Bi-Feng Yuan

Wuhan University | WHU · College of Chemistry and Molecular Sciences; School of Public Health

Chemical modifications in DNA have profound influences on the structures and functions of DNA. Uracil, a naturally occurring DNA modification, can originate from the deamination of cytosine or arise from misincorporation of dUTP into DNA during DNA replication. Uracil in DNA will imperil genomic stability due to their potential in producing detrime...

DNA methylation (5-methylcytosine, 5mC) is the most important epigenetic modification in mammals. Deciphering the roles of 5mC relies on the quantitative detection of 5mC at the single-base resolution. Bisulfite sequencing (BS-seq) is the most often employed technique for mapping 5mC in DNA. However, bisulfite treatment may cause serious degradatio...

Phosphomonoesters are important biosynthetic and energy metabolism intermediates in microorganisms. A comprehensive analysis of phosphomonoester metabolites is of great significance for the understanding of their metabolic phosphorylation process and inner mechanism. In this study, we established a pair of isotope reagent d0/d5-2-diazomethyl-N-meth...

Background RNA modifications are essential for the establishment of cellular identity. Although increasing evidence indicates that RNA modifications regulate the innate immune response, their role in monocyte-to-macrophage differentiation and polarisation is unclear. To date, most studies have focused on m ⁶ A, while other RNA modifications, includ...

DNA methylation (5-methylcytosine, 5mC) is the most prevalent epigenetic modification that is predominantly found in CG dinucleotides in mammalian genomes. In-depth investigation of the functions of 5mC heavily relies on the quantitative measurement of 5mC at single-base resolution in genomes. Here, we proposed a methyltransferase-directed labeling...

RNA molecules contain diverse modifications that play crucial roles in a wide variety of biological processes. Inosine is one of the most prevalent modifications in RNA and dysregulation of inosine is correlated with many human diseases. Herein, we established an acrylonitrile labeling-mediated elongation stalling (ALES) method for quantitative and...

RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosi...

N ⁴-methylcytosine (4mC) is a natural DNA modification occurring in thermophiles and plays important roles in restriction-modification (R-M) systems in bacterial genomes. However, the precise location and sequence context of 4mC in the whole genome are limited. In this study, we developed an APOBEC3A-mediated deamination sequencing (4mC-AMD-seq) me...

The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed as a critical epigenetic modification. Deciphering the functions of 5hmC necessitates the location analysis of 5hmC in genomes. Here, we proposed an engineered deaminase-mediated sequencing (EDM-...

Ribosomal RNAs (rRNAs) provide the structural framework of ribosomes and play critical roles in protein translation. In ribosome biogenesis, rRNAs acquire various modifications that can influence the structure and catalytic activity of ribosomes. However, rRNA modifications in plants have yet to be fully defined. Herein, we proposed a method to pur...

6-Thioguanine (6TG) is a widely used chemotherapeutic agent for the treatment of a variety of human diseases including acute lymphoblastic leukemia. After entry into cells, 6TG is metabolically converted into 6-thioguanosine (SG) nucleotide that can be incorporated into the genome during DNA replication. SG in genomic DNA could induce cell death by...

As the connecting part of diet and host physiology, intestinal microbes can convert the ingested diet into a huge number of physiologically active small molecules. Indole metabolites of tryptophan are precursors or signal molecules for many biologically active substances, which are involved in serotonin and microbial catabolism pathways. To underst...

DNA adenine methylation (N⁶-methyladenine, 6mA) widely exists in bacteria and regulates various biological processes including gene transcription and restriction-modification system. In recent years, it has been reported that 6mA is also present in genomic DNA of higher eukaryotes. However, the accurate determination of 6mA in DNA of higher eukaryo...

Understanding the functional roles of DNA modifications relies on the accurate detection, quantification, and mapping of DNA modifications. Methods for deciphering DNA modifications have substantially improved over the last several years, which greatly revolutionize the field of DNA modifications. In addition to DNA cytosine methylation (5-methylcy...

RNA molecules contain diverse modifications that display important functions in a variety of physiological and pathological processes. So far over 150 chemical modifications have been characterized to be present in various RNA species, such as in messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Previous studies revealed that cer...

DNA 5-hydroxymethyluracil (5hmU) is a thymine modification existing in the genomes of various organisms. The post-replicative formation of 5hmU occursviahydroxylation of thymine by ten-eleven translocation (TET) dioxygenases in mammals and J-binding proteins (JBPs) in protozoans, respectively. In addition, 5hmU can also be generated through oxidati...

Alcohol consumption is a critical risk factor contributing to a verity of human diseases. The incidence of alcohol use disorder increases across adolescence in recent years. Accumulating line of evidence suggests that alcohol-induced changes of DNA cytosine methylation (5-methyl-2′-deoxycytidine, 5mC) in genomes play an important role in the develo...

DNA cytosine methylation (5-methylcytosine, 5mC) is the most important epigenetic mark in higher eukaryotes. 5mC in genomes is dynamically controlled by writers and erasers. DNA (cytosine-5)-methyltransferases (DNMTs) are responsible for the generation and maintenance of 5mC in genomes. Active demethylation of 5-methylcytosine (5mC) is achieved by...

In active DNA demethylation, DNA cytosine methylation (5-methylcytosine, 5-mC) can be converted to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine (5-caC) by ten-eleven translocation (TET) proteins. These cytosine derivatives play important functions in various biological processes. 5-HmC, 5-fC, and 5-caC in genomic...

Reactive oxygen species (ROS) can induce DNA damages in cells. 8-Oxo-7,8-dihydroguanine (OG) is viewed as one of the most frequent oxidative modifications in human genomes. It was reported that OG was also capable to facilitate the G-quadruplex formation and participate in the transcription process. Thus, OG might have potential functions in regula...

The recent discovery of reversible chemical modifications on mRNA has opened a new era of post-transcriptional gene regulation in eukaryotes. Among these modifications identified in eukaryotic mRNA, N7-methylguanosine (m7G) is unique owing to its presence in the 5′ cap structure. Recently, it has been reported that m7G also exists internally in mRN...

Post-transcriptional modifications of RNA constitute an emerging regulatory layer of gene expression. The demethylase fat mass- and obesity-associated protein (FTO), an eraser of N6-methyladenosine (m6A), has been shown to play a role in cancer, but its contribution to tumor progression and the underlying mechanisms remain unclear. Here, we report...

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to man...

RNA modifications play critical roles in regulating a variety of physiological processes. Methylation is the most prevalent modification occurring in RNA. Three isomeric cytosine methylation modifications have been reported in...

5-Methylcytosine (5mC) is the most important epigenetic modification in mammals. The active DNA demethylation could be achieved through the ten-eleven translocation (TET) protein-mediated oxidization of 5mC with the generation of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). It has been known that 5mC, 5hmC a...

The discovery of dynamic and reversible modifications in RNA expands their functional repertoires. Now, RNA modifications have been viewed as new regulators involved in a variety of biological processes. Among these modifications, thiolation is one kind of special modification in RNA. Several thiouridines have been identified to be present in RNA,...

Polar phosphorylated metabolites are involved in a variety of biological processes and play vital roles in energetic metabolism, cofactor regeneration, and nucleic acid synthesis. However, it is often challenging to interrogate polar phosphorylated metabolites and compounds from biological samples. Liquid chromatography-mass spectrometry (LC/MS) no...

Gain-of-function mutations of isocitrate dehydrogenase 1 and 2 (IDH1/2) were demonstrated to induce the production and accumulation of oncometabolite 2-hydroxyglutarate (2HG). 2HG is a potent competitor of α-ketoglutarate (α-KG) and can inhibit multiple α-KG-dependent dioxygenases that are critical for regulating the metabolic and epigenetic state...

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysi...

RNA molecules contain many chemical modifications that can regulate a variety of biological processes. Messenger RNA (mRNA) molecules are critical components in the central dogma of molecular biology. The discovery of reversible chemical modifications in eukaryotic mRNA brings forward a new research field in RNA modification-mediated regulation of...

G-Quadruplex (G4) is a noncanonical nucleic acid secondary structure with multiple biofunctions. Identifying G4-related proteins (G4RPs) is important for understanding the roles of G4 in biology. Current methods to identify G4RPs include discovery from specific biological processes or in vitro pull-down assays with specific G4 sequences. Here, we r...

RNA modification, such as N1-methyladenosine (m1A), affect the secondary structure of RNA and its ability to recognize specific reader proteins. Methods for detecting site-specific m1A are in demand. We report here a ligation-assisted differentiation approach for quantitative detection of m1A in mRNA with single-base resolution. The methyl group in...

The discovery of dynamic and reversible modifications in messenger RNA (mRNA) is opening new directions in RNA modification-mediated regulation of biological processes. Methylation is the most prevalent modification occurring in mRNA and the methyl group is mainly decorated in the adenine, cytosine, and guanine base, or in the 2’-hydroxyl group of...

Ribonucleotide analogues and their related phosphorylated metabolites play critical roles in tumor metabolism. However, determination of the endogenous ribonucleotides from the complex biological matrix is still a challenge due to their high structural similarity and high polarity that will lead to the low retention and low detection sensitivities...

DNA molecules utilize adenine, thymine, cytosine, and guanine for coding genetic information. In addition to these four canonical nucleobases, DNA molecules also contain a variety of modified nucleobases that can control and regulate gene expression and chromosome structure. Elucidating the functions of DNA modifications relies on the sensitive det...

RNA molecules carry diverse modifications that exert important influences in many cellular processes. In addition to the single modification occurring in either nucleobase or 2' hydroxyl of ribose in RNA, some dual modifications occur in both the nucleobase and 2' hydroxyl of ribose in RNA. 2'-O-methyl-5-methylcytidine (m5Cm), the dual modification...

Hexavalent chromium [Cr(VI)] compounds that are generated during industrial processes are widely recognized as highly toxic and carcinogenic. It has been reported that exposure to Cr(VI) can produce some chromium intermediates and reactive oxygen species (ROS), which causes DNA damages, genetic instability and eventually leads to the elevated risk...

RNA molecules harbor diverse chemical modifications that play important regulatory roles in a variety of biological processes. Up to date, more than 150 modifications have been identified in various RNA species. Most of these modifications occurring in nucleic acids are the methylation of nucleic acids. It has been demonstrated that many of these m...

Both DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC) and RNA cytosine methylation (5-methylcytidine, m5rC) are important epigenetic marks that play regulatory roles in diverse biological processes. m5dC and m5rC can be further oxidized by the ten-eleven translocation (TET) proteins to form 5-hydroxymethyl-2'-deoxycytidine (hm5dC) and 5-h...

RNA contains diverse modifications that exert important influences in a variety of cellular processes. So far more than 150 modifications have been identified in various RNA species, mainly in rRNA and tRNA. Recent research advances in RNA modifications have been sparked by the discovery of dynamic and reversible modifications in mRNA. Moving beyon...

The extensive use of toxic metals in industry and agriculture leads to their wide distribution in the environment, which raises critical concerns over their toxic effects on human health. Many toxic metals are reported to be mildly mutagenic or non-mutagenic, indicating that genetic-based mechanisms may not be primarily responsible for toxic metal-...

Trehalose-6-phosphate (T6P) is an important signaling metabolite that is involved in many physiological processes. However, the mechanism of the biological functions of T6P is not fully understood. Quantification of T6P in plants will be beneficial to elucidate the mechanism. However, it is still a challenge to chromatographically separate and sens...

Short-chain fatty acids (SCFAs) are one class of bacterial metabolites mainly formed by gut microbiota from undigested fibers and proteins. These molecules are able to mediate signal conduction processes of cells, acting as G protein-coupled receptors (GPR) activators and histone deacetylases (HDAC) inhibitors. It was reported that SCFAs were close...

Accumulating lines of evidence indicate that reactive oxygen species (ROS) are important signalling molecules for various cellular processes. 8-Oxo-7,8-dihydroguanine (OG) is a prominent oxidative modification formed in DNA by ROS. Recently, it has been proposed that OG may have regulatory and possibly epigenetic-like properties in modulating gene...

The past decade has witnessed remarkable progress in our understanding of the important roles that gut microbial metabolites play in modulating the human health. The dynamic interplay between the host and gut microbiota is critical for maintaining the host homeostasis. The gut microbial metabolites are increasingly being recognized as an important...

In addition to the canonical nucleobases, a variety of chemical modifications have been identified presence in nucleic acids. These modifications have been demonstrated to involve in regulating the spatiotemporal expression of genes. Up to date, over 150 types of chemical modifications have been found existence in nucleic acids. Understanding the f...

In addition to DNA cytosine methylation (5-methyl-2'-deoxycytidine, m5dC), DNA adenine methylation (N6-methyl-2'-deoxyadenosine, m6dA) is another DNA modification that has been discovered in eukaryotes. Recent studies demonstrated that the content and distribution of m6dA in genomic DNA of vertebrates and mammals exhibit dynamic regulation, indicat...

The report of the existence of 5-hydroxymethylcytosine (hm5C) in mammalian genomes is a milestone discovery. hm5C is now generally viewed as the sixth base of DNA with important functions on epigenetic regulation. The in-depth investigation of the biological functions of hm5C requires elucidating the distribution patterns of hm5C in genomes, better...

RNA modification has recently been proposed to play important roles in biological regulation. The detection and quantification of RNA modifications generally are challenging tasks since most of the modifications exist in low abundance in vivo. Here we developed an on-line trapping/capillary hydrophilic-interaction liquid chromatography/electrospray...

Methyltransferase-involved DNA methylation is one of the most important epigenetic processes, making the ultrasensitive MTase assay highly desirable in clinical diagnosis as well as biomedical research. Traditional single-stage amplification means often achieve linear amplification that might not fulfil the increasing demands for detecting trace am...

Over 150 different types of modifications have been found in nucleic acids so far. The modification in nucleic acids now is recognized as a new layer in regulating gene expression. Elucidation of the functional roles of these modifications is critical to understand living organisms and the molecular mechanism of diseases. The abundance of most of t...

RNA molecules harbor various levels of diverse chemical modifications. So far, more than 150 structurally distinct modifications have been identified in cellular RNAs. Different with previous views that these modifications are mostly static, recent advances demonstrate a much more dynamic landscape of RNA modifications. The diverse and dynamic modi...

Context N⁶-methyladenosine (m⁶A) in mRNA is the most abundant and reversible modification. However, the mechanism behind the decrease in m⁶A in patients with type 2 diabetes (T2D) has not yet been thoroughly investigated. Objective To clarify whether glucose is involved in the dynamic regulation of m6A in T2D and to identify a possible underlying...

DNA and RNA contain diverse chemical modifications that exert important influences in a variety of cellular processes. In addition to enzyme-mediated modifications of DNA and RNA, previous in-vitro study showed that pre-modified nucleoside triphosphates (NTPs) can be incorporated into DNA and RNA during replication and transcription. Herein, we est...

Now increasing chemical modifications are discovered on genomic DNA and RNA. Up to date, more than 150 chemical modifications are identified in nucleic acids. These chemical modifications do not change the sequence of DNA and RNA, but alter their structures and biochemical properties, and eventually control or regulate the spatial and temporal expr...

RNA contains diverse modifications that exert important influences in a variety of cellular processes. So far more than 150 modifications have been identified in various RNA species, mainly in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). In contrast to rRNA, tRNA and mRNA, the known modifications in small RNAs have been prim...

Gut microbiota plays important roles in the host health. The host and symbiotic gut microbiota coproduce a large numbers of metabolites during the metabolism of food and xenobiotics. Analysis of fecal metabolites can provide a non-invasive manner to study the outcome of the host-gut microbiota interaction. Herein we reported the comprehensive profi...

Low-molecular-weight thiols play important roles in a variety of pathological processes and are closely associated with a wide range of diseases. In this study, a selective and sensitive method was developed for the simultaneous determination of all the 7 thiols occurring in the transsulfuration pathway (Cysteine (Cys), homocysteine (Hcys), glutath...

Background Alterations in DNA methylation are demonstrated in atherosclerosis pathogenesis. However, changing rules of global DNA methylation and hydroxymethylation in peripheral blood leukocytes (PBLs) and different blood cell subtypes of coronary artery disease (CAD) patients are still inconclusive, and much less is known about mechanisms underly...

The spatiotemporal expression of genes is sophisticatedly controlled through three main layers: transcriptional, translational and post-translational. Now increasing chemical modifications are discovered on genomic DNA, RNA and proteins. These modifications are recognized as additional layer of regulatory mechanisms in controlling gene expression t...

The recent discovery of reversible chemical modifications on messenger RNA (mRNA) has opened a new era of post-transcriptional gene regulation in eukaryotes. Among the 15 types of modifications identified in mRNA of eukaryotes, N7-methylguanosine (m7G) is unique ow-ing to its presence in the 5’ cap structure. It remains unknown whether m7G is also...

Brassinosteroids (BRs) play crucial roles in a variety of physiological processes in plants. The full elucidation of the functions of RBs relies on sensitive detection and accurate measurement of BRs in plants. However, the identification and quantification of BRs are challenging due to their low abundance as well as poor ionization efficiencies du...

Protein glycosylation is an important post-translational modification that plays a crucial role in many biological processes. Due to the low abundance of glycoproteins and high complexity of clinical samples, the development of methods to selectively capture glycoproteins/glycopeptides is crucial to glycoproteomics study. In this work, a kind of hi...

Tumor metastasis is attributed to circulating tumor cells (CTC) or CTC clusters. Many strategies have hitherto been designed to isolate CTCs, but there are few methods that can capture and gently release CTC clusters as efficient as single CTCs. Herein, we developed a three-dimensional (3D) scaffold chip with thermosensitive coating for high-effici...

Ketone bodies are small lipid-derived molecules and the metabolism of ketone bodies interfaces with various physiological processes. 3-Hydroxybutyric acid (3HB) is the most stable ketone body and can be employed to supply energy source. 2-Hydroxybutyric acid (2HB), an isomer of 3HB, was demonstrated to be an early biomarker for both insulin resista...

Nucleic acids carry diverse chemical modifications that exert critical influences in a variety of cellular processes in living organisms. In addition to methylation, the emerging DNA and RNA formylation has been reported to play functional roles in various physiological processes. However, the amounts of formylated DNA and RNA are extremely low and...

Recently, a new class of endogenous lipids, branched fatty acid esters of hydroxy fatty acids (FAHFAs), was discovered with anti-diabetic and anti-inflammatory effects in mammals. FAHFAs attracted increasing attention because of their critical physiological function. However, accurate quantitation of FAHFAs is still a challenge due to their high st...

5-methylcysine (5-mC) and N 6-methyladenosine (m6A) are important epigenetic marks occurring in nucleic acids of plants with regulatory roles in a broad range of biological processes. Recently, some novel modifications with potential regulatory roles such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC) h...

Toxic heavy metals have been considered to be harmful environmental contaminations. The molecular mechanisms of heavy metals-induced cytotoxicity and carcinogenicity are still not well elucidated. Previous reports showed exposures to toxic heavy metals can cause change of DNA cytosine methylation (5-methylcytosine, 5-mC). However, it is still not c...

Dynamic RNA modifications recently were considered to constitute another realm for biological regulation in the form of “RNA epigenetics”. N 6-methyladenosine (m6A), one of the most important modifications on RNA, plays a fundamental role in epigenetic regulation of the mammalian transcriptome. We recently established various liquid chromatography-...

5-Methylcytosine (5-mC) is an important epigenetic mark that plays critical roles in a variety of cellular pro-cesses. To properly exert physiological functions, the distribution of 5-mC needed to be tightly controlled in both DNA and RNA. In addition to methyltransferase-mediated DNA and RNA methylation, pre-methylated nucleotides can be potential...

Carbonyl compounds are considered as the potential biomarkers for oxidative stress and many types of diseases; therefore their determination may serve as indicator for early clinical diagnosis. Here we developed a strategy based on isotope labeling combined with liquid chromatography-double precursor ion scan-mass spectrometry (IL-LC-DPIS-MS) analy...

Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility. The pathogenesis of PCOS remains unclear and early diagnosis of PCOS is challenging. Follicular fluid provides a unique window in the critical processes during oocyte and follicular maturation, and the metabolic level of follicular fluid has important impact on th...

Grafting copolymerization, especially “grafting from” approach, has attracted a great attention for the preparation of cellulose-based materials with various functionalities. In this study, a novel phosphate group-containing cotton fiber-based material, CF-NH2-AZO-p(VPA-x), was successfully synthesized by a “grafting from” radical polymerization ap...