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Essays in Biochemistry Dec 2019Bisulfite sequencing is a powerful technique to detect 5-methylcytosine in DNA that has immensely contributed to our understanding of epigenetic regulation in plants and... (Review)
Review
Bisulfite sequencing is a powerful technique to detect 5-methylcytosine in DNA that has immensely contributed to our understanding of epigenetic regulation in plants and animals. Meanwhile, research on other base modifications, including 6-methyladenine and 4-methylcytosine that are frequent in prokaryotes, has been impeded by the lack of a comparable technique. Bisulfite sequencing also suffers from a number of drawbacks that are difficult to surmount, among which DNA degradation, lack of specificity, or short reads with low sequence diversity. In this review, we explore the recent refinements to bisulfite sequencing protocols that enable targeting genomic regions of interest, detecting derivatives of 5-methylcytosine, and mapping single-cell methylomes. We then present the unique advantage of long-read sequencing in detecting base modifications in native DNA and highlight the respective strengths and weaknesses of PacBio and Nanopore sequencing for this application. Although analysing epigenetic data from long-read platforms remains challenging, the ability to detect various modified bases from a universal sample preparation, in addition to the mapping and phasing advantages of the longer read lengths, provide long-read sequencing with a decisive edge over short-read bisulfite sequencing for an expanding number of applications across kingdoms.
Topics: 5-Methylcytosine; Adenine; Animals; DNA; DNA Methylation; Epigenomics; Humans; Nanopores; Sequence Analysis, DNA; Sulfites
PubMed: 31755932
DOI: 10.1042/EBC20190027 -
Molecular Cell Jul 2018DNA N-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human...
DNA N-methyladenine (6mA) modification is the most prevalent DNA modification in prokaryotes, but whether it exists in human cells and whether it plays a role in human diseases remain enigmatic. Here, we showed that 6mA is extensively present in the human genome, and we cataloged 881,240 6mA sites accounting for ∼0.051% of the total adenines. [G/C]AGG[C/T] was the most significantly associated motif with 6mA modification. 6mA sites were enriched in the coding regions and mark actively transcribed genes in human cells. DNA 6mA and N-demethyladenine modification in the human genome were mediated by methyltransferase N6AMT1 and demethylase ALKBH1, respectively. The abundance of 6mA was significantly lower in cancers, accompanied by decreased N6AMT1 and increased ALKBH1 levels, and downregulation of 6mA modification levels promoted tumorigenesis. Collectively, our results demonstrate that DNA 6mA modification is extensively present in human cells and the decrease of genomic DNA 6mA promotes human tumorigenesis.
Topics: Adenine; AlkB Homolog 1, Histone H2a Dioxygenase; Animals; Carcinogenesis; DNA; DNA Methylation; Genome, Human; Heterografts; Humans; Mice; Mice, Nude; Site-Specific DNA-Methyltransferase (Adenine-Specific)
PubMed: 30017583
DOI: 10.1016/j.molcel.2018.06.015 -
Proceedings of the National Academy of... Feb 1977DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments...
DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify the positions of that base. We describe reactions that cleave DNA preferentially at guanines, at adenines, at cytosines and thymines equally, and at cytosines alone. When the products of these four reactions are resolved by size, by electrophoresis on a polyacrylamide gel, the DNA sequence can be read from the pattern of radioactive bands. The technique will permit sequencing of at least 100 bases from the point of labeling.
Topics: Adenine; Base Sequence; Biochemical Phenomena; Biochemistry; Cytosine; DNA; DNA Restriction Enzymes; Guanine; Hydrazines; Methods; Nucleic Acid Hybridization; Thymine
PubMed: 265521
DOI: 10.1073/pnas.74.2.560 -
HIV Medicine May 2016
Topics: Adenine; Alanine; Anti-HIV Agents; Clinical Trials as Topic; Drug Approval; Drug-Related Side Effects and Adverse Reactions; HIV Infections; Humans; Tenofovir
PubMed: 27061461
DOI: 10.1111/hiv.12405 -
Cellular and Molecular Life Sciences :... Aug 2019DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done... (Review)
Review
DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done elucidating the role of 5-methylcytosine over the past several decades, only recently has it been recognized that N(6)-methyladenine (N-mA) is present in quantifiable and biologically active levels in the DNA of eukaryotic cells. Unlike prokaryotes which utilize N-mA to recognize "self" from "foreign" DNA, eukaryotes have been found to use N-mA in varying ways, from regulating transposable elements to gene regulation in response to hypoxia and stress. In this review, we examine the current state of the N-mA in research field, and the current understanding of the biochemical mechanisms which deposit and remove N-mA from the eukaryotic genome.
Topics: Adenine; Animals; DNA Methylation; DNA Repair Enzymes; Epigenomics; Eukaryota; Humans; Neoplasms; Oxidoreductases, N-Demethylating; Stress, Physiological
PubMed: 31143960
DOI: 10.1007/s00018-019-03146-w -
Proceedings of the National Academy of... Mar 2020Proteins' interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment...
Proteins' interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein-adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein-adenine interactions in the Watson-Crick edge of adenine and shows that all of adenine's edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments ("themes") that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
Topics: Adenine; Binding Sites; Evolution, Molecular; Hydrogen Bonding; Molecular Docking Simulation; Protein Binding; Protein Conformation; Sequence Analysis, Protein; Software
PubMed: 32079721
DOI: 10.1073/pnas.1911349117 -
Biochimica Et Biophysica Acta. Gene... Mar 2019
Review
Topics: Adenine; Animals; Humans; Protein Biosynthesis; RNA Processing, Post-Transcriptional; RNA, Messenger
PubMed: 30342175
DOI: 10.1016/j.bbagrm.2018.10.006 -
Blood Jun 2021
Topics: Adenine; Biomechanical Phenomena; Piperidines; Pyrazoles; Pyrimidines
PubMed: 34165548
DOI: 10.1182/blood.2021011574 -
Frontiers in Immunology 2021RNA modification represents one of the most ubiquitous mechanisms of epigenetic regulation and plays an essential role in modulating cell proliferation, differentiation,... (Review)
Review
RNA modification represents one of the most ubiquitous mechanisms of epigenetic regulation and plays an essential role in modulating cell proliferation, differentiation, fate determination, and other biological activities. At present, over 170 types of RNA modification have been discovered in messenger RNA (mRNA) and noncoding RNA (ncRNA). RNA methylation, as an abundant and widely studied epigenetic modification, is crucial for regulating various physiological or pathological states, especially immune responses. Considering the biological significance of T cells as a defense against viral infection and tumor challenge, in this review, we will summarize recent findings of how RNA methylation regulates T cell homeostasis and function, discuss the open questions in this rapidly expanding field of RNA modification, and provide the theoretical basis and potential therapeutic strategies involving targeting of RNA methylation to orchestrate beneficial T cell immune responses.
Topics: Adenine; Epigenesis, Genetic; Humans; Methylation; Methyltransferases; RNA; RNA Processing, Post-Transcriptional; T-Lymphocytes
PubMed: 33912158
DOI: 10.3389/fimmu.2021.627455 -
Advances in Experimental Medicine and... 2016Chromatin, consisting of deoxyribonucleic acid (DNA) wrapped around histone proteins, facilitates DNA compaction and allows identical DNA codes to confer many different... (Review)
Review
Chromatin, consisting of deoxyribonucleic acid (DNA) wrapped around histone proteins, facilitates DNA compaction and allows identical DNA codes to confer many different cellular phenotypes. This biological versatility is accomplished in large part by posttranslational modifications to histones and chemical modifications to DNA. These modifications direct the cellular machinery to expand or compact specific chromatin regions and mark regions of the DNA as important for cellular functions. While each of the four bases that make up DNA can be modified (Iyer et al. 2011), this chapter will focus on methylation of the sixth position on adenines (6mA), as this modification has been poorly characterized in recently evolved eukaryotes, but shows promise as a new conserved layer of epigenetic regulation. 6mA was previously thought to be restricted to unicellular organisms, but recent work has revealed its presence in metazoa. Here, we will briefly describe the history of 6mA, examine its evolutionary conservation, and evaluate the current methods for detecting 6mA. We will discuss the enzymes that bind and regulate this mark and finally examine known and potential functions of 6mA in eukaryotes.
Topics: Adenine; Chromatin; DNA; DNA Methylation; Epigenesis, Genetic; Eukaryota; Evolution, Molecular; Histones; Protein Processing, Post-Translational
PubMed: 27826841
DOI: 10.1007/978-3-319-43624-1_10