Literature DB >> 32645449

Modern epigenetics methods in biological research.

Yuanyuan Li1.   

Abstract

The definition of epigenetics refers that molecular modifications on DNA that can regulate gene activity are independent of DNA sequence and mitotically stable. Notably, epigenetics studies have grown exponentially in the past few years. Recent progresses that lead to exciting discoveries and groundbreaking nature of this area demand thorough methodologies and advanced technologies to move epigenetics to the forefront of molecular biology. The most recognized epigenetic regulations are DNA methylation, histone modifications, and non-coding RNAs (ncRNAs). This review will discuss the modern techniques that are available to detect locus-specific and genome-wide changes for all epigenetic codes. Furthermore, updated analysis of technologies, newly developed methods, recent breakthroughs and bioinformatics pipelines in epigenetic analysis will be presented. These methods, as well as many others presented in this specific issue, provide comprehensive guidelines in the area of epigenetics that facilitate further developments in this promising and rapidly developing field.
Copyright © 2020 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Advanced technologies; DNA methylation; Epigenetics; Histone modifications; Methods; Non-coding RNAs

Mesh:

Substances:

Year:  2020        PMID: 32645449      PMCID: PMC7785612          DOI: 10.1016/j.ymeth.2020.06.022

Source DB:  PubMed          Journal:  Methods        ISSN: 1046-2023            Impact factor:   3.608


  106 in total

Review 1.  MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship.

Authors:  Amy E Pasquinelli
Journal:  Nat Rev Genet       Date:  2012-03-13       Impact factor: 53.242

Review 2.  Chromatin modifications and their function.

Authors:  Tony Kouzarides
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

3.  Epigenetics: a historical overview.

Authors:  Robin Holliday
Journal:  Epigenetics       Date:  2006-03-15       Impact factor: 4.528

Review 4.  The current state of chromatin immunoprecipitation.

Authors:  Philippe Collas
Journal:  Mol Biotechnol       Date:  2010-05       Impact factor: 2.695

Review 5.  Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications.

Authors:  Brian D Brown; Luigi Naldini
Journal:  Nat Rev Genet       Date:  2009-08       Impact factor: 53.242

6.  Characterization of Long Noncoding RNA-Associated Proteins by RNA-Immunoprecipitation.

Authors:  Youyou Zhang; Yi Feng; Zhongyi Hu; Xiaowen Hu; Chao-Xing Yuan; Yi Fan; Lin Zhang
Journal:  Methods Mol Biol       Date:  2016

7.  A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression.

Authors:  Gang Liu; Yang-Mei Jiang; Yong-Cheng Liu; Lin-Li Han; Hong Feng
Journal:  Appl Microbiol Biotechnol       Date:  2020-02-22       Impact factor: 4.813

Review 8.  Long non-coding RNAs: new players in cell differentiation and development.

Authors:  Alessandro Fatica; Irene Bozzoni
Journal:  Nat Rev Genet       Date:  2013-12-03       Impact factor: 53.242

9.  Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

Authors:  Eric E Schadt; Onureena Banerjee; Gang Fang; Zhixing Feng; Wing H Wong; Xuegong Zhang; Andrey Kislyuk; Tyson A Clark; Khai Luong; Alona Keren-Paz; Andrew Chess; Vipin Kumar; Alice Chen-Plotkin; Neal Sondheimer; Jonas Korlach; Andrew Kasarskis
Journal:  Genome Res       Date:  2012-10-23       Impact factor: 9.043

10.  WASP: allele-specific software for robust molecular quantitative trait locus discovery.

Authors:  Bryce van de Geijn; Graham McVicker; Yoav Gilad; Jonathan K Pritchard
Journal:  Nat Methods       Date:  2015-09-14       Impact factor: 28.547

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  14 in total

1.  DNA Methylation Analysis Using Bisulfite Pyrosequencing.

Authors:  Ken Higashimoto; Satoshi Hara; Hidenobu Soejima
Journal:  Methods Mol Biol       Date:  2023

Review 2.  The Relationship between Cancer and Paraoxonase 1.

Authors:  Irma Martha Medina-Díaz; Néstor Ponce-Ruíz; Aurora Elizabeth Rojas-García; José Francisco Zambrano-Zargoza; Yael Y Bernal-Hernández; Cyndia Azucena González-Arias; Briscia S Barrón-Vivanco; José Francisco Herrera-Moreno
Journal:  Antioxidants (Basel)       Date:  2022-03-31

Review 3.  Epigenetic Inheritance: Intergenerational Effects of Pesticides and Other Endocrine Disruptors on Cancer Development.

Authors:  Heloiza Diniz Nicolella; Sonia de Assis
Journal:  Int J Mol Sci       Date:  2022-04-23       Impact factor: 6.208

Review 4.  Chromatin Structure and Function in Mosquitoes.

Authors:  Óscar M Lezcano; Miriam Sánchez-Polo; José L Ruiz; Elena Gómez-Díaz
Journal:  Front Genet       Date:  2020-12-07       Impact factor: 4.599

Review 5.  Role of epigenetic transgenerational inheritance in generational toxicology.

Authors:  Eric E Nilsson; Millissia Ben Maamar; Michael K Skinner
Journal:  Environ Epigenet       Date:  2022-02-16

Review 6.  Epigenetic Transgenerational Modifications Induced by Xenobiotic Exposure in Zebrafish.

Authors:  Luis Terrazas-Salgado; Alejandra García-Gasca; Miguel Betancourt-Lozano; Raúl Llera-Herrera; Isabel Alvarado-Cruz; Beatriz Yáñez-Rivera
Journal:  Front Cell Dev Biol       Date:  2022-02-25

Review 7.  Regulation of ADAMTS Proteases.

Authors:  Keron W J Rose; Nandaraj Taye; Stylianos Z Karoulias; Dirk Hubmacher
Journal:  Front Mol Biosci       Date:  2021-06-29

Review 8.  Epigenetic Changes Induced by Maternal Factors during Fetal Life: Implication for Type 1 Diabetes.

Authors:  Ilaria Barchetta; Jeanette Arvastsson; Luis Sarmiento; Corrado M Cilio
Journal:  Genes (Basel)       Date:  2021-06-08       Impact factor: 4.096

Review 9.  Can Forest Trees Cope with Climate Change?-Effects of DNA Methylation on Gene Expression and Adaptation to Environmental Change.

Authors:  Ewelina A Klupczyńska; Ewelina Ratajczak
Journal:  Int J Mol Sci       Date:  2021-12-16       Impact factor: 5.923

10.  Epigenetics of obstructive sleep apnea syndrome: a systematic review.

Authors:  Brittany A Leader; Bala S C Koritala; Charles A Moore; Elaine H Grigg Dean; Leah C Kottyan; David F Smith
Journal:  J Clin Sleep Med       Date:  2021-12-01       Impact factor: 4.062

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