Epigenetics In Human Reproduction And Development

Anna K Naumova, Teruko Taketo

• Publisher: WSPC
• Year: 2016
• ISBN:
  9789813144286
• Topic: Biowissenschaften
• Subtopic: Genetik & Genomik

Epigenetics is defined as heritable changes that do not affect the DNA sequence but influence gene expression. Epigenetic changes occur at the levels of DNA, histone, protein, and chromatin structures. Proper epigenetic modifications are essential for cell differentiation and function during development, while some epigenetic modifications are passed on from parents to offspring through gametes. Therefore, alterations of epigenetic states would have serious consequences for human development and health. This realization and the advent of new technologies have encouraged the advance of epigenetic studies in recent years. Nonetheless, many aspects of epigenetics, such as regulatory mechanisms and evolutional advantages, remain to be better understood.

Written by 26 scientists at the forefront of epigenetics research, this book discusses the different facets of epigenetics: from gametogenesis to child development, as well as from mechanistic studies in animal models to reviews of human clinical data.

Editor Anna K Naumova, Editor Teruko Taketo 0Mammalian Development, Epigenetics, Spermatogenesis, Oogenesis, DNA Methylation, Human Reproduction

• Focuses on the functions of epigenetics during gametogenesis and embryonic development
• Covers both the basic science in animal models and humans as well as overviews of human clinical data
• Presents the current ideas and approaches that address epigenetic phenomena from different angles

Epigenetics and Transposon Control in the Mammalian Germline

1

Safia Malki and Alex Bortvin

Department of Embryology,
Carnegie Institution for Science,
Baltimore, MD USA

Germ cells bridge generations and are critical for the successful propagation of species. Early in development, a small group of embryonic cells embarks on a long but fascinating journey that will take them through most dramatic changes in their genomic architecture, epigenetic makeup and cellular morphology (Lesch and Page 2012). The germ cell lineage will multiply, protect and prepare a few original copies of the newly created embryonic genome for the ultimate purpose of fertilization. Failure to precisely fulfill these functions at any level of cellular organization leads to deleterious mutations, chromosomal numerical and structural abnormalities, subfertility or infertility of an organism.

Integrity of germ cells’ genomes is critical for reproduction. In addition to numerous exogenous factors constantly bombarding somatic and germ cells of any organism throughout its life cycle, each of those cells’ genomes has a dark secret in the form of massive amounts of apparently non-functional DNA sequences. While not coding for any of the regulatory or structural proteins that make up a successful gamete, these DNA sequences possess a tremendous potential power to harm the germ cell and its genome. This chapter will introduce these DNA sequences in some detail and describe the complex love–hate relationship between them and germ cells.

1.1What are Transposons?

Barbara McClintock’s discovery of “controlling elements” in maize in the late 1940s marked the critical departure from the earlier vision of the constant character of the genome (Comfort 1999, 2001, McClintock 1948, 1951, 1956, 1984). Now known as transposable elements (TEs) or transposons, these discrete segments of DNA capable of integrating into a new location in the genome remain phenotypically invisible unless specifically looked for or presented with a chance to cause an observable change in an organism such as variegated coloring of maize kernels studied by McClintock. Since then, owing to the incredible advances in molecular biology, we have gained an extensive knowledge of the immense variety of plant and animal transposons, their structures and mechanisms of spreading throughout host genomes (Craig et al. 2015, Kazazian 2011). This knowledge empowers ongoing and future exploration of TEs’ roles in genome structure and evolution. Furthermore, transposons have become critical tools in every day biological research and have a great promise in human gene therapy (Hou et al. 2014, Ivics and Izsvak 2006, Rubin and Spradling 1983).

As we learn more about evolution and mechanisms of transposition of transposons, their classification continues to evolve (Finnegan 1989, Piégu et al. 2015, Wicker et al. 2007). According to their dependency on an RNA intermediate for insertion to a new location in the host genome, any TE belongs to one of two broad classes. A DNA transposon generally uses a “cut and paste” mechanism whereby it physically excises its entire body and inserts it at a new site in the genome (Craig et al. 2015, Pace and Feschotte 2007). This transposition process is possible because DNA transposons encode a specific enzyme “transposase”, which binds in a sequence-specific manner to terminal inverted repeats (TIRs) flanking transposon sequence and catalyzes both the excision and integration reactions of transposition (Hickman et al. 2005, Yuan and Wessler 2011). Some DNA transposons, such as miniature inverted-repeat transposable elements (MITEs), lack transposases and jump around the genome in a non-autonomous manner using transposases of other elements (Fattash et al. 2013).

In contrast, RNA intermediate-dependent elements transpose by a “copy and paste” mechanism (Goodier and Kazazian 2008). Here, DNA sequence of an element remains intact at the original genomic site but its RNA transcript templates the synthesis of DNA by reverse transcriptase. Based on their absolute dependency on reverse transcriptase, these TEs are classified as retrotransposons. There are two principle types of retrotransposons — those flanked by long terminal repeats (LTR retrotransposons) and those lacking LTRs altogether (non-LTR retrotransposons). The LTR retrotransposons (also known as Endogenous RetroViruses, ERVs) encode GAG and POL and, in some cases, ENV proteins and therefore, might represent ancestors of true retroviruses (Dewannieux and Heidmann 2013, Maksakova et al. 2006, Ribet et al. 2008, Weiss 2005). In mice, low copy number ERVs bearing similarity to murine leukemia virus (MLV) exhibit significantly higher activity than copious Intracisternal A particle (IAP) elements. In addition to hundreds of full-length copies of ERVs, the genome contains large numbers of solitary LTRs that arise by way of homologous recombination between the 5′ and 3′ LTRs of the full-length ERV. It is also quite possible that ERVs encoding the ENV protein have retained infectivity and propagate, at least in part, by infecting germ cells (Maksakova et al. 2006).

The non-LTR retrotransposons are subdivided into autonomous elements called long interspersed nuclear element (LINEs) and non-autonomous short interspersed nuclear element (SINEs) (Han 2010, Kramerov and Vassetzky 2010, Ohshima and Okada 2004). Full-length LINEs such as those in the LINE-1 (L1) super-family encode an RNA-binding chaperon ORF1p and a reverse transcriptase/endonuclease ORF2p (Babushok and Kazazian 2007, Feng et al. 1996, Martin 2006, 2010, Martin and Bushman 2001, Mathias et al. 1991, Moran et al. 1996). Although the mechanism of LINE-1 retrotransposition requires reverse transcription, it is distinct from that of LTR retrotransposons. Instead of forming a cytoplasmic virus-like particle, LINE-1-encoded ORF1p and ORF2p proteins form cytoplasmic ribonucleoprotein particles (RNPs) with their L1 mRNA that must reach the nuclear genome not only to integrate but also to create LINE-1 cDNA in the first place (Doucet et al. 2010, Martin 1991, 2006). Once in the nucleus, endonuclease activity of ORF2p nicks genomic DNA (predominantly at 5′TTAAAA/3′AA|TTTT sequences) to provide a T-rich template sequence to anneal LINE-1 mRNA poly(A)-tail and to initiate synthesis of the cDNA by reverse transcriptase activity of ORF2p (Cost and Boeke 1998; Feng et al. 1996, Jurka 1997). Details of later steps in this retrotransposition mechanism (known as Target-Primed Reverse Transcription or TPRT) remain await further elucidation (Gilbert et al. 2005, Han 2010, Kojima 2010).

Non-autonomous SINEs have originated from tRNA, 7SL RNA or 5S rRNAs. SINE-B1 (∼140 bp) and Alu (∼300 bp) are predominant elements, respectively, in mouse and human species (Kramerov and Vassetzky 2010). Transcription of gene-embedded SINEs occurs by RNA polymerase II while polymerase III transcribes individual SINEs utilizing internal promoter. The presence of a 3′- terminal L1-common sequence and an A-rich tail facilitates recognition of SINE RNA by L1 reverse transcriptase and retrotransposition (Dewannieux et al. 2003, Dewannieux and Heidmann 2005, Wallace et al. 2008). In addition, the human genome encodes ∼2700 copies of another non-LTR retrotransposon — 700–4,000 bp-long composite SINE-VNTR-Alu (SVA) elements (Hancks and Kazazian 2010). Like SINEs, these “repeat of repeats” elements rely on L1 reverse transcriptase but possess sequence features most consistent with their RNA polymerase II transcription using internal or upstream promoters.

1.2How Many Transposons are There in a Mammalian Genome?

As early as 1968, Britten and Kohne demonstrated a high repeat content of plant and animal genomes (Britten and Kohne 1968). Over the past two decades, genome sequencing projects revealed that much of that repeat content is of transposon origin. For example, at least 42% of the human genome is made up of sequences of intact and mutated transposable elements (19% of LINE-1, 12% of SINEs, 8% LTR and 3% DNA transposons) (Chalopin et al. 2015, Lander et al. 2001). Likewise, the mouse genome contains 31% of transposon sequences (15% LINE, 6% SINE, 9% LTR and 1% DNA TEs) while transposons account for 54% of the Zebrafish genome (3.6% LINE, 1.8% SINE, 5% LTR and 41% DNA TEs) (Chalopin et al. 2015, Waterston et al. 2002). While these are already very impressive numbers, they likely underestimate the true contribution of TEs to genomes due to the challenge of genome assembly from highly similar repeated elements (de Koning et al. 2011).

Most TEs populating modern genomes have lost their ability to transpose due to truncation and mutations introduced during transposition or accumulated over time. For example, there is no evidence of active DNA transposons since ∼40 million years in mouse and human genome (Goodier and Kazazian 2008, Pace and Feschotte 2007, Ray et al. 2008, Smit and Riggs 1996). A census of DNA transposons of the Hg19 human genome assembly listed 383,000 DNA sequences derived from DNA transposons (Pace and Feschotte 2007). These elements are subdivided within 125 families counting 100 to 1,000 copies per family. With mouse genome that counts 110,000 DNA transposon elements, the human genome contains the highest copy number among eukaryotic species (Chalopin et al. 2015, Lander et al. 2001). Loss of DNA transposons activity in mammals throughout evolution (with the exception for PiggyBat elements recently described in Bat) is puzzling with respect to their quantitative importance in the genome (Mitra et al. 2013, Ray et al. 2008).

Only about 100 of 500,000 LINE-1 elements in the human genomes remain competent for retrotransposition but just 6 of those could account for most of the ongoing LINE-1 activity (Brouha et al. 2003, Sassaman et al. 1997). The mouse genome encodes upwards of 10,000 full-length LINE-1 elements belonging to evolutionarily “young” families (DeBerardinis et al. 1998, Goodier et al. 2001). LTR transposons are still active in the mouse, for example IAP elements, but not in the human genomes (Horie et al. 2007, Lander et al. 2001, McCarthy and McDonald 2003, Qin et al. 2010, Smit and Riggs 1996).

Transposons reside throughout mammalian genomes with no clear preference for specific locations yet LINE-1 appears to amass in G-banding regions and the X chromosome while SINEs favor R-banding regions (Sandmeyer et al. 1989, Wichman et al. 1992) and both sequence and chromatin features could play significant role in targeting integration of transposons (Gao et al. 2008). Interestingly, both human and mouse genomes possess transposon-free regions some of which include Hox gene clusters (Simons et al. 2006a, 2006b).

1.3Transposons — Genomic Junk or Agents of Change?

What purpose do transposons have in the genome — is it solely that of selfish propagation or are they accidental building blocks or, more precisely, the clay of evolution? The functionality of transposable elements has been and remains one of the most exciting and contentious questions that go back to the original ideas of McClintock. In fact, contrary to the wide-spread belief it was not the mere existence of transposons but rather McClintock’s vision of them as “controlling elements” that received an overwhelmingly cold reception by contemporaries (Comfort 1999, 2001). In the early days of the molecular biology era, evolutional considerations and the C-value paradox of marked disparity between size of the genome and morphological complexity of the organism raised a strong argument that transposable elements are most likely “selfish”, “parasitic” or “junk” bits of modern genomes (Doolittle and Sapienza 1980, Orgel and Crick 1980). While such view did not exclude sporadic advantageous roles of junk DNA, little experimental evidence at the time could argue against it otherwise. Yet, careful consideration of these features leads to a conclusion that not a single description could account for the complexity of interactions between transposons and their host genomes (Kidwell and Lisch 2000). Over the years, ample although not yet systematic evidence of transposon impact on genome structure and gene expression has erode to some extent the purely negative perception of transposons (Britten 1996, Britten and Davidson 1971, Bucheton 1990, Corces and Geyer 1991, Fedoroff 1989, Kazazian et al. 1988, Pardue et al. 1996, Smit 1996, Spradling 1994, Weiner et al. 1986, Wichman et al. 1992). With the emergence of sequenced genomes and next generation sequencing technologies over the last decade, transposons continued to gain further recognition as “potent agents of change” (Kidwell and Lisch 2000). The recently completed Encyclopedia of DNA Elements (ENCODE) project has claimed a functional role of 80% of the human genome sequence thus reigniting an enthusiastic debate on this subject (Doolittle 2013, Dunham 2012, Eddy 2012). Whether or not transposons will remain qualified as junk DNA or be upgraded to a more attractive status, this discourse underscores an important fact that we are still in the very active phase of understanding the structure and function of the genome (Doolittle et al. 2012, Stencel and Crespi 2013). The ongoing exploration of the world of short and long non-coding RNAs promises to further expand the boundaries of our knowledge and it is without any doubt that transposable elements will be an important part of the new vision of the genome (Hangauer et al. 2013, Kelley and Rinn 2011, Rory and Roderic 2014). In all likelihood, future studies of vast numbers of eukaryotic genomes will illuminate additional roles of transposons in the evolution of species thus proving correct once again Dobzhansky’s aphorism that “Nothing in biology makes sense except in the light of evol...

Table of contents

• Cover Page
• Title
• Copyright
• Preface
• Contents
• Chapter 1 Epigenetics and Transposon Control in the Mammalian Germline
• Chapter 2 Epigenetic Modifications during Mammalian Oogenesis: Emerging Roles of Chromatin Structure during Oocyte Growth and Meiotic Maturation
• Chapter 3 Meiotic Recombination in the Human Germ Line
• Chapter 4 Epigenetics of Male Infertility
• Chapter 5 Epigenetic Regulation of X-Chromosome Inactivation
• Chapter 6 Placentation and Genomic Imprinting
• Chapter 7 Genetic and Epigenetic Variation at the H19 Imprinted Region and Its Effect on Birth Weight
• Chapter 8 Disturbances in Folate Metabolism and Their Impact on Development
• Chapter 9 Early Life Experiences and Their Influence on Epigenetic Marks and Human Brain Development
• Chapter 10 Epigenetic Consequences of Human Assisted Reproductive Technologies