Chromatin Unlimited: An Evolutionary View of Chromatin

Chromatin is a fundamental and highly conserved structure that carries genetic and epigenetic information in eukaryotic cells [...]

Epigenetics in the Transgenerational Transmission of Chronic Diseases in the Context of Poverty with a Perinatal Approach

Introduction: Epigenetics is relevant in obstetrics for its action during pregnancy, in embryo-fetal life and even for the events that exist at birth. Objective: To investigate and analyze information about the role that epigeomics plays in the transgenerational transmission of chronic diseases in the context of poverty with a perinatal approach. Methods: Through a non-systematic bibliographic review through the search engines: LILACS, CINAHL, COCHRANE, EBSCO, MEDLINE, SCIELO, SCOPUS and PUBMED. Results: 32 bibliographic publications were found, of which 30 articles containing information related to the topic were included. Discussion: The genome has been compared to the hardware of a computer, while the epigenetic information is compared to the software that controls the operation of the hardware. Furthermore, the factors affecting epigenetic information can be analog as parameters to operate the software. Conclusion: The epigenomics studies the process by which the expression of certain genes occurs, in order to reduce the probability of the appearance of chronic diseases, having a potential effect during pregnancy and neonatal period. Keywords: epigenomics, transcription, genetic, poverty, chronic disease. RESUMEN Introducción: La epigenética tiene relevancia en la obstetricia por su acción durante el embarazo, en la vida embrio-fetal e inclusive, por los sucesos que existen al nacimiento. Objetivo: Investigar y analizar de información acerca del rol que juega la epigenómica en la transmisión transgeneracional de las enfermedades crónicas en el contexto de la pobreza con enfoque perinatal. Métodos: Por medio de una revisión bibliográfica no sistemática a través de los buscadores: LILACS, CINAHL, COCHRANE, EBSCO, MEDLINE, SCIELO, SCOPUS y PUBMED. Resultados: Se encontraron 32 publicaciones bibliográficas, de las cuales se incluyeron 30 artículos que contenían la información relacionada al tema. Discusión: El genoma se lo ha comparado con el hardware de una computadora, mientras que la información epigenética se lo compara con el software que controla el funcionamiento del hardware. Además, los factores que afectan la información epigenética pueden ser analógicos como parámetros para operar el software. Conclusiones: La epigenómica estudia proceso por el cual se da la expresión de determinados genes, con la finalidad de disminuir la probabilidad de la aparición de enfermedades crónicas, teniendo un efecto potencial durante el embarazo y periodo neonatal. Palabras clave: epigenómica, transcripción genética, pobreza, enfermedad crónica.

A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis

Forming an embryo from a zygote poses an apparent conflict for epigenetic regulation. On the one hand, the de novo induction of cell fate identities requires the establishment and subsequent maintenance of epigenetic information to harness developmental gene expression. On the other hand, the embryo depends on cell proliferation, and every round of DNA replication dilutes preexisting histone modifications by incorporation of new unmodified histones into chromatin. Here, we investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis. We systemically inhibited cell proliferation during the G1/S transition in gastrula embryos and followed their development until the tadpole stage. Comparing wild-type and cell cycle–arrested embryos, we show that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation. In parallel, we quantified by mass spectrometry the abundance of a large set of histone modification states, which reflects the developmental maturation of the embryonic epigenome. The arrested embryos developed abnormal stage-specific histone modification profiles (HMPs), in which transcriptionally repressive histone marks were overrepresented. Embryos released from the cell cycle block during neurulation reverted toward normality on morphological, molecular, and epigenetic levels. These results suggest that the cell cycle block by HUA alters stage-specific HMPs. We propose that this influence is strong enough to control developmental decisions, specifically in cell populations that switch between resting and proliferating states such as stem cells.

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization

Background Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell potency changes cyclically, accompanied by dynamic transcriptional changes and epigenetic reprogramming. Recently, to understand these dynamic and regulatory mechanisms, multiomic analyses, including transcriptomic and epigenomic analyses of DNA methylation, chromatin accessibility and histone modifications of germline cells, have been performed for different stages in human and mouse germline cycles. However, the long time span of the germline cycle and material scarcity of germline cells have largely limited the understanding of these dynamic characteristic changes. A tool that integrates the existing multiomics data and visualizes the overall continuous dynamic trends in the germline cycle can partially overcome such limitations. Results Here, we present GLEANER, a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization. GLEANER provides a comprehensive collection of the transcriptome, DNA methylome, chromatin accessibility, and H3K4me3, H3K27me3, and H3K9me3 histone modification characteristics in human and mouse germline cycles. For each input gene, GLEANER shows the integrative analysis results of its transcriptional and epigenetic features, the genes with correlated transcriptional changes, and the overall continuous dynamic trends in the germline cycle. We further used two case studies to demonstrate the detailed functionality of GLEANER and highlighted that it can provide valuable clues to the epigenetic regulation mechanisms in the genetic and epigenetic information transmitted during the germline cycle. Conclusions To the best of our knowledge, GLEANER is the first web server dedicated to the analysis and visualization of multiomics data related to the mammalian germline cycle. GLEANER is freely available at http://compbio-zhanglab.org/GLEANER.

Spermatogonial Dio3 as a Potential Germ Line Sensor for Thyroid Hormone-Driven Epigenetic Inheritance

Summary Sentence: Thyroid hormone-clearing type 3 deiodinase is located in spermatogonia, where it may serve as a critical modulator of the thyroid hormone exposure of the male germ line and its epigenetic information, with implications for neurodevelopmental and endocrine disorders in subsequent generations.

AGO104 is an RdDM effector of paramutation at the maize b1 locus

Paramutation is an exception among eukaryotes, in which epigenetic information is conserved through mitosis and meiosis. It has been studied for over 70 years in maize, but the mechanisms involved are largely unknown. Previously described actors of paramutation encode components of the RNA-dependent DNA-methylation (RdDM) pathway all involved in the biogenesis of 24-nt small RNAs. However, no actor of paramutation have been identified in the effector complex of RdDM. Here, through a combination of reverse genetics, immunolocalization and immunoprecipitation (siRNA-IP) we found that ARGONAUTE104 (AGO104), AGO105 and AGO119 are members of the RdDM effector complex in maize and bind siRNAs produced from the tandem repeats required for paramutation at the b1 locus. We also showed that AGO104 is an effector of the b1 paramutation in maize.

The impact of epigenetic information on genome evolution

Epigenetic information affects gene function by interacting with chromatin, while not changing the DNA sequence itself. However, it has become apparent that the interactions between epigenetic information and chromatin can, in fact, indirectly lead to DNA mutations and ultimately influence genome evolution. This review evaluates the ways in which epigenetic information affects genome sequence and evolution. We discuss how DNA methylation has strong and pervasive effects on DNA sequence evolution in eukaryotic organisms. We also review how the physical interactions arising from the connections between histone proteins and DNA affect DNA mutation and repair. We then discuss how a variety of epigenetic mechanisms exert substantial effects on genome evolution by suppressing the movement of transposable elements. Finally, we examine how genome expansion through gene duplication is also partially controlled by epigenetic information. Overall, we conclude that epigenetic information has widespread indirect effects on DNA sequences in eukaryotes and represents a potent cause and constraint of genome evolution.This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

Breaking symmetry: the asymmetries in epigenetic inheritance

Symmetry and asymmetry are the fundamental aspects of life. Most cells within a multicellular organism contain the same genetic information, passed on from one originating cell, the zygote; however, these cells can take on a variety of different identities, with diverse appearances and functions. A fundamental question in biology ponders how cells containing identical DNA content can take on different cell identities. Epigenetic mechanisms could be the symmetry-breaking factor, as they are able to change the gene expression in cells without changing the DNA sequence. While the process of duplication and segregation of DNA during cell division has been well studied, it is less understood how the epigenetic information is established and inherited in the cells within a multicellular organism. Studies of asymmetric stem cell division, where a stem cell division gives rise to a self-renewed stem cell and a differentiating daughter cell, provide a model to study how epigenetic information is maintained or changed to produce daughter cells with identical genetic information but distinct cell fates. Here, we discuss the findings and ideas of how epigenetic information is maintained or changed during asymmetric cell division and the importance of this asymmetry in influencing cell fate.