To analyse the biological role of 5‐methylation of cytosine residues in DNA requires precise and efficient methods for detecting individual 5‐methylcytosines (5‐MeCs) in genomic DNA. The methods developed over the past decade rely on either differential enzymatic or chemical cleavage of DNA, or more recently on differential sensitivity to chemical conversion of one base to another. The most commonly used methods for studying the methylation profile of DNA, including the bisulphite base‐conversion method, are reviewed.

5‐methylcytosine (5mC) was long thought to be the only enzymatically created modified DNA base in mammalian cells. The discovery of 5‐hydroxymethylcytosine, 5‐formylcytosine, and 5‐carboxylcytosine as reaction products of the TET family 5mC oxidases has prompted extensive searches for proteins that specifically bind to these oxidized bases. However, only a few of such “reader” proteins have been identified and verified so far. In this review, we discuss potential biological functions of oxidized 5mC as well as the role the presumed reader proteins (...) may play in interpreting the genomic signals of 5mC oxidation products. (shrink)

Properties of non‐canonical GC base pairs and their relations with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the transient GC wobble base pairs both in the mechanisms of the mechanochemical cleavage of DNA and epigenetic mechanisms involving of 5‐methylcytosine, is proposed. The hypothesis explains the increase in the frequency of the breaks of the sugar‐phosphate backbone of DNA after cytosines, the asymmetric character of these breaks, and an increase in break frequency in CpG after cytosine (...) methylation. As an alternative hypothesis, probable implication of GC+ Hoogsteen base pairs is considered, which now exemplify the best‐studied non‐canonical GC base pairs in the DNA double helix. Also see the video abstract here https://youtu.be/EUunVWL0ptw. (shrink)

We here review primary methods used in quantifying and mapping 5‐hydroxymethylcytosine (5hmC), including global quantification, restriction enzyme‐based detection, and methods involving DNA‐enrichment strategies and the genome‐wide sequencing of 5hmC. As discovered in the mammalian genome in 2009, 5hmC, oxidized from 5‐methylcytosine (5mC) by ten‐eleven translocation (TET) dioxygenases, is increasingly being recognized as a biomarker in biological processes from development to pathogenesis, as its various detection methods have shown. We focus in particular on an ultrasensitive single‐molecule imaging technique that can detect (...) and quantify 5hmC from trace samples and thus offer information regarding the distance‐based relationship between 5hmC and 5mC when used in combination with fluorescence resonance energy transfer. (shrink)

N6‐methyladenine (6mA) is one of the most abundant types of DNA methylation, and plays an important role in bacteria; however, its roles in higher eukaryotes, such as plants, insects, and mammals, have been considered less important. Recent studies highlight that 6mA does indeed occur, and that it plays an important role in eukaryotes, such as worm, fly, and green algae, and thus the regulation of 6mA has emerged as a novel epigenetic mechanism in higher eukaryotes. Despite this intriguing development, a (...) number of important issues regarding its biological roles are yet to be addressed. In this review, we focus on the 5mC and 6mA modifications in terms of their production, distribution, and the erasure of 6mA in higher eukaryotes including mammals. We perform an analysis of the potential functions of 6mA, hence widening understanding of this new epigenetic mark in higher eukaryotes, and suggesting future studies in this field. (shrink)

RNA modifications have recently emerged as an important regulatory layer of gene expression. The most prevalent and reversible modification on messenger RNA (mRNA), N6‐methyladenosine, regulates most steps of RNA metabolism and its dysregulation has been associated with numerous diseases. Other modifications such as 5‐methylcytosine and N1‐methyladenosine have also been detected on mRNA but their abundance is lower and still debated. Adenosine to inosine RNA editing is widespread on coding and non‐coding RNA and can alter mRNA decoding as well as protect (...) against autoimmune diseases. 2′‐O‐methylation of the ribose and pseudouridine are widespread on ribosomal and transfer RNA and contribute to proper RNA folding and stability. While the understanding of the individual role of RNA modifications has now reached an unprecedented stage, still little is known about their interplay in the control of gene expression. In this review we discuss the examples where such interplay has been observed and speculate that with the progress of mapping technologies more of those will rapidly accumulate. (shrink)

Contrary to mammalian DNA, which is thought to contain only 5-methylcytosine (m5C), bacterial DNA contains two additional methylated bases, namely N6-methyladenine (m6A), and N4-methylcytosine (m4C). However, if the main function of m5C and m4C in bacteria is protection against restriction enzymes, the roles of m6A are multiple and include, for example, the regulation of virulence and the control of many bacterial DNA functions such as the replication, repair, expression and transposition of DNA. Interestingly, even if adenine methylation is usually considered (...) a bacterial DNA feature, the presence of m6A has been found in protist and plant DNAs. Furthermore, indirect evidence suggests the presence of m6A in mammal DNA, raising the possibility that this base has remained undetected due to the low sensitivity of the analytical methods used. This highlights the importance of considering m6A as the sixth element of DNA. BioEssays 28: 309–315, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

While N6‐methyladenosine (m6A) is a well‐known epigenetic modification in bacterial DNA, it remained largely unstudied in eukaryotes. Recent studies have brought to fore its potential epigenetic role across diverse eukaryotes with biological consequences, which are distinct and possibly even opposite to the well‐studied 5‐methylcytosine mark. Adenine methyltransferases appear to have been independently acquired by eukaryotes on at least 13 occasions from prokaryotic restriction‐modification and counter‐restriction systems. On at least four to five instances, these methyltransferases were recruited as RNA methylases. Thus, (...) m6A marks in eukaryotic DNA and RNA might be more widespread and diversified than previously believed. Several m6A‐binding protein domains from prokaryotes were also acquired by eukaryotes, facilitating prediction of potential readers for these marks. Further, multiple lineages of the AlkB family of dioxygenases have been recruited as m6A demethylases. Although members of the TET/JBP family of dioxygenases have also been suggested to be m6A demethylases, this proposal needs more careful evaluation. (shrink)

The fifth base in human DNA, 5‐methylcytosine, is inherently mutagenic. This has led to marked changes in the distribution of the CpG methyl acceptor site and an 80% depletion in its frequency of occurrence in vertebrate DNA. The coding regions of many genes contain CpGs which are methylated in sperm and serve as hot spots for mutation in human genetic diseases. Fully 30–40% of all human germline point mutations are thought to be methylation induced even though the CpG dinucleotide is (...) under‐represented and efficient cellular repair systems exist. Importantly, tumor suppressor genes such as p53 also contain methylated CpGs and these serve as hot spots for mutations in some, but not all, human cancers. Comparison of the spectrum of mutations present in this gene in different human cancers allows for predictions to be made on the molecular mechanisms of tumorigenesis. (shrink)

Drosophila melanogaster is often considered to lack genomic 5‐methylcytosine (m5C), an opinion reinforced by two whole genome bisulfite‐sequencing studies that failed to find m5C. New evidence, however, indicates that genomic methylation is indeed present in the fly, albeit in small quantities and in unusual patterns. At embryonic stage 5, m5C occurs in short strand‐specific regions that cover ∼1% of the genome, at tissue levels suggesting a distribution restricted to a subset of nuclei. Its function is not obvious, but methylation in (...) subsets of nuclei would obscure functional associations since transcript levels and epigenetic modifications are assayed in whole embryos. Surprisingly, Mt2, the fly's only candidate DNA methyltransferase, is not necessary for the observed methylation. Full evaluation of the functions of genome methylation in Drosophila must await discovery and experimental inactivation of the DNA methyltransferase, as well as a better understanding of the pattern and developmental regulation of genomic m5C. (shrink)

DNA methylation is a quintessential epigenetic mechanism. Widely considered a stable regulator of gene silencing, it represents a form of “molecular braille,” chemically printed on DNA to regulate its structure and the expression of genetic information. However, there was a time when methyl groups simply existed in cells, mysteriously speckled across the cytosine building blocks of DNA. Why was the code of life chemically modified, apparently by “no accident of enzyme action” (Wyatt 1951 )? If all cells in a body (...) share the same genome sequence, how do they adopt unique functions and maintain stable developmental states? Do cells remember? In this historical perspective, I review epigenetic history and principles and the tools, key scientists, and concepts that brought us the synthesis and discovery of prokaryotic and eukaryotic methylated DNA. Drawing heavily on Gerard Wyatt’s observation of asymmetric levels of methylated DNA across species, as well as to a pair of visionary 1975 DNA methylation papers, 5-methylcytosine is connected to DNA methylating enzymes in bacteria, the maintenance of stable cellular states over development, and to the regulation of gene expression through protein-DNA binding. These works have not only shaped our views on heritability and gene regulation but also remind us that core epigenetic concepts emerged from the intrinsic requirement for epigenetic mechanisms to exist. Driven by observations across prokaryotic and eukaryotic worlds, epigenetic systems function to access and interpret genetic information across all forms of life. Collectively, these works offer many guiding principles for our epigenetic understanding for today, and for the next generation of epigenetic inquiry in a postgenomics world. (shrink)

To decode the function and molecular recognition of several recently discovered cytosine derivatives in the human genome – 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine – a detailed understanding of their effects on the structural, chemical, and biophysical properties of DNA is essential. Here, we review recent literature in this area, with particular emphasis on features that have been proposed to enable the specific recognition of modified cytosine bases by DNA-binding proteins. These include electronic factors, modulation of base-pair stability, flexibility, and radical changes (...) in duplex conformation. We explore these proposals and assess whether or not they are supported by current biophysical data. This analysis is focused primarily on the properties of epigenetically modified DNA itself, which provides a basis for discussion of the mechanisms of recognition by different proteins. 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine have recently been discovered in mammalian DNA and appear to have essential regulatory roles. Here, we summarize recent investigations into their effects on the structural, chemical, and biophysical properties of DNA, an understanding of which is essential to decoding their behavior in the genome. (shrink)

Methylation of DNA plays an important role in the control of gene expression in higher eukaryotes. This is largely achieved by the packaging of methylated DNA into chromatin structures that are inaccessible to transcription factors and other proteins. Methylation involves the addition of a methyl group to the 5‐position of the cytosine base in DNA, a reaction catalysed by a DNA (cytosine‐5) methyltransferase. This reaction occurs in nuclear replication foci where the chromatin structure is loosened for replication, thereby allowing access (...) to methyltransferases. Partly as a result of their recognising the presence of a methylcytosine on the parental strand following replication, these large enzymes are able to maintain the distribution of methyl groups along the DNA of somatic cells and, thereby, maintain tissue‐specific patterns of gene expression. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:BOOK REVIEWS 91 The passage which permitted such an interpretation is the following: This self-command is very different at different times.... Can we give any reason for these variations, except experience? Where then is the power of which we pretend to be conscious? Is there not here, either in a spiritual or a material substance, or both, some secret mechanism or structure of parts, upon which the effect depends...?" (...) (Enquiry, p. 68). This rhetorical question is, on the contrary, intended as the part of the third argument for the thesis "that even this command of the will gives us no real idea of force or energy" (Enquiry, p. 67). There is no evidence in the Enquiries that Hume concluded that self is a substance. On p. 45, Anderson "suggests that Hume employs 'impression'...in a less frequent usage, however.., to be a pressure, or pattern of light, or other means whereby objects are applied to the external organs of sense"t On p. 65 and also on p. 173, it is argued fallaciously that, "Hume considers mathematical ideas, like all other ideas, to be existences. If this be true, then the necessary relations ~mpposed to obtain among mathematical ideas cannot be discerned even though these ideas themselves be fully known." Now it is a matter of debate whether Hume believed that all mathematical ideas are derived from impressions (see my controversy with Flew on this issue, in Ratio, Vol. VI, No. 2, "Hume on Pure and Applied Geometry," and Flew's article, "Did Hume Distinguish Pure and Applied Geometry?," Ratio, Vol. VIII, No. 1). But even if we assume that this is his belief, it does not follow at all that the logical relations among these ideas are contingent. As Pap argued a long time ago, "A sensationalist might maintain that all the concepts that constitute a given proposition are derived from experience and might nevertheless admit that proposition itself is a priori in the sense of requiring no empirical verification in order to be assertable as true." Thus, Hume the sensationalist admitted that a priori knowledge is possible in mathematics, which is conversant exclusively about "relations of ideas" and not about "matters of fact." Finally, in the last chapter, it is argued that, "Hume's own suggestion concerning these three natural relations (resemblance, contiguity, and cause and effect) is that they are fundamentally material--that they consist in a certain characteristic movement of the animal spirit in the brain" (p. 163)I1 That, "The necessity is the relationship between cause and effect, Hume's remarks suggest, is ultimately their identity in essence. One passage which we have noted indicates that cause and effect are inseparable, and by use of Hume's own maxims we may strictly infer from their inseparability their identity" (p. 165)II And that, "Although Hume's doctrine of matter is ultimately of central importance in his system, his beginnings in moral philosophy doubtless led him to turn his attention away from the topic of matter" (p. 175). This book, though replete with quotations from Hume's works and exhibiting a great amount of microscopic observations, represents a mistaken view of Hume's epistemology. ~ARHANG ZABEEIq Roosevelt University, Chicago Hegel's Phenomenology. Dialogues on the Life of Mind. By Jacob Loewenberg. (La Salle, Ill. : The Open Court Publ. Co., 1965.Pp. xv + 377.) Hegel's Phenomenology o] Spirit, intriguing in its richness, has long remained one of the most forbidding of philosophical classics. Unfortunately, commentaries, though altogether indispensable, are sparse. Heretofore, the reader found himself referred mainly to two foreign language studies, G. A. Gabler's Kritik des Be~usst~ein~ of 1835, and J. Hyppolite's Gen~se et structure de la Phdnomdnologie de l'esprit; no full-scale work in English was available. And 92 HISTORY OF PHILOSOPHY even the reader prepared to turn to these works might register disenchantment: Gabler deals with two fifths of the book only, and Hyppolite is at times too close to the text to be much help. What remains is comment in the framework of more general studies of Hegel's philosophy (Royce, Haering, Kroner, Stace, Findlay and others). In this situation Loewenberg's contribution marks a... (shrink)

Known as 'Darwin's Bulldog', the biologist Thomas Henry Huxley was a tireless supporter of the evolutionary theories of his friend Charles Darwin. Huxley also made his own significant scientific contributions, and he was influential in the development of science education despite having had only two years of formal schooling. He established his scientific reputation through experiments on aquatic life carried out during a voyage to Australia while working as an assistant surgeon in the Royal Navy; ultimately he became President of (...) the Royal Society. Throughout his life Huxley struggled with issues of faith, and he coined the term 'agnostic' to describe his beliefs. This nine-volume collection of Huxley's essays, which he edited and published in 1893–4, demonstrates the wide range of his intellectual interests. In Volume 5, Huxley discusses the doctrines of Christianity and explains how his dissatisfaction with conventional religion led him to agnosticism. (shrink)

A celebration of a distinctly American form of commercial architecture The only comprehensive history of America's 5-&-10-cent stores It was where you went to browse the latest issues of Life and Photoplay, where the folks bought reading glasses, and where your mom took you for a hot dog and a malted. It was the local 5-&-10-cent store, and it was an integral part of everyday life. In this lavishly illustrated homage to the 5-&-10-cent store, architectural historian Bernice Thomas looks at (...) the architectural achievements of the Kress Company. Devoted to bringing outstanding design to Main Street America, Kress supported an architectural division of more than 100 architects and draftsmen. The over 200 stores these people designed and built between 1900 and 1950 set a new standard in commercial architecture. Thomas takes us on an illustrated tour of sites across the United States —from New Orleans to Honolulu, Albuquerque to New York. She introduces us to the architects and how they deftly balanced sound merchandising principles with aesthetics. (shrink)

Introduction -- Evolution: how life and we came about -- Medicine: our health, illnesses and healing -- Order, disorder and chaos: complex phenomena around us -- Motion, space and time: where and when we are -- Cosmology: how did our universe come about -- Religion, science and scientists -- Science for life.

Abnormalities in the ability of cells to properly degrade proteins have been identified in many neurodegenerative diseases. Recent work has implicated synaptojanin 1 (SynJ1) in Alzheimer's disease and Parkinson's disease, although the role of this polyphosphoinositide phosphatase in protein degradation has not been thoroughly described. Here, we dissected in vivo the role of SynJ1 in endolysosomal trafficking in zebrafish cone photoreceptors using a SynJ1‐deficient zebrafish mutant, nrca14. We found that loss of SynJ1 leads to specific accumulation of late endosomes and (...) autophagosomes early in photoreceptor development. An analysis of autophagic flux revealed that autophagosomes accumulate because of a defect in maturation. In addition we found an increase in vesicles that are highly enriched for PI(3)P, but negative for an early endosome marker in nrca14 cones. A mutational analysis of SynJ1 enzymatic domains found that activity of the 5'phosphatase, but not the Sac1 domain, is required to rescue both aberrant late endosomes and autophagosomes. Finally, modulating activity of the PI(4,5)P2 regulator, Arf6, rescued the disrupted trafficking pathways in nrca14 cones. Our study describes a specific role for SynJ1 in autophagosomal and endosomal trafficking and provides evidence that PI(4,5)P2 participates in autophagy in a neuronal cell type. -/- . (shrink)