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Journal articles on the topic 'Reduced representation bisulfite sequencing'

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Published: 3 June 2025

Last updated: 31 July 2025

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1

van Gurp, Thomas P., Niels C. A. M. Wagemaker, Björn Wouters, Philippine Vergeer, Joop N. J. Ouborg, and Koen J. F. Verhoeven. "epiGBS: reference-free reduced representation bisulfite sequencing." Nature Methods 13, no. 4 (2016): 322–24. http://dx.doi.org/10.1038/nmeth.3763.

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2

Tanas, Alexander S., Marina E. Borisova, Ekaterina B. Kuznetsova, et al. "Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing." Epigenomics 9, no. 6 (2017): 833–47. http://dx.doi.org/10.2217/epi-2017-0031.

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3

Chatterjee, Aniruddha, Euan J. Rodger, Peter A. Stockwell, Robert J. Weeks, and Ian M. Morison. "Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries." Journal of Biomedicine and Biotechnology 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/741542.

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Reduced representation bisulfite sequencing (RRBS), which couples bisulfite conversion and next generation sequencing, is an innovative method that specifically enriches genomic regions with a high density of potential methylation sites and enables investigation of DNA methylation at single-nucleotide resolution. Recent advances in the Illumina DNA sample preparation protocol and sequencing technology have vastly improved sequencing throughput capacity. Although the new Illumina technology is now widely used, the unique challenges associated with multiplexed RRBS libraries on this platform hav

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4

Chatterjee, Aniruddha, Yuichi Ozaki, Peter A. Stockwell, Julia A. Horsfield, Ian M. Morison, and Shinichi Nakagawa. "Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing." Epigenetics 8, no. 9 (2013): 979–89. http://dx.doi.org/10.4161/epi.25797.

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5

Chen, Yunshun, Bhupinder Pal, Jane E. Visvader, and Gordon K. Smyth. "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR." F1000Research 6 (November 28, 2017): 2055. http://dx.doi.org/10.12688/f1000research.13196.1.

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Studies in epigenetics have shown that DNA methylation is a key factor in regulating gene expression. Aberrant DNA methylation is often associated with DNA instability, which could lead to development of diseases such as cancer. DNA methylation typically occurs in CpG context. When located in a gene promoter, DNA methylation often acts to repress transcription and gene expression. The most commonly used technology of studying DNA methylation is bisulfite sequencing (BS-seq), which can be used to measure genomewide methylation levels on the single-nucleotide scale. Notably, BS-seq can also be c

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Chen, Yunshun, Bhupinder Pal, Jane E. Visvader, and Gordon K. Smyth. "Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR." F1000Research 6 (October 8, 2018): 2055. http://dx.doi.org/10.12688/f1000research.13196.2.

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Cytosine methylation is an important DNA epigenetic modification. In vertebrates, methylation occurs at CpG sites, which are dinucleotides where a cytosine is immediately followed by a guanine in the DNA sequence from 5' to 3'. When located in the promoter region of a gene, DNA methylation is often associated with transcriptional silencing of the gene. Aberrant DNA methylation is associated with the development of various diseases such as cancer. Bisulfite sequencing (BS-seq) is the current "gold-standard" technology for high-resolution profiling of DNA methylation. Reduced representation bisu

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7

Lee, Yew, Shengnan Jin, Shiwei Duan, et al. "Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples." Biological Procedures Online 16, no. 1 (2014): 1. http://dx.doi.org/10.1186/1480-9222-16-1.

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8

Meissner, A. "Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis." Nucleic Acids Research 33, no. 18 (2005): 5868–77. http://dx.doi.org/10.1093/nar/gki901.

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9

Yamane, Junko, Tomoya Mori, Nobuko Taniyama, Kenta Kobayashi, and Wataru Fujibuchi. "Development of Enhanced Reduced Representation Bisulfite Sequencing Method for Single-cell Methylome Analysis." Genomics and Computational Biology 3, no. 2 (2017): 49. http://dx.doi.org/10.18547/gcb.2017.vol3.iss2.e49.

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Single-cell analysis provides molecular signatures to define cell identity. To characterize cell types, DNA methylation patterns are often used as a flag of internal molecular status. There are a few reports of single-cell methylome techniques that involves bisulfite conversion. However, the step often causes DNA fragmentation, which leads to severe PCR substrate reduction. Here we developed a new version of single-cell reduced representation bisulfite sequencing (scRRBS) method to recover more CpG sites to be analysed. Our method succeeded to increase of 4.1 times in sample yield and 1.6 time

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10

Longtin, Amy, Marina M. Watowich, Baptiste Sadoughi, et al. "Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing." PLOS Genetics 21, no. 5 (2025): e1011667. https://doi.org/10.1371/journal.pgen.1011667.

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Characterizing DNA methylation patterns is important for addressing key questions in evolutionary biology, development, geroscience, and medical genomics. While costs are decreasing, whole-genome DNA methylation profiling remains prohibitively expensive for most population-scale studies, creating a need for cost-effective, reduced representation approaches (i.e., assays that rely on microarrays, enzyme digests, or sequence capture to target a subset of the genome). Most common whole genome and reduced representation techniques rely on bisulfite conversion, which can damage DNA resulting in DNA

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11

Sun, Xiwei, Yi Han, Liyuan Zhou, et al. "A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data." Bioinformatics 34, no. 16 (2018): 2715–23. http://dx.doi.org/10.1093/bioinformatics/bty174.

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12

Paun, Ovidiu, Koen J. F. Verhoeven, and Christina L. Richards. "Opportunities and limitations of reduced representation bisulfite sequencing in plant ecological epigenomics." New Phytologist 221, no. 2 (2018): 738–42. http://dx.doi.org/10.1111/nph.15388.

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13

Sun, Zhifu, Saurabh Baheti, Sumit Middha, et al. "SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing." Bioinformatics 28, no. 16 (2012): 2180–81. http://dx.doi.org/10.1093/bioinformatics/bts337.

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14

Panchapakesa, Vaishnavi, Chaithanya Ponnaluri, Daniel Evanich, Ariel Erijman, Bradley Langhorst, and Louise Williams. "Abstract 7022: Whole genome and reduced representation enzymatic methyl-seq enable cost effective methylomes." Cancer Research 84, no. 6_Supplement (2024): 7022. http://dx.doi.org/10.1158/1538-7445.am2024-7022.

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Abstract DNA methylation is an epigenetic regulator of gene expression with important functions in development and diseases such as cancer. Traditionally, sodium bisulfite conversion was used to distinguish 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) from cytosines. However, this method damages DNA and introduces significant sequencing bias. NEBNext® Enzymatic Methyl-seq (EM-seq™) is an enzymatic conversion approach that minimizes DNA damage therefore enabling longer insert sizes, lower duplication rates and a more accurate quantification of methylation in DNA samples with inpu

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15

Begue, Gwénaëlle, Ulrika Raue, Bozena Jemiolo, and Scott Trappe. "DNA methylation assessment from human slow- and fast-twitch skeletal muscle fibers." Journal of Applied Physiology 122, no. 4 (2017): 952–67. http://dx.doi.org/10.1152/japplphysiol.00867.2016.

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A new application of the reduced representation bisulfite sequencing method was developed using low-DNA input to investigate the epigenetic profile of human slow- and fast-twitch skeletal muscle fibers. Successful library construction was completed with as little as 15 ng of DNA, and high-quality sequencing data were obtained with 32 ng of DNA. Analysis identified 143,160 differentially methylated CpG sites across 14,046 genes. In both fiber types, selected genes predominantly expressed in slow or fast fibers were hypomethylated, which was supported by the RNA-sequencing analysis. These are th

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16

Choi, Minkyeung, Jongin Lee, Min Thong Le, et al. "Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing." DNA Research 22, no. 5 (2015): 343–55. http://dx.doi.org/10.1093/dnares/dsv017.

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17

Gu, Hongcang, Zachary D. Smith, Christoph Bock, Patrick Boyle, Andreas Gnirke, and Alexander Meissner. "Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling." Nature Protocols 6, no. 4 (2011): 468–81. http://dx.doi.org/10.1038/nprot.2010.190.

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18

Boyle, Patrick, Kendell Clement, Hongcang Gu, et al. "Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling." Genome Biology 13, no. 10 (2012): R92. http://dx.doi.org/10.1186/gb-2012-13-10-r92.

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19

Yin, Danqing, Matthew E. Ritchie, Jafar S. Jabbari, Tamara Beck, Marnie E. Blewitt, and Andrew Keniry. "High concordance between Illumina HiSeq2500 and NextSeq500 for reduced representation bisulfite sequencing (RRBS)." Genomics Data 10 (December 2016): 97–100. http://dx.doi.org/10.1016/j.gdata.2016.10.002.

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20

Wang, Xuefeng, Xiaoqing Yu, Wei Zhu, et al. "A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing: Fig. 1." Bioinformatics 31, no. 12 (2015): 2040–42. http://dx.doi.org/10.1093/bioinformatics/btv089.

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21

Wang, Tao, Qi Liu, Xianfeng Li, et al. "RRBS-Analyser: A Comprehensive Web Server for Reduced Representation Bisulfite Sequencing Data Analysis." Human Mutation 34, no. 12 (2013): 1606–10. http://dx.doi.org/10.1002/humu.22444.

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22

Guo, Hongshan, Ping Zhu, Fan Guo, et al. "Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing." Nature Protocols 10, no. 5 (2015): 645–59. http://dx.doi.org/10.1038/nprot.2015.039.

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23

Xi, Yuanxin, Christoph Bock, Fabian Müller, Deqiang Sun, Alexander Meissner, and Wei Li. "RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing." Bioinformatics 28, no. 3 (2011): 430–32. http://dx.doi.org/10.1093/bioinformatics/btr668.

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24

Wang, Kangli, Xianfeng Li, Shanshan Dong, et al. "Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses." Epigenetics 10, no. 9 (2015): 775–83. http://dx.doi.org/10.1080/15592294.2015.1075690.

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25

Karetnikov, Dmitry I., Stanislav E. Romanov, Vladimir P. Baklaushev, and Petr P. Laktionov. "Age Prediction Using DNA Methylation Heterogeneity Metrics." International Journal of Molecular Sciences 25, no. 9 (2024): 4967. http://dx.doi.org/10.3390/ijms25094967.

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Dynamic changes in genomic DNA methylation patterns govern the epigenetic developmental programs and accompany the organism's aging. Epigenetic clock (eAge) algorithms utilize DNA methylation to estimate the age and risk factors for diseases as well as analyze the impact of various interventions. High-throughput bisulfite sequencing methods, such as reduced-representation bisulfite sequencing (RRBS) or whole genome bisulfite sequencing (WGBS), provide an opportunity to identify the genomic regions of disordered or heterogeneous DNA methylation, which might be associated with cell-type heteroge

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26

Grehl, Claudius, Markus Kuhlmann, Claude Becker, Bruno Glaser, and Ivo Grosse. "How to Design a Whole-Genome Bisulfite Sequencing Experiment." Epigenomes 2, no. 4 (2018): 21. http://dx.doi.org/10.3390/epigenomes2040021.

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Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation can be found in both prokaryotes and eukaryotes. In the latter, dynamic variation is shown across species, along development, and by cell type. DNA methylation usually leads to a lower binding affinity of DNA-interacting proteins and often results in a lower expression rate of the subsequent genome region, a process

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27

Schmidt, Martin, Bel Michiel Van, Magdalena Woloszynska, et al. "Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions." BMC Plant Biology 17, no. 1 (2017): 115. https://doi.org/10.1186/s12870-017-1070-y.

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<strong>Background: </strong>Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome-w

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28

Johnson, Kevin, Ming Tang, Marcos Estécio, Paul Robson, and Roel Verhaak. "GENE-59. CHARACTERIZING EPIGENETIC INTRATUMORAL HETEROGENEITY IN GLIOMA USING SINGLE-CELL REDUCED REPRESENTATION BISULFITE SEQUENCING." Neuro-Oncology 19, suppl_6 (2017): vi105—vi106. http://dx.doi.org/10.1093/neuonc/nox168.431.

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29

Chatterjee, Aniruddha, Erin C. Macaulay, Antonio Ahn, et al. "Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis." Epigenomics 9, no. 6 (2017): 823–32. http://dx.doi.org/10.2217/epi-2016-0176.

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30

Tao, Xin, Yiping Zhan, Katherine Scott, Richard Thomas Scott, and Emre Seli. "Comparative analysis of DNA methylation in euploid and aneuploid human embryos using reduced representation bisulfite sequencing." Fertility and Sterility 112, no. 3 (2019): e129-e130. http://dx.doi.org/10.1016/j.fertnstert.2019.07.458.

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31

Tanas, A. S., E. B. Kuznetsova, M. E. Borisova, V. V. Rudenko, D. V. Zaletayev, and V. V. Strelnikov. "Reduced representation bisulfite sequencing design for assessing the methylation of human CpG islands in large samples." Molecular Biology 49, no. 4 (2015): 618–26. http://dx.doi.org/10.1134/s0026893315040184.

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32

Nair, Venugopalan D., Hanna Pincas, Mary Anne S. Amper, et al. "Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing." STAR Protocols 5, no. 2 (2024): 103007. http://dx.doi.org/10.1016/j.xpro.2024.103007.

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33

Guan, Yuting, Hongbo Liu, Ziyuan Ma, et al. "Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease." Journal of the American Society of Nephrology 31, no. 4 (2020): 765–82. http://dx.doi.org/10.1681/asn.2019080797.

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BackgroundCytosine methylation is an epigenetic mark that dictates cell fate and response to stimuli. The timing and establishment of methylation logic during kidney development remains unknown. DNA methyltransferase 3a and 3b are the enzymes capable of establishing de novo methylation.MethodsWe generated mice with genetic deletion of Dnmt3a and Dnmt3b in nephron progenitor cells (Six2CreDnmt3a/3b) and kidney tubule cells (KspCreDnmt3a/3b). We characterized KspCreDnmt3a/3b mice at baseline and after injury. Unbiased omics profiling, such as whole genome bisulfite sequencing, reduced representa

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34

Du, Rose, Vince Carey, and Scott T. Weiss. "deconvSeq: deconvolution of cell mixture distribution in sequencing data." Bioinformatics 35, no. 24 (2019): 5095–102. http://dx.doi.org/10.1093/bioinformatics/btz444.

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Abstract Motivation Although single-cell sequencing is becoming more widely available, many tissue samples such as intracranial aneurysms are both fibrous and minute, and therefore not easily dissociated into single cells. To account for the cell type heterogeneity in such tissues therefore requires a computational method. We present a computational deconvolution method, deconvSeq, for sequencing data (RNA and bisulfite) obtained from bulk tissue. This method can also be applied to single-cell RNA sequencing data. Results DeconvSeq utilizes a generalized linear model to model effects of tissue

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35

Roberts, Michelle L., Theodore A. Kotchen, Xiaoqing Pan, et al. "Unique Associations of DNA Methylation Regions With 24-Hour Blood Pressure Phenotypes in Black Participants." Hypertension 79, no. 4 (2022): 761–72. http://dx.doi.org/10.1161/hypertensionaha.121.18584.

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Background: Epigenetic marks (eg, DNA methylation) may capture the effect of gene-environment interactions. DNA methylation is involved in blood pressure (BP) regulation and hypertension development; however, no studies have evaluated its relationship with 24-hour BP phenotypes (daytime, nighttime, and 24-hour average BPs). Methods: We examined the association of whole blood DNA methylation with 24-hour BP phenotypes and clinic BPs in a discovery cohort of 281 Black participants using reduced representation bisulfite sequencing. We developed a deep and region-specific methylation sequencing me

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36

Rohde, Christian, Till Schoofs, Katja Hebestreit та ін. "Identification of the PML-RARα Associated DNA Methylome Using Reduced Representation Bisulfite Sequencing in Primary Patient Samples". Blood 118, № 21 (2011): 2436. http://dx.doi.org/10.1182/blood.v118.21.2436.2436.

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Abstract Abstract 2436 The origin of altered DNA methylation in cancer and more specifically in leukemia remains incompletely understood. One favored hypothesis suggests that aberrant methylation is recruited to direct genomic target regions of transcriptional repressor oncogenes. PML-RARα, as a transcriptional repressor oncogene, mediates a repressed chromatin structure at its genomic targets and leads to a rather uniform leukemia subtype. In the current study we aimed to identify patterns and variability of DNA methylation changes in PML-RARα associated acute promyelocytic leukemia (APL). We

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37

Batcheller, A. E., G. L. Christensen, Y. Leung, et al. "Dietary Bisphenol-A exposure alters the methylome of rat tropectoderm as determined by reduced representation bisulfite sequencing." Fertility and Sterility 104, no. 3 (2015): e138. http://dx.doi.org/10.1016/j.fertnstert.2015.07.426.

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38

Sun, Zhifu, Manuel Bonfim Braga Neto, Yuning Xiong, et al. "Sa526 DNA METHYLATION LANDSCAPE AND SIGNATURE OF CD4+ LYMPHOCYTES IN CROHN'S PATIENTS BY REDUCED REPRESENTATION AND BISULFITE SEQUENCING." Gastroenterology 160, no. 6 (2021): S—536. http://dx.doi.org/10.1016/s0016-5085(21)01982-x.

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39

Izzi, Benedetta, Juan J. Carmona, Alexandra M. Binder, et al. "Application of multiplexed reduced representation bisulfite sequencing (mRRBS) to environmental epigenetic studies: comparison to the 450K Illumina BeadChip." ISEE Conference Abstracts 2013, no. 1 (2013): 5363. http://dx.doi.org/10.1289/isee.2013.p-2-26-01.

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40

Guo, H., P. Zhu, X. Wu, X. Li, L. Wen, and F. Tang. "Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing." Genome Research 23, no. 12 (2013): 2126–35. http://dx.doi.org/10.1101/gr.161679.113.

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41

García-García, Isabel, Belén Méndez-Cea, Jose Luis Horreo, Juan Carlos Linares, and Francisco Javier Gallego. "DNA methylation analysis in plant gigagenomes: comparing two bisulfite sequencing techniques in Abies alba trees affected by dieback." Silvae Genetica 73, no. 1 (2024): 201–5. https://doi.org/10.2478/sg-2024-0020.

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Abstract Phenotypic plasticity is a fundamental mechanism that enables plants to adapt to shifting environmental conditions, such as those induced by climate change. Epigenetic modifications, notably DNA methylation, may play a pivotal role in such process. However, this field remains largely unstudied in non-model organisms with large, complex genomes. Here, we focus on silver fir (Abies alba), more precisely on a natural population subjected to climate stress, comparing the results obtained from two different bisulfite sequencing techniques in the study of the epigenetic patterns of its giga

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42

Johnson, Kevin C., Kevin Anderson, Elise Courtois, et al. "GENE-40. CHARACTERIZING EPIGENETIC INTRATUMORAL HETEROGENEITY IN GLIOMA USING SINGLE-CELL BISULFITE SEQUENCING." Neuro-Oncology 21, Supplement_6 (2019): vi106. http://dx.doi.org/10.1093/neuonc/noz175.442.

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Abstract Genetic and epigenetic alterations contribute to the observed intratumoral heterogeneity in adult glioma. Current glioma classification, based on genotype (e.g., IDH1 mutations) and DNA methylation profiles (e.g., glioma CpG Island Methylator Phenotype), can provide clinically relevant tumor subgroups. However, traditional bulk sampling fails to adequately capture the full complement of epigenomic heterogeneity, and may mask deadly features present in less abundant glioma cells. To more precisely characterize the glioma epigenome, we separately profiled single-cell DNA methylation (Re

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43

Ashktorab, Hassan, Afnan Shakoori, Shatha Zarnogi, et al. "Reduced Representation Bisulfite Sequencing Determination of Distinctive DNA Hypermethylated Genes in the Progression to Colon Cancer in African Americans." Gastroenterology Research and Practice 2016 (2016): 1–8. http://dx.doi.org/10.1155/2016/2102674.

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Background and Aims. Many studies have focused on the determination of methylated targets in colorectal cancer. However, few analyzed the progressive methylation in the sequence from normal to adenoma and ultimately to malignant tumors. This is of utmost importance especially in populations such as African Americans who generally display aggressive tumors at diagnosis and for whom markers of early neoplasia are needed. We aimed to determine methylated targets in the path to colon cancer in African American patients using Reduced Representation Bisulfite Sequencing (RRBS).Methods. Genomic DNA w

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44

Jackson, Jamaal C., Darren Sanchez, Aron Y. Joon, et al. "Bilateral Germ Cell Tumor of the Testis: Biological and Clinical Implications for a Stem Versus Genetic Origin of Cancers." Cells 14, no. 9 (2025): 658. https://doi.org/10.3390/cells14090658.

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Germ cell tumors of the testis (GCTs) provide an ideal tumor model to investigate the cellular versus genetic origin of cancers. In this single institutional study, we evaluated 38 patients with bilateral GCT, including tumors that occurred simultaneously (synchronous) and those occurring at different times (metachronous). For nine of these patients, DNA was isolated from the right and left GCT to determine the genomic and epigenetic differences between tissues using whole-exome sequencing (WES) and reduced representation bisulfite sequencing (RRBS). We found that seminomas and non-seminomas a

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45

Motwani, Jyoti, Euan J. Rodger, Peter A. Stockwell, Bruce C. Baguley, Erin C. Macaulay, and Michael R. Eccles. "Genome-wide DNA methylation and RNA expression differences correlate with invasiveness in melanoma cell lines." Epigenomics 13, no. 8 (2021): 577–98. http://dx.doi.org/10.2217/epi-2020-0440.

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Aims & objectives: The aim of this study was to investigate the role of DNA methylation in invasiveness in melanoma cells. Materials & methods: The authors carried out genome-wide transcriptome (RNA sequencing) and reduced representation bisulfite sequencing methylome profiling between noninvasive (n = 4) and invasive melanoma cell lines (n = 5). Results: The integration of differentially expressed genes and differentially methylated fragments (DMFs) identified 12 DMFs (two in AVPI1, one in HMG20B, two in BCL3, one in NTSR1, one in SYNJ2, one in ROBO2 and four in HORMAD2) that overlapp

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46

Ajithkumar, Priyadarshana, Gregory Gimenez, Peter A. Stockwell, et al. "DNA Methylome and Transcriptome Maps of Primary Colorectal Cancer and Matched Liver Metastasis." Data 9, no. 1 (2023): 8. http://dx.doi.org/10.3390/data9010008.

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Sequencing-based genome-wide DNA methylation, gene expression studies and associated data on paired colorectal cancer (CRC) primary and liver metastasis are very limited. We have profiled the DNA methylome and transcriptome of matched primary CRC and liver metastasis samples from the same patients. Genome-scale methylation and expression levels were examined using Reduced Representation Bisulfite Sequencing (RRBS) and RNA-Seq, respectively. To investigate DNA methylation and expression patterns, we generated a total of 1.01 × 109 RRBS reads and 4.38 x 108 RNA-Seq reads from the matched cancer

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47

Wang, Junwen, Yudong Xia, Lili Li, et al. "Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing." BMC Genomics 14, no. 1 (2013): 11. http://dx.doi.org/10.1186/1471-2164-14-11.

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48

Wang, Li, Jihua Sun, Honglong Wu, et al. "Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies." Journal of Biotechnology 157, no. 1 (2012): 1–6. http://dx.doi.org/10.1016/j.jbiotec.2011.06.034.

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49

Tsymbal, Olga S., Daria S. Isubakova, Evgenia V. Bronikovskaya та ін. "Assessment of the Degree Of DNA Methylation in Lymphocytes аfter а Single Blood Irradiation in vitro". Radiation biology. Radioecology 64, № 2 (2024): 126–35. http://dx.doi.org/10.31857/s0869803124020021.

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DNA methylation is one of the processes of epigenetic regulation of the genome, which is sensitive to the influence of endogenous and exogenous factors. The effect of ionizing radiation on the genome is accompanied by a change in the degree of DNA methylation, which can be dose-dependent and persist for a long time after radiation exposure. The objective of the study was to assess the degree of DNA methylation of blood lymphocytes after a single exposure to gamma radiation at a dose of 1.5 Gy using wide-genome bisulfite sequencing. The study included 10 conditionally healthy male employees of

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Murdoch, Brenda M., Kimberly M. Davenport, Shangqian Xie, et al. "378 Characterizing Functional Genetic Regulatory Elements in Sheep Reference Genome." Journal of Animal Science 100, Supplement_3 (2022): 185. http://dx.doi.org/10.1093/jas/skac247.340.

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Abstract:

Abstract Characterizing the locations of genetic regulatory elements is critical for understanding the regulatory mechanisms of complex phenotypic traits related to production traits and health in livestock species. The Ovine Functional Annotation of Animal Genomes (FAANG) Project aims to characterize transcriptional regulatory elements across the sheep genome to facilitate a better understanding of the biological mechanisms influencing phenotypic traits in sheep. Assays including sequencing of messenger RNA (mRNA-seq), cap analysis of gene expression (CAGE), chromatin immunoprecipitation of h

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