Epigenetic Regulatory Network Research Articles

Structure and function of long noncoding RNAs in epigenetic regulation

Genomes of complex organisms encode an abundance and diversity of long noncoding RNAs (lncRNAs) that are expressed throughout the cell and fulfill a wide variety of regulatory roles at almost every stage of gene expression. These roles, which encompass sensory, guiding, scaffolding and allosteric capacities, derive from folded modular domains in lncRNAs. In this diverse functional repertoire, we focus on the well-characterized ability for lncRNAs to function as epigenetic modulators. Many lncRNAs bind to chromatin-modifying proteins and recruit their catalytic activity to specific sites in the genome, thereby modulating chromatin states and impacting gene expression. Considering this regulatory potential in combination with the abundance of lncRNAs suggests that lncRNAs may be part of a broad epigenetic regulatory network.

Long Non-Coding RNA Targeting and Transcriptional De-Repression

Our current understanding of the molecular events that functionally characterize cellular biology continues to be revised. Recent observations find that the vast majority of the human genome is transcribed and may be functionally relevant. Many of these previously unrecognized transcripts, both short and long non-coding RNAs, have been found to be active modulators of protein coding gene function. While such observations were in the past relegated to imprinted genes, it is now becoming apparent that several different genes in differentiated cells may be under some form of non-coding RNA based regulatory control. Emerging evidence suggests that some of these long non-coding RNAs are functional in controlling gene transcription by the targeted recruitment of epigenetic silencing complexes to homology-containing loci in the genome. Most notably when these repressor non-coding RNAs are targeted using small RNA-based inhibitors (such as with RNA interference), a de-repression of the targeted gene can occur resulting in activation of gene expression. Knowledge of this emerging RNA based epigenetic regulatory network has implications not only in cellular evolution but also for the development of an entirely new area of pharmacology.

One, Two, Three: How Histone Methylation is Read

Methylation of histone lysine and arginine residues constitutes a highly complex control system directing diverse functions of the genome. Owing to their immense signaling potential with distinct sites of methylation and defined methylation states of mono-, di- or trimethylation as well as their higher biochemical stability compared with other histone modifications, these marks are thought to be part of epigenetic regulatory networks. Biological principles of how histone methylation is read and translated have emerged over the last few years. Only very few methyl marks directly impact chromatin. Conversely, a large number of histone methylation binding proteins has been identified. These contain specialized modules that are recruited to chromatin in a methylation site- and state-specific manner. Besides the molecular mechanisms of interaction, patterns of regulation of the binding proteins are becoming evident.

Mapping recently identified nucleotide variants in the genome and transcriptome

Nucleotide variants, especially those related to epigenetic functions, provide critical regulatory information beyond simple genomic sequence, and they define cell status in higher organisms. 5-methylcytosine, which is found in DNA, was until recently the only nucleotide variant studied in terms of epigenetics in eukaryotes. However, 5-methylcytosine has turned out to be just one component of a dynamic DNA epigenetic regulatory network that also includes 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine. Reversible methylation of N6-methyladenosine in RNA has also been demonstrated. The discovery of new nucleotide variants triggered an explosion of new information in the epigenetics field. This rapid research progress has benefited significantly from timely developments of new technologies that specifically recognize, enrich, and sequence nucleotide modifications, as evidenced by the wide application of the bisulfite sequencing of 5-methylcytosine and very recent modifications of bisulfite sequencing to revolve 5-hydroxymethylcytosine from 5-methylcytosine with base-resolution information.

Transcriptome analysis of a rotenone model of parkinsonism reveals complex I-tied and -untied toxicity mechanisms common to neurodegenerative diseases.

The pesticide rotenone, a neurotoxin that inhibits the mitochondrial complex I, and destabilizes microtubules (MT) has been linked to Parkinson disease (PD) etiology and is often used to model this neurodegenerative disease (ND). Many of the mechanisms of action of rotenone are posited mechanisms of neurodegeneration; however, they are not fully understood. Therefore, the study of rotenone-affected functional pathways is pertinent to the understanding of NDs pathogenesis. This report describes the transcriptome analysis of a neuroblastoma (NB) cell line chronically exposed to marginally toxic and moderately toxic doses of rotenone. The results revealed a complex pleiotropic response to rotenone that impacts a variety of cellular events, including cell cycle, DNA damage response, proliferation, differentiation, senescence and cell death, which could lead to survival or neurodegeneration depending on the dose and time of exposure and cell phenotype. The response encompasses an array of physiological pathways, modulated by transcriptional and epigenetic regulatory networks, likely activated by homeostatic alterations. Pathways that incorporate the contribution of MT destabilization to rotenone toxicity are suggested to explain complex I-independent rotenone-induced alterations of metabolism and redox homeostasis. The postulated mechanisms involve the blockage of mitochondrial voltage-dependent anions channels (VDACs) by tubulin, which coupled with other rotenone-induced organelle dysfunctions may underlie many presumed neurodegeneration mechanisms associated with pathophysiological aspects of various NDs including PD, AD and their variant forms. Thus, further investigation of such pathways may help identify novel therapeutic paths for these NDs.

MiRNAs regulate stem cell self-renewal and differentiation.

Stem cells undergo symmetric and asymmetric divisions to generate differentiated cells and more stem cells. The balance between self-renewal and differentiation of stem cells is controlled by transcription factors, epigenetic regulatory networks, and microRNAs (miRNAs). Herein the miRNA involvement in the regulation of stem cell self-renewal and differentiation is summarized. miRNA contribution to malignancy through regulating cancer stem cells is described. In addition, the reciprocal associations between miRNAs and epigenetic modifications in control of stem cell fate are discussed.

Tackling Skeletal Muscle Cells Epigenome in the Next-Generation Sequencing Era

Recent advances in high-throughput technologies have transformed methodologies employed to study cell-specific epigenomes and the approaches to investigate complex cellular phenotypes. Application of next-generation sequencing technology in the skeletal muscle differentiation field is rapidly extending our knowledge on how chromatin modifications, transcription factors and chromatin regulators orchestrate gene expression pathways guiding myogenesis. Here, we review recent biological insights gained by the application of next-generation sequencing techniques to decode the epigenetic profile and gene regulatory networks underlying skeletal muscle differentiation.

High-Throughput Computational Approaches to Analyzing Histone Modification Next-Generation Sequencing Data

Chromatin immunoprecipitation followed by sequencing (ChIP–seq) facilitates systematic analysis of chemical modifications of histone tails. As the cost of next-generation sequencing continues to drop, genome-wide histone modification sequencing becomes a common approach in a variety of researches in the epigenetic area. However, challenges of efficient ChIP–seq data analysis are now the main hurdle to interpret the histone modification ChIP-seq data, calling for continued enhancements of computational approaches. Here we provide a pragmatic overview of available computational approaches for the study of histone modification ChIP-seq data. We present the latest advances of computational methods for systematically detecting and functionally characterizing various types of histone modification ChIP-seq data, discuss the software packages currently available for performing tasks from short read mapping, peak calling to downstream genomic characterization and genome-wide visualization. We also present that the regulatory roles of histone modifications upon gene expression can be inferred by developing algorithms and methods specifically for histone modification ChIP-seq data. Such approaches will facilitate the epigenetic regulatory network construction and provide explicit biological hypothesis for further experiment testing. We also describe some challenges and important directions for histone modification analysis based on ChIP-seq data in future. We envision that the advances of computational approaches will bring more about a bright future for large-scale histone modification studies.

EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans

The advances of high throughput profiling methods, such as microarray gene profiling and RNA-seq, have enabled researchers to identify thousands of differentially expressed genes under a certain perturbation. Much work has been done to understand the genetic factors that contribute to the expression changes by searching the over-represented regulatory motifs in the promoter regions of these genes. However, the changes could also be caused by epigenetic regulation, especially histone modifications, and no web server has been constructed to study the epigenetic factors responsible for gene expression changes. Here, we pre-sent a web tool for this purpose. Provided with different categories of genes (e.g., up-regulated, down-regulated or unchanged genes), the server will find epigenetic factors responsible for the difference among the categories and construct an epigenetic regulatory network. Furthermore, it will perform co-localization analyses between these epigenetic factors and transcription factors, which were collected from large scale experimental ChIP-seq or computational predicted data. In addition, for users who want to analyze dynamic change of a histone modification mark under different cell conditions, the server will find direct and indi-rect target genes of this mark by integrative analysis of experimental data and computational prediction, and present a regulatory network around this mark. Both networks can be visualized by a user friendly in-terface and the data are downloadable in batch. The server currently supports 12 cell types in human, including ESC and CD4+ T cells, and will expand as more public data are available. It also allows user to create a self-defined cell type, upload and analyze multiple ChIP-seq data. It is freely available to academic users at http://jjwanglab.org/EpiRegNet.

Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification

BackgroundTranscription promoters are fundamental genomic cis-elements controlling gene expression. They can be classified into two types by the degree of imprecision of their transcription start sites: peak promoters, which initiate transcription from a narrow genomic region; and broad promoters, which initiate transcription from a wide-ranging region. Eukaryotic transcription initiation is suggested to be associated with the genomic positions and modifications of nucleosomes. For instance, it has been recently shown that histone with H3K9 acetylation (H3K9ac) is more likely to be distributed around broad promoters rather than peak promoters; it can thus be inferred that there is an association between histone H3K9 and promoter architecture.ResultsHere, we performed a systematic analysis of transcription promoters and gene expression, as well as of epigenetic histone behaviors, including genomic position, stability within the chromatin, and several modifications. We found that, in humans, broad promoters, but not peak promoters, generally had significant associations with nucleosome positioning and modification. Specifically, around broad promoters histones were highly distributed and aligned in an orderly fashion. This feature was more evident with histones that were methylated or acetylated; moreover, the nucleosome positions around the broad promoters were more stable than those around the peak ones. More strikingly, the overall expression levels of genes associated with broad promoters (but not peak promoters) with modified histones were significantly higher than the levels of genes associated with broad promoters with unmodified histones.ConclusionThese results shed light on how epigenetic regulatory networks of histone modifications are associated with promoter architecture.

Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications

BackgroundThe advent of ChIP-seq technology has made the investigation of epigenetic regulatory networks a computationally tractable problem. Several groups have applied statistical computing methods to ChIP-seq datasets to gain insight into the epigenetic regulation of transcription. However, methods for estimating enrichment levels in ChIP-seq data for these computational studies are understudied and variable. Since the conclusions drawn from these data mining and machine learning applications strongly depend on the enrichment level inputs, a comparison of estimation methods with respect to the performance of statistical models should be made.ResultsVarious methods were used to estimate the gene-wise ChIP-seq enrichment levels for 20 histone methylations and the histone variant H2A.Z. The Multivariate Adaptive Regression Splines (MARS) algorithm was applied for each estimation method using the estimation of enrichment levels as predictors and gene expression levels as responses. The methods used to estimate enrichment levels included tag counting and model-based methods that were applied to whole genes and specific gene regions. These methods were also applied to various sizes of estimation windows. The MARS model performance was assessed with the Generalized Cross-Validation Score (GCV). We determined that model-based methods of enrichment estimation that spatially weight enrichment based on average patterns provided an improvement over tag counting methods. Also, methods that included information across the entire gene body provided improvement over methods that focus on a specific sub-region of the gene (e.g., the 5' or 3' region).ConclusionThe performance of data mining and machine learning methods when applied to histone modification ChIP-seq data can be improved by using data across the entire gene body, and incorporating the spatial distribution of enrichment. Refinement of enrichment estimation ultimately improved accuracy of model predictions.

Modulation of gene-specific epigenetic states and transcription by non-coding RNAs

Emerging evidence points to a role for long non-coding RNAs in the modulation of epigenetic states and transcription in human cells. New insights, using various forms of small non-coding RNAs, suggest that a mechanism of action is operative in human cells, which utilizes non-coding RNAs to direct epigenetic marks to homology containing loci resulting ultimately in the epigenetic-based modulation of gene transcription. Importantly, insights into this mechanism of action have allowed for certain target sequences, which are either actively involved in RNA mediated epigenetic regulation or targets for non-coding RNA based epigenetic regulation, to be selected. As such, it is now feasible to utilize small antisense RNAs to either epigenetically silence a gene expression or remove epigenetic silencing of endogenous non-coding RNAs and essentially turn on a gene expression. Knowledge of this emerging RNA-based epigenetic regulatory network and our ability to cognitively control gene expression has deep implications in the development of an entirely new area of pharmacopeia.

Methyltransferase‐Directed Derivatization of 5‐Hydroxymethylcytosine in DNA

Cytosine modification by AdoMet–dependent DNA methyltransferases is part of an epigenetic regulatory network in vertebrates. Here we show that, in the absence of AdoMet, bacterial cytosine-5 methyltransferases can catalyze condensation of aliphatic thiols and selenols to 5-hydroxymethylcytosine in DNA yielding 5-chalcogenomethyl derivatives. These new atypical reactions open new ways for sequence-specific derivatization and analysis of 5-hydroxymethylcytosine, a recently discovered nucleobase in mammalian DNA

A Model for Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways for Transcription Factor Induced Pluripotency

With relatively low efficiency, differentiated cells can be reprogrammed to a pluripotent state by ectopic expression of a few transcription factors. An understanding of the mechanisms that underlie data emerging from such experiments can help design optimal strategies for creating pluripotent cells for patient-specific regenerative medicine. We have developed a computational model for the architecture of the epigenetic and genetic regulatory networks which describes transformations resulting from expression of reprogramming factors. Importantly, our studies identify the rare temporal pathways that result in induced pluripotent cells. Further experimental tests of predictions emerging from our model should lead to fundamental advances in our understanding of how cellular identity is maintained and transformed.

Arabidopsis DNA methyltransferase AtDNMT2 associates with histone deacetylase AtHD2s activity

DNA methyltransferase2 (DNMT2) is always deemed to be enigmatic, because it contains highly conserved DNA methyltransferase motifs but lacks the DNA methylation catalytic capability. Here we show that Arabidopsis DNA methyltransferase2 (AtDNMT2) is localized in nucleus and associates with histone deacetylation. Bimolecular fluorescence complementation and pull-down assays show AtDNMT2 interacts with type-2 histone deacetylases (AtHD2s), a unique type of histone deacetylase family in plants. Through analyzing the expression of AtDNMT2: ß-glucuronidase (GUS) fusion protein, we demonstrate that AtDNMT2 has the ability to repress gene expression at transcription level. Meanwhile, the expression of AtDNMT2 gene is altered in athd2c mutant plants. We propose that AtDNMT2 possibly involves in the activity of histone deacetylation and plant epigenetic regulatory network.

A Model For Genetic and Epigenetic Regulatory Networks Identifies Rare Pathways For Transcription Factor Induced Pluripotency

With relatively low efficiency, differentiated cells can be reprogrammed to a pluripotent state by ectopic expression of a few transcription factors. An understanding of the mechanisms that underlie data emerging from such experiments can help design optimal strategies for creating pluripotent cells for patient-specific regenerative medicine. We have developed a computational model for the architecture of the epigenetic and genetic regulatory networks which describes transformations resulting from expression of reprogramming factors. Importantly, our studies identify the rare temporal pathways that result in induced pluripotent cells. Further experimental tests of predictions emerging from our model should lead to fundamental advances in our understanding of how cellular identity is maintained and transformed.

Epigenetic Signatures In Stem Cells And Cancer Stem Cells

The physiological properties of pluripotency in stem cells and the processes of cell specialization are governed by epigenetic mechanisms, as they are inheritable but not dependent on the cell genotype. There is cumulating evidence demonstrating the presence of cells with stem cell properties within tumors, suggesting that these cells are responsible for tumor growth and heterogeneity. As epigenetic control of self-renewal and pluripotency is a hallmark of stem cells, there is increased interest in studying similar epigenetic mechanisms governing these stemness properties in cancer stem cells. Here we will review the evidence supporting a role for epigenetic mechanisms in the induction of cancer stem cells, with an emphasis on the epigenetic regulatory networks involved in the establishment of normal self-renewal and pluripotency, and their potential deregulation in cancer. We will also discuss the data supporting the plasticity of these mechanisms and its potential therapeutic implications.

ChIP'ing the mammalian genome: technical advances and insights into functional elements

Characterization of the functional components in mammalian genomes depends on our ability to completely elucidate the genetic and epigenetic regulatory networks of chromatin states and nuclear architecture. Such endeavors demand the availability of robust and effective approaches to characterizing protein-DNA associations in their native chromatin environments. Consider able progress has been made through the applica tion of chromatin immunoprecipitation (ChIP) to study chromatin biology in cells. Coupled with genome-wide analyses, ChIP-based assays enable us to take a global, unbiased and comprehensive view of transcriptional control, epigenetic regulation and chromatin structures, with high precision and versatility. The integrated knowledge derived from these studies is used to decipher gene regulatory networks and define genome organization. In this review, we discuss this powerful approach and its current advances. We also explore the possible future developments of ChIP-based approaches to interrogating long-range chromatin interactions and their impact on the mechanisms regulating gene expression.

Chromosomal fragility, structural rearrangements and mobile element activity may reflect dynamic epigenetic mechanisms of importance in neurobehavioural genetics

Advances in human genome analyses have not yet allowed identification of specific genetic mechanisms underlying the expression of human neurobehavioural disorders. There is an increasing awareness that several genes may contribute to behavioural phenotypes and these genes appear to interact in as yet undetermined ways. It has been suggested that the problem needs elucidation from an epigenetic, gene expression perspective. Cytogenetic instability manifesting as chromosomal fragile sites, translocations, duplications, deletions and inversions, when co-occurring with neurobehavioural disorders, may offer a doorway to the investigation of such chromatin level, regulatory region, epigenetic processes. Due to earlier indications of non-specificity of chromosomal aberrations, poor phenotype:genotype correlations and a shift to analysing candidate coding regions on high resolution map level, the only utility of chromosomal breakpoints came to be seen as harbouring possible candidate genes of interest when segregating together with particular neurobehavioural disorders. More recent findings of the expression of highly specific subsets of fragile sites in association with Tourette and Rett syndromes need to be extended to other neurobehavioural disorders to ascertain whether observed patterns can be considered representative of 'chromatin endophenotypes' correlating with discrete sets of neurobehavioural symptoms. Environmental/epigenetic factors could affect the chromatin characteristics of the genome arising through DNA strand breakage, mobile element activity and retroinsertion, establishing new architectural features of regulatory control networks very rapidly in comparison to coding region evolution rates. Microarray-based techniques for the genome-wide mapping of in vivo protein-DNA interactions offer increasingly comprehensive views of genetic and epigenetic regulatory networks. It may be informative to include functionally significant chromatin structural variation analyses when considering candidate genes for neurobehavioural disorders.

Mapping of genetic and epigenetic regulatory networks using microarrays

The highly coordinated expression of thousands of genes in an organism is regulated by the concerted action of hundreds of transcription factors and chromatin proteins, as well as by epigenetic mechanisms. Understanding the architecture of these vastly complex regulatory networks is one of the main challenges in the postgenomic era. New microarray-based techniques have become available for the genome-wide mapping of in vivo protein-DNA interactions and epigenetic marks. Data sets obtained with these techniques begin to offer the first comprehensive views of genetic and epigenetic regulatory networks.