Epigenetics, Volume 17, Issue 13 (2022)

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Epigenetics, Volume 17, Issue 13 (2022)

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Brief Report

Brief Report
Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis
Kristina M. Garske, Caroline Comenho, David Z. Pan, Marcus Alvarez, Karen Mohlke, Markku Laakso, Kirsi H. Pietiläinen & Päivi Pajukanta
Pages: 1849-1862
Published online: 23 Jun 2022
AbstractforLong-range chromosomal interactions increase and mark repressed gene expression during adipogenesis | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
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Research Paper

Article
Residential green space in association with the methylation status in a CpG site within the promoter region of the placental serotonin receptor HTR2A
Yinthe Dockx, Esmée Bijnens, Nelly Saenen, Raf Aerts, Jean-Marie Aerts, Lidia Casas, Andy Delcloo, Nicolas Dendoncker, Catherine Linard, Michelle Plusquin, Michiel Stas, an Van Nieuwenhuyse, Jos Van Orshoven, Ben Somers & Tim Nawrot
Pages: 1863-1874
Published online: 19 Jun 2022
AbstractforResidential green space in association with the methylation status in a CpG site within the promoter region of the placental serotonin receptor HTR2A | Full Text | References | PDF (776.6 KB) | EPUB | Supplemental
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Brief Report

Brief Report
Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro
Johanna Huoman, Shumaila Sayyab, Eirini Apostolou, Lovisa Karlsson, Lucas Porcile, Muhammad Rizwan, Sumit Sharma, Jyotirmoy Das, Anders Rosén & Maria Lerm
Pages: 1875-1891
Published online: 26 Jun 2022
AbstractforEpigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
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Research Paper

Article
Oleic acid-related anti-inflammatory effects in force-stressed PdL fibroblasts are mediated by H3 lysine acetylation associated with altered IL10 expression
Lisa Schuldt, Katrin von Brandenstein, Collin Jacobs & Judit Symmank
Pages: 1892-1904
Published online: 28 Jun 2022
AbstractforOleic acid-related anti-inflammatory effects in force-stressed PdL fibroblasts are mediated by H3 lysine acetylation associated with altered IL10 expression | Full Text | References | PDF (1.7 MB) | EPUB
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Article
Maternal depression and adverse neighbourhood conditions during pregnancy are associated with gestational epigenetic age deceleration
Allison A. Appleton, Betty Lin, Elizabeth M. Kennedy & Elizabeth A. Holdsworth
Pages: 1905-1919
Published online: 30 Jun 2022
AbstractforMaternal depression and adverse neighbourhood conditions during pregnancy are associated with gestational epigenetic age deceleration | Full Text | References | PDF (382.4 KB) | EPUB
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Article
Genomic map of candidate human imprint control regions: the imprintome
Dereje D. Jima, David A. Skaar, Antonio Planchart, Alison Motsinger-Reif, Sebnem E. Cevik, Sarah S. Park, Michael Cowley, Fred Wright, John House, Andy Liu, Randy L. Jirtle & Cathrine Hoyo
Pages: 1920-1943
Published online: 04 Jul 2022
AbstractforGenomic map of candidate human imprint control regions: the imprintome | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
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Article
Comparison of DNA methylation measurements from EPIC BeadChip and SeqCap targeted bisulphite sequencing in PON1 and nine additional candidate genes
Dennis Khodasevich, Anna R. Smith, Karen Huen, Brenda Eskenazi, Andres Cardenas & Nina Holland
Pages: 1944-1955
Published online: 02 Jul 2022
AbstractforComparison of DNA methylation measurements from EPIC BeadChip and SeqCap targeted bisulphite sequencing in PON1 and nine additional candidate genes | Full Text | References | PDF (2 MB) | EPUB | Supplemental
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Brief Report

Brief Report
Evaluating DNA recovery efficiency following bisulphite modification from plasma samples submitted for cell-free DNA methylation analysis
Daniel RA Cox, Boris Ka Leong Wong, Eunice Lee, Adam Testro, Vijayaragavan Muralidharan, Alexander Dobrovic & Su Kah Goh
Pages: 1956-1960
Published online: 28 Jun 2022
AbstractforEvaluating DNA recovery efficiency following bisulphite modification from plasma samples submitted for cell-free DNA methylation analysis | Full Text | References | PDF (319.6 KB) | EPUB | Supplemental
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Research Paper

Article
Whole human genome 5’-mC methylation analysis using long read nanopore sequencing
Catarina Silva, Miguel Machado, José Ferrão, António Sebastião Rodrigues & Luís Vieira
Pages: 1961-1975
Published online: 20 Jul 2022
AbstractforWhole human genome 5’-mC methylation analysis using long read nanopore sequencing | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
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Article
Prenatal Socioeconomic Disadvantage and Epigenetic Alterations at Birth Among Children Born to White British and Pakistani Mothers in the Born in Bradford Study
Amanda M. Simanek, Regina Manansala, Jennifer M.P. Woo, Helen C. S. Meier, Belinda L. Needham & Paul L. Auer
Pages: 1976-1990
Published online: 14 Jul 2022
AbstractforPrenatal Socioeconomic Disadvantage and Epigenetic Alterations at Birth Among Children Born to White British and Pakistani Mothers in the Born in Bradford Study | Full Text | References | PDF (431.7 KB) | EPUB | Supplemental
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Article
Digital methylation assessments of alcohol and cigarette consumption account for common variance in accelerated epigenetic ageing
Man-Kit Lei, Frederick X. Gibbons, Meg Gerrard, Steven R.H. Beach, Kelsey Dawes & Robert Philibert
Pages: 1991-2005
Published online: 22 Jul 2022
AbstractforDigital methylation assessments of alcohol and cigarette consumption account for common variance in accelerated epigenetic ageing | Full Text | References | PDF (1 MB) | EPUB | Supplemental
  • 436 Views
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Article
Prenatal and birth associations of epigenetic gestational age acceleration in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort
Saher Daredia, Karen Huen, Lars Van Der Laan, Philip A. Collender, Jamaji C. Nwanaji-Enwerem, Kim Harley, Julianna Deardorff, Brenda Eskenazi, Nina Holland & Andres Cardenas
Pages: 2006-2021
Published online: 01 Aug 2022
AbstractforPrenatal and birth associations of epigenetic gestational age acceleration in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 2417 Views
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Article
Genome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome
Shirley Chu, Anne Avery, Janna Yoshimoto & Jeffrey N. Bryan
Pages: 2022-2038
Published online: 31 Jul 2022
AbstractforGenome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome | Full Text | References | PDF (857.9 KB) | EPUB | Supplemental
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Article
Long non-coding RNA Gm10561 promotes myogenesis by sponging miR-432
Shanshan Wang, Baohua Tan, Liyao Xiao, Jiekang Zeng, Xinming Zhao, Linjun Hong, Zicong Li, Gengyuan Cai, Enqin Zheng, Ting Gu & Zhenfang Wu
Pages: 2039-2055
Published online: 31 Jul 2022
AbstractforLong non-coding RNA Gm10561 promotes myogenesis by sponging miR-432 | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
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Article
MYCN and HIF-1 directly regulate TET1 expression to control 5-hmC gains and enhance neuroblastoma cell migration in hypoxia
Anastasia E. Hains, Sakshi Uppal, John Z. Cao, Helen R. Salwen, Mark A. Applebaum, Susan L. Cohn & Lucy A. Godley
Pages: 2056-2074
Published online: 08 Aug 2022
AbstractforMYCN and HIF-1 directly regulate TET1 expression to control 5-hmC gains and enhance neuroblastoma cell migration in hypoxia | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 458 Views
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Brief Report

Brief Report
Precise epigenomic editing with a SunTag-based modular epigenetic toolkit
Subhrangshu Guhathakurta, Levi Adams, Inhye Jeong, Anishaa Sivakumar, Mingyu Cha, Mariana Bernardo Fiadeiro, Haiyan Nancy Hu & Yoon-Seong Kim
Pages: 2075-2081
Published online: 03 Aug 2022
AbstractforPrecise epigenomic editing with a SunTag-based modular epigenetic toolkit | Full Text | References | PDF (1,014.9 KB) | EPUB | Supplemental
  • 2210 Views
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Research Paper

Article
Weight loss reduces circulating micro-RNA related to obesity and breast cancer in postmenopausal women
Catherine Duggan, Jean de Dieu Tapsoba, John Scheel, Ching-Yun Wang & Anne McTiernan
Pages: 2082-2095
Published online: 08 Aug 2022
AbstractforWeight loss reduces circulating micro-RNA related to obesity and breast cancer in postmenopausal women | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
  • 808 Views
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Article
Using Cg05575921 methylation to predict lung cancer risk: a potentially bias-free precision epigenetics approach
Rob Philibert, Kelsey Dawes, Joanna Moody, Richard Hoffman, Jessica Sieren & Jeffrey Long
Pages: 2096-2108
Published online: 03 Aug 2022
AbstractforUsing Cg05575921 methylation to predict lung cancer risk: a potentially bias-free precision epigenetics approach | Full Text | References | PDF (2.4 MB) | EPUB
  • 318 Views
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Article
Placental DNA methylation changes in gestational diabetes mellitus
Fujia Chen, Xiaoping Fei, Weiqiang Zhu, Zhaofeng Zhang, Yupei Shen, Yanyan Mao, Qianxi Zhu, Jianhua Xu, Weijin Zhou, Min Li & Jing Du
Pages: 2109-2121
Published online: 21 Aug 2022
AbstractforPlacental DNA methylation changes in gestational diabetes mellitus | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 663 Views
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Article
Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38
Claire Marchal, Pierre-Antoine Defossez & Benoit Miotto
Pages: 2122-2143
Published online: 24 Aug 2022
AbstractforContext-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38 | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
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Article
In silico identification and in vitro expression analysis of breast cancer-related m6A-SNPs
Tamara Kleinbielen, Felix Olasagasti, Daniel Azcarate, Elena Beristain, Amparo Viguri-Díaz, Isabel Guerra-Merino, África García-Orad & Marian M. de Pancorbo
Pages: 2144-2156
Published online: 29 Aug 2022
AbstractforIn silico identification and in vitro expression analysis of breast cancer-related m6A-SNPs | Full Text | References | PDF (1,021.6 KB) | EPUB | Supplemental
  • 661 Views
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Article
Gestational diabetes mellitus placentas exhibit epimutations at placental development genes
Laetitia P. Meyrueix, Raad Gharaibeh, Jing Xue, Cory Brouwer, Corbin Jones, Linda Adair, Shane A. Norris & Folami Ideraabdullah
Pages: 2157-2177
Published online: 21 Aug 2022
AbstractforGestational diabetes mellitus placentas exhibit epimutations at placental development genes | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 1894 Views
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Article
Epigenetic Aging Mediates the Association between Pain Impact and Brain Aging in Middle to Older Age Individuals with Knee Pain
Jessica A. Peterson, Larissa J. Strath, Chavier Laffitte Nodarse, Asha Rani, Zhiguang Huo, Lingsong Meng, Sean Yoder, James H. Cole, Thomas C. Foster, Roger B. Fillingim & Yenisel Cruz-Almeida
Pages: 2178-2187
Published online: 17 Aug 2022
AbstractforEpigenetic Aging Mediates the Association between Pain Impact and Brain Aging in Middle to Older Age Individuals with Knee Pain | Full Text | References | PDF (468.2 KB) | EPUB
  • 577 Views
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Review

Review
Placental DNA methylation in pregnancies complicated by maternal diabetes and/or obesity: State of the art and research gaps
Line Hjort, Boris Novakovic, Silvija Cvitic, Richard Saffery, Peter Damm & Gernot Desoye
Pages: 2188-2208
Published online: 05 Sep 2022
AbstractforPlacental DNA methylation in pregnancies complicated by maternal diabetes and/or obesity: State of the art and research gaps | Full Text | References | PDF (1 MB) | EPUB
  • 1880 Views
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Research Paper

Article
Maternal high-fat diet modifies epigenetic marks H3K27me3 and H3K27ac in bone to regulate offspring osteoblastogenesis in mice
Jin-Ran Chen, Perry C. Caviness, Haijun Zhao, Beau Belcher, Umesh D. Wankhade, Kartik Shankar, Michael L Blackburn & Oxana P. Lazarenko
Pages: 2209-2222
Published online: 17 Aug 2022
AbstractforMaternal high-fat diet modifies epigenetic marks H3K27me3 and H3K27ac in bone to regulate offspring osteoblastogenesis in mice | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 795 Views
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Article
Polymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort
Freida A. Blostein, Jonah Fisher, John Dou, Lisa Schneper, Erin B. Ware, Daniel A. Notterman, Colter Mitchell & Kelly M. Bakulski
Pages: 2223-2240
Published online: 18 Aug 2022
AbstractforPolymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort | Full Text | References | PDF (985.6 KB) | EPUB | Supplemental
  • 416 Views
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Article
An evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays
Yuanchao Zheng, Kathryn L. Lunetta, Chunyu Liu, Seyma Katrinli, Alicia K. Smith, Mark W. Miller & Mark W. Logue
Pages: 2241-2258
Published online: 01 Sep 2022
AbstractforAn evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 421 Views
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Article
Epigenome-wide association studies of occupational exposure to benzene and formaldehyde
Rachael V. Phillips, Linqing Wei, Andres Cardenas, Alan E. Hubbard, Cliona M. McHale, Roel Vermeulen, Hu Wei, Martyn T. Smith, Luoping Zhang, Qing Lan & Nathaniel Rothman
Pages: 2259-2277
Published online: 25 Aug 2022
AbstractforEpigenome-wide association studies of occupational exposure to benzene and formaldehyde | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 719 Views
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Article
mir152 hypomethylation as a mechanism for non-syndromic cleft lip and palate
Lucas Alvizi, Luciano Abreu Brito, Gerson Shigeru Kobayashi, Bárbara Bischain, Camila Bassi Fernandes da Silva, Sofia Ligia Guimaraes Ramos, Jaqueline Wang & Maria Rita Passos-Bueno
Pages: 2278-2295
Published online: 01 Sep 2022
Abstractformir152 hypomethylation as a mechanism for non-syndromic cleft lip and palate | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 860 Views
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Article
CircCLTH promotes skeletal muscle development and regeneration
Mengjie Chen, Qingyou Liu, Mingming Song, Xingyu Liu, Kongwei Huang, Dandan Zhong, Yaling Chen, Mingsheng Jiang, Junming Sun, Yiqiang Ouyang, Suren R Sooranna, Deshun Shi & Hui Li
Pages: 2296-2317
Published online: 08 Sep 2022
AbstractforCircCLTH promotes skeletal muscle development and regeneration | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 553 Views
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Review

Review
Aberrant regulation of CXCR4 in cancer via deviant microRNA-targeted interactions
Alexei J. Stuckel, Tripti Khare, Marc Bissonnette & Sharad Khare
Pages: 2318-2331
Published online: 06 Sep 2022
AbstractforAberrant regulation of CXCR4 in cancer via deviant microRNA-targeted interactions | Full Text | References | PDF (388.6 KB) | EPUB
  • 419 Views
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Research Paper

Article
DNA hypermethylation of Kiss1r promoter and reduction of hepatic Kiss1r in female rats with type 2 diabetes
Kamil Ziarniak, Tony Yang, Cayla Boycott, Megan Beetch, Maciej Sassek, Emilia Grzeda, Yuexi Ma, Joanna H. Sliwowska & Barbara Stefanska
Pages: 2332-2346
Published online: 12 Sep 2022
AbstractforDNA hypermethylation of Kiss1r promoter and reduction of hepatic Kiss1r in female rats with type 2 diabetes | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
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Brief Report

Brief Report
Dominant effects of the histone mutant H3-L61R on Spt16-gene interactions in budding yeast
Alex Pablo-Kaiser, McKenzie G. Tucker, Grace A. Turner, Elijah G. Dilday, Avery G. Olmstead, Caroline L. Tackett & Andrea A. Duina
Pages: 2347-2355
Published online: 08 Sep 2022
AbstractforDominant effects of the histone mutant H3-L61R on Spt16-gene interactions in budding yeast | Full Text | References | PDF (767.2 KB) | EPUB | Supplemental
  • 1415 Views
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Research Paper

Article
Additive and non-additive epigenetic signatures of natural hybridization between fish species with different mating systems
Waldir M. Berbel-Filho, George Pacheco, Mateus G. Lira, Carlos Garcia de Leaniz, Sergio M. Q. Lima, Carlos M. Rodríguez-López, Jia Zhou & Sofia Consuegra
Pages: 2356-2365
Published online: 15 Sep 2022
AbstractforAdditive and non-additive epigenetic signatures of natural hybridization between fish species with different mating systems | Full Text | References | PDF (680.1 KB) | EPUB | Supplemental
  • 1330 Views
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Article
The impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip
Sarah Holmes Watkins, Karen Ho, Christian Testa, Louise Falk, Patrice Soule, Linda V. Nguyen, Sophie FitzGibbon, Catherine Slack, Jarvis T. Chen, George Davey Smith, Immaculata De Vivo, Andrew J. Simpkin, Kate Tilling, Pamela D. Waterman, Nancy Krieger, Matthew Suderman & Caroline Relton
Pages: 2366-2376
Published online: 14 Oct 2022
AbstractforThe impact of low input DNA on the reliability of DNA methylation as measured by the Illumina Infinium MethylationEPIC BeadChip | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 1142 Views
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Article
Methylation profiles of global LINE-1 DNA and the GSTP1 promoter region in children exposed to lead (Pb)
Yared Beyene Yohannes, Shouta M.M. Nakayama, John Yabe, Haruya Toyomaki, Andrew Kataba, Hokuto Nakata, Kaampwe Muzandu, Chihiro Miyashita, Yoshinori Ikenaka, Kennedy Choongo & Mayumi Ishizuka
Pages: 2377-2388
Published online: 21 Sep 2022
AbstractforMethylation profiles of global LINE-1 DNA and the GSTP1 promoter region in children exposed to lead (Pb) | Full Text | References | PDF (1.8 MB) | EPUB
  • 305 Views
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Article
Placental epigenetic gestational aging in relation to maternal sociodemographic factors and smoking among infants born extremely preterm: a descriptive study
Jeliyah Clark, Catherine M. Bulka, Chantel L. Martin, Kyle Roell, Hudson P. Santos, T. Michael O’Shea, Lisa Smeester, Rebecca Fry & Radhika Dhingra
Pages: 2389-2403
Published online: 22 Sep 2022
AbstractforPlacental epigenetic gestational aging in relation to maternal sociodemographic factors and smoking among infants born extremely preterm: a descriptive study | Full Text | References | PDF (903.8 KB) | EPUB | Supplemental
  • 626 Views
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Article
Prenatal lead (Pb) exposure is associated with differential placental DNA methylation and hydroxymethylation in a human population
Pei Wen Tung, Elizabeth M. Kennedy, Amber Burt, Karen Hermetz, Margaret Karagas & Carmen J. Marsit
Pages: 2404-2420
Published online: 23 Sep 2022
AbstractforPrenatal lead (Pb) exposure is associated with differential placental DNA methylation and hydroxymethylation in a human population | Full Text | References | PDF (1,001.9 KB) | EPUB | Supplemental
  • 562 Views
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Research Article

Article
Epigenetic mechanisms underlying the association between maternal climate stress and child growth: characterizing severe drought and its impact on a Kenyan community engaging in a climate change-sensitive livelihood
Bilinda Straight, Xi Qiao, Duy Ngo, Charles E. Hilton, Charles Owuor Olungah, Amy Naugle, Claudia Lalancette & Belinda L. Needham
Pages: 2421-2433
Published online: 15 Oct 2022
AbstractforEpigenetic mechanisms underlying the association between maternal climate stress and child growth: characterizing severe drought and its impact on a Kenyan community engaging in a climate change-sensitive livelihood | Full Text | References | PDF (380.5 KB) | EPUB | Supplemental
  • 750 Views
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Research Paper

Article
Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods
Martin Bizet, Matthieu Defrance, Emilie Calonne, Gianluca Bontempi, Christos Sotiriou, François Fuks & Jana Jeschke
Pages: 2434-2454
Published online: 10 Nov 2022
AbstractforImproving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 2146 Views
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