chromatin structure in the human myeloperoxidase gene during myeloid differentiation

Blood ◽  
1991 ◽  
Vol 78 (2) ◽  
pp. 345-356 ◽  
Author(s):  
M Lubbert ◽  
CW Miller ◽  
HP Koeffler
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Chromatin Structure ◽  
Messenger Rna ◽  
Hybrid Cell ◽  
Myeloid Cells ◽  
Dnase I ◽  
Lymphoid Cells ◽  
Upstream Region ◽  
Myeloid Differentiation

Expression of the myeloperoxidase (MPO) gene is tightly regulated in a tissue- and development-specific manner. Accumulation of MPO messenger RNA (mRNA) occurs only at the late myeloblastic and promyelocytic stages of myeloid differentiation and is negligible at other stages of myeloid development and in other tissues. The goal of our studies was to begin to understand the events that occur to control MPO gene expression during normal granulocytopoiesis. Chromatin structure of the MPO gene was evaluated by DNase I treatment of isolated nuclei and Southern blot analysis. No detectable DNase I hypersensitive sites were found in the region of the MPO gene in non-myeloid cells. One site was present in the 5′ upstream region in myeloid cells that are developmentally too immature to transcribe MPO. Three sites of hypersensitivity in the regions of the putative MPO promoter and upstream region occurred in MPO-expressing promyelocytes. These sites were markedly reduced in terminally differentiated, non-expressing myeloid cells. Analysis of DNA methylation of the MPO gene using methylation-sensitive restriction enzymes showed that the gene was highly methylated in non-myeloid cells. Stepwise demethylation occurred in myeloid cells developmentally too immature to transcribe MPO. Maximal demethylation in the 5′ gene region occurred in MPO-expressing promyelocytes. This methylation pattern did not change in terminally differentiated, MPO non-expressing myeloid cells. A somatic hybrid cell formed by fusion of HL-60 (MPO-expressing cells) and PUT (MPO non- expressing lymphoid cells) extinguished expression of MPO and showed a chimeric pattern of MPO gene methylation, suggesting that demethylation is necessary but not sufficient for expression of the MPO gene. Our studies show that demethylation and DNase I hypersensitivity of the MPO gene were associated with a tissue-dependent potential for MPO gene expression that preceded the developmental ability to express MPO mRNA.

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