665 results match your criteria bisulfite conversion


Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA.

Genome Res 2021 Jun 17. Epub 2021 Jun 17.

New England Biolabs, Incorporated, Ipswich, Massachusetts 01938, USA.

Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. Read More

View Article and Full-Text PDF

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N.

Genome Res 2021 Jun 8. Epub 2021 Jun 8.

University of Texas Southwestern Medical Center

Sequencing technologies utilizing nucleotide conversion techniques such as cytosine-to-thymine in bisulfite-seq and thymine-to-cytosine in SLAM-seq are powerful tools to explore the chemical intricacies of cellular processes. To date, no one has developed a unified methodology for aligning converted sequences and consolidating alignment of these technologies in one package. In this paper, we describe HISAT-3N (hierarchical indexing for spliced alignment of transcripts - 3 nucleotides), which can rapidly and accurately align sequences consisting of any nucleotide conversion by leveraging the powerful hierarchical index and repeat index algorithms originally developed for the HISAT software. Read More

View Article and Full-Text PDF

Quantitative and Single-Nucleotide Resolution Profiling of RNA 5-Methylcytosine.

Methods Mol Biol 2021 ;2298:135-151

Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.

RNA has coevolved with numerous posttranscriptional modifications to sculpt interactions with proteins and other molecules. One of these modifications is 5-methylcytosine (mC) and mapping the position and quantifying the level in different types of cellular RNAs and tissues is an important objective in the field of epitranscriptomics. Both in plants and animals bisulfite conversion has long been the gold standard for detection of mC in DNA but it can also be applied to RNA. Read More

View Article and Full-Text PDF

Long-read whole-genome methylation patterning using enzymatic base conversion and nanopore sequencing.

Nucleic Acids Res 2021 May 21. Epub 2021 May 21.

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

Long-read whole-genome sequencing analysis of DNA methylation would provide useful information on the chromosomal context of gene expression regulation. Here we describe the development of a method that improves the read length generated by using the bisulfite-sequencing-based approach. In this method, we combined recently developed enzymatic base conversion, where an unmethylated cytosine (C) should be converted to thymine (T), with nanopore sequencing. Read More

View Article and Full-Text PDF

Methylation of TGM-3 Promoter and Its Association with Oral Squamous Cell Carcinoma (OSCC).

Avicenna J Med Biotechnol 2021 Apr-Jun;13(2):65-73

Department of Immunology, Faculty of Public Health, Tehran University of Medical Sciences, Tehran, Iran.

Background: Oral Squamous Cell Carcinoma (OSCC) is among the ten most common cancers worldwide. Hypermethylation of CpG sites in the promoter region and subsequent down-regulation of a tumor suppressor gene, TGM-3 has been proposed to be linked to different types of human cancers including OSCC. In this study, methylation status of CpG sites in the promoter region of TGM-3 has been evaluated in a cohort of patients with OSCC compared to normal controls. Read More

View Article and Full-Text PDF

Bioinformatic Estimation of DNA Methylation and Hydroxymethylation Proportions.

Methods Mol Biol 2021 ;2272:141-162

Department of Statistics, State University of Campinas, Campinas, SP, Brazil.

Simultaneous measurement of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) at the single-nucleotide level can be obtained by combining data from DNA processing methods including traditional bisulfite (BS), oxidative bisulfite (oxBS), or Tet-assisted (TAB) bisulfite conversion. Array-based technologies have been widely used in this task, due to their time and cost efficiency. For methylation studies using BS data, many protocols and related packages have been suggested in the literature to deal with limitations and confounders that arise from array data. Read More

View Article and Full-Text PDF

Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays.

Methods Mol Biol 2021 ;2272:97-140

Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.

The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Read More

View Article and Full-Text PDF

Reduced Bisulfite Sequencing: Quantitative Base-Resolution Sequencing of 5-Formylcytosine.

Methods Mol Biol 2021 ;2272:3-12

Department of Chemistry, University of Cambridge, Cambridge, UK.

The generation of tools to study mammalian epigenetics is vital to understanding normal biological function and to identify how it is dysregulated in disease. The well-studied epigenetic DNA modification 5-methylcytosine can be enzymatically oxidized to 5-formylcytosine (5fC) in vivo. 5fC has been demonstrated to be an intermediate in demethylation, but recent evidence suggests that 5fC may have an epigenetic function of its own. Read More

View Article and Full-Text PDF

Cas9-targeted nanopore sequencing reveals epigenetic heterogeneity after assembly of native full-length hepatitis B virus genomes.

Microb Genom 2021 May;7(5)

INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, France.

Hepatitis B virus (HBV) contains a 3.2 kb DNA genome and causes acute and chronic hepatitis. HBV infection is a global health problem, with 350 million chronically infected people at increased risk of developing liver disease and hepatocellular carcinoma (HCC). Read More

View Article and Full-Text PDF

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.

Nat Biotechnol 2021 May 6. Epub 2021 May 6.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Read More

View Article and Full-Text PDF

The FKBP5 genotype and childhood trauma effects on FKBP5 DNA methylation in patients with psychosis, their unaffected siblings, and healthy controls.

Psychoneuroendocrinology 2021 Jun 23;128:105205. Epub 2021 Mar 23.

Clinic for Psychiatry, Clinical Centre of Serbia, Pasterova 2, Belgrade 11000, Serbia; Faculty of Medicine, University of Belgrade, Dr Subotica 8, Belgrade 11000, Serbia.

Hypothalamic-pituitary-adrenal (HPA) axis activity mediates the relationship between childhood trauma (CT) and psychosis. The FKBP5 gene, one of the key regulators of HPA axis activity after stress exposure, has been found associated with psychosis. Allele-specific and CT related FKBP5 demethylation in intron 7 was revealed in different psychiatric disorders. Read More

View Article and Full-Text PDF

DNA Methylation in Solid Tumors: Functions and Methods of Detection.

Int J Mol Sci 2021 Apr 19;22(8). Epub 2021 Apr 19.

Masaryk Memorial Cancer Institute, Zluty Kopec 7, 656 53 Brno, Czech Republic.

DNA methylation, i.e., addition of methyl group to 5'-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Read More

View Article and Full-Text PDF

Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum.

J Plant Res 2021 Apr 22. Epub 2021 Apr 22.

Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07059, Antalya, Turkey.

The nuclear ribosomal DNA (nrDNA) sequences are often used for phylogenetic analysis among organisms. Because DNA cytosine methylation and nucleolar dominancy are two common epigenetic mechanisms of nrDNA, we hypothesized that internal transcribed spacer 1 (ITS1), 5.8S rRNA and ITS2 of nrDNA sequences could be used as epigenetic biomarkers. Read More

View Article and Full-Text PDF

Clinical evaluation of Bladder CARE, a new epigenetic test for bladder cancer detection in urine samples.

Clin Epigenetics 2021 Apr 21;13(1):84. Epub 2021 Apr 21.

Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

Background: Bladder cancer (BC) is the 5th most common cancer in the USA. Non-muscle invasive bladder cancer represents about 70% of all cases and has generally a favorable outcome. However, recurrence rates as high as 60 to 70% and progression rates of 10 to 20% necessitate intensive surveillance with cystoscopy. Read More

View Article and Full-Text PDF

Synthesis of Natural Starch from Trunk Biomass Applying Bisulphite Steeping Method: Optimization by RSM.

J Air Waste Manag Assoc 2021 Apr 19. Epub 2021 Apr 19.

School of Civil Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Penang, Malaysia.

A massive quantity of (oil palm) trunk biomass, containing a significant amount of natural starch, is available in Malaysia as bio-waste because of annual replantation. The efficient extraction of this starch (carbohydrate polymer) would be worthwhile concerning the environmental sustainability and economy through conversion to bio-resources. This study investigated the effectiveness of the bisulphite steeping method for starch synthesis from oil palm trunk (OPT) bio-waste. Read More

View Article and Full-Text PDF

Evaluation of genome-wide DNA methylation profile of human embryos with different developmental competences.

Hum Reprod 2021 05;36(6):1682-1690

IVIRMA, New Jersey, Basking Ridge, NJ, USA.

Study Question: Do embryos with different developmental competence exhibit different DNA methylation profiles at the blastocyst stage?

Summary Answer: We established genome-wide DNA methylome analysis for embryo trophectoderm (TE) biopsy samples and our findings demonstrated correlation of methylation profile of trophectoderm with euploidy status and with maternal age, indicating that genome-wide methylation level might be negatively correlated with embryo quality.

What Is Known Already: DNA methylation is a fundamental epigenetic regulatory mechanism that affects differentiation of cells into their future lineages during pre-implantation embryo development. Currently there is no established approach available to assess the epigenetic status of the human preimplantation embryo during routine IVF treatment. Read More

View Article and Full-Text PDF

Barrierless HONO and HOS(O)2-NO Formation via NH-Promoted Oxidation of SO by NO.

J Phys Chem A 2021 Apr 23;125(12):2666-2672. Epub 2021 Mar 23.

State Key Joint Laboratory of Environment Simulation and Pollution Control (Peking University), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.

In the troposphere, the knowledge about nitrous acid (HONO) sources is incomplete. The missing source of sulfate and fine particles cannot be explained during haze events. Air quality models cannot predict high levels of secondary fine-particle pollution. Read More

View Article and Full-Text PDF

Adiponectin DNA methylation in South African women with gestational diabetes mellitus: Effects of HIV infection.

PLoS One 2021 22;16(3):e0248694. Epub 2021 Mar 22.

Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council, Tygerberg, Cape Town, South Africa.

DNA methylation is increasingly recognized as a potential biomarker of metabolic disease. However, there is limited information on the impact of human immunodeficiency virus (HIV) infection on the candidacy of DNA methylation to serve as molecular biomarkers. This study investigated the effect of HIV infection on DNA methylation patterns in the peripheral blood of South African women with (n = 95) or without (n = 191) gestational diabetes mellitus (GDM). Read More

View Article and Full-Text PDF

Bisulfite-Converted DNA Quantity Evaluation: A Multiplex Quantitative Real-Time PCR System for Evaluation of Bisulfite Conversion.

Front Genet 2021 25;12:618955. Epub 2021 Feb 25.

Department of Forensic Medicine and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.

Bisulfite (BS) conversion, which includes a series of chemical reactions using bisulfite, is a prerequisite to most DNA methylation analysis methods, and thus is an essential step in the associated research process. Unfortunately, BS conversion leads to the degradation or loss of DNA, which can hinder further downstream analysis. In addition, it is well known that incomplete BS conversion is crucial, as it causes an exaggeration of the DNA methylation level, which can adversely affect the results. Read More

View Article and Full-Text PDF
February 2021

The prognostic impact of circulating homeobox A9 methylated DNA in advanced non-small cell lung cancer.

Transl Lung Cancer Res 2021 Feb;10(2):855-865

Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark.

Background: The homeobox A9 gene encodes a transcription factor, and aberrantly methylated homeobox A9 in the circulation has been suggested as a prognostic marker in early stage non-small cell lung cancer (NSCLC). The aim of the present study was to investigate the prognostic impact of methylated homeobox A9 in plasma from patients with advanced NSCLC.

Methods: Blood samples were prospectively collected from patients with NSCLC stage III and IV receiving standard first line chemotherapy. Read More

View Article and Full-Text PDF
February 2021

Consistency of the S5 DNA methylation classifier in formalin-fixed biopsies versus corresponding exfoliated cells for the detection of pre-cancerous cervical lesions.

Cancer Med 2021 04 12;10(8):2668-2679. Epub 2021 Mar 12.

Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, UK.

Methylation biomarkers are promising tools for diagnosis and disease prevention. The S5 classifier is aimed at the prevention of cervical cancer by the early detection of cervical intraepithelial neoplasia (CIN). S5 is based on pyrosequencing a promoter region of EPB41L3 and five late regions of HPV types 16, 18, 31, and 33 following bisulfite conversion of DNA. Read More

View Article and Full-Text PDF

Reliable Sea Water Ro Operation with High Water Recovery and No-Chlorine/No-Sbs Dosing in Arabian Gulf, Saudi Arabia.

Membranes (Basel) 2021 Feb 17;11(2). Epub 2021 Feb 17.

Saline Water Conversion Corporation, Desalination Technologies Research Institute, Al-Jubail 31951, Saudi Arabia.

For providing advanced desalination the combination of the improvement of water recovery ratio in the reverse osmosis (RO) process and the No-Chlorine/No-Sodium Bisulfite (SBS) Dosing process was studied. In order to prevent membrane fouling even in high recovery water operations, an advanced two-stage design was implemented to (1) control the permeate flux through the RO membrane module, (2) optimize the system to reduce contaminant build-up and (3) eliminate the use of chlorine and SBS, which can accelerate membrane fouling. The system was evaluated by monitoring the biofouling and the microorganisms proliferation on the membrane surface based on membrane biofilm formation rate (mBFR). Read More

View Article and Full-Text PDF
February 2021

A workflow for simultaneous DNA copy number and methylome analysis of inner cell mass and trophectoderm cells from human blastocysts.

Fertil Steril 2021 Jun 12;115(6):1533-1540. Epub 2021 Feb 12.

Department of Genetics, Albert Einstein College of Medicine, Bronx, New York; Center for Single-Cell Omics in Aging and Disease, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.

Objective: To establish a workflow for isolating single trophectoderm (TE) and inner cell mass (ICM) cells and to simultaneously evaluate these cells for copy number variation (CNV) as well as methylome development.

Design: Experimental.

Setting: Academic medical center. Read More

View Article and Full-Text PDF

Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment.

Int J Mol Sci 2020 Dec 3;21(23). Epub 2020 Dec 3.

Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI Vigo, 36213 Vigo, Spain.

Different methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Read More

View Article and Full-Text PDF
December 2020

A newly developed age estimation method based on CpG methylation of teeth-derived DNA using real-time methylation-specific PCR.

J Oral Sci 2020 Dec 7;63(1):54-58. Epub 2020 Dec 7.

Division of Anatomical Science, Department of Functional Morphology, Nihon University School of Medicine.

Age estimation of unidentified bodies is important in forensic medicine and crime scenes. There is accumulating evidence that DNA methylation in the human genome isolated from body fluids changes with age. Most of the data have been obtained by pyrosequencing. Read More

View Article and Full-Text PDF
December 2020

Molecular evaluation of a multiplex methylation panel for epigenetic analysis of FNAB samples from Greek patients with suspicious breast lesions.

J BUON 2020 Sep-Oct;25(5):2244-2254

2nd Department of Obstetrics and Gynaecology, Medical Faculty Aristotle University of Thessaloniki, Hippokration General Hospital of Thessaloniki, Thessaloniki, Greece.

Purpose: Aberrant DNA methylation in promoter regions has been found in many cancers, including breast cancer (BC). A Methylation Specific PCR (MSP) was applied in breast Fine Needle Aspiration Biopsy (FNAB) material, which has been rarely used in the literature, to estimate the methylation frequencies of CND2, APC, HIN1 & CDH13 and to assess whether this multiplex methylation panel can be possibly used as an indicator-biomarker for BC detection in a Greek population.

Methods: A total of 104 participants were subjected to FNAB and both cytological evaluation and epigenetic analysis were carried out. Read More

View Article and Full-Text PDF
December 2020

Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution.

Elife 2020 11 13;9. Epub 2020 Nov 13.

Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, United States.

Displacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Read More

View Article and Full-Text PDF
November 2020

DNA promoter methylation of CCM genes in human cerebral cavernous malformations: Importance of confirming MSP data through sequencing.

Eur J Med Genet 2020 Dec 22;63(12):104090. Epub 2020 Oct 22.

Department of Neurosurgery, University Hospital Essen, Hufelandstrasse 55, 45122, Essen, Germany. Electronic address:

Background: Cerebral cavernous malformations (CCMs) is the second most common cerebrovascular disease and is classified as familial (20%) and sporadic (80%) forms. Loss of function mutation of three CCM genes results in the familial CCM. Considering the similar clinic presentation of familial and sporadic CCMs, and based on enriched CpG islands in the DNA promoter region of three CCM genes, we hypothesized that DNA methylation of the CpG islands of the CCM genes is involved in human CCM, thereby leading to loss of CCM genes. Read More

View Article and Full-Text PDF
December 2020

The effect of laser-assisted hatching on the methylation and expression pattern of imprinted gene IGF2/H19 in mouse blastocysts and offspring.

J Assist Reprod Genet 2020 Dec 21;37(12):3057-3067. Epub 2020 Oct 21.

Department of Reproductive Medical Center, The Affiliated Hospital of Guilin Medical University, Guilin, 541001, China.

Purpose: This study aimed to determine the effects of drilling and thinning treatment of laser-assisted hatching on the expression and methylation of imprinted gene IGF2/H19 in embryos and offspring.

Methods: The prehatching blastocysts with treatment of drilling or thinning, or control prehatching blastocysts, were transplanted in surrogate uteri. The DNA methylation of IGF2/H19 imprinting control region (ICR) and the expression of IGF2 and H19 were respectively evaluated using bisulfite conversion-mediated sequencing and real-time PCR. Read More

View Article and Full-Text PDF
December 2020

Azacitidine regulates DNA methylation of GADD45γ in myelodysplastic syndromes.

J Clin Lab Anal 2021 Feb 20;35(2):e23597. Epub 2020 Oct 20.

Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.

Background: Myelodysplastic syndrome (MDS) is a heterogeneous clonal disease originated from hematopoietic stem cells. Epigenetic studies had demonstrated that DNA methylation and histone acetylation were abnormal in MDS. Azacitidine is an effective drug in the treatment of demethylation. Read More

View Article and Full-Text PDF
February 2021