Reasons to Believe

Fearfully and Wonderfully Made

Have you ever wondered if human cloning might be a real possibility? And if so, how close might we be to seeing mini-me’s walking about? I think about this periodically. And I have to admit, I’ve met very few people who I think would be clone-worthy. I’m certainly not one of them!

Even though almost all of my cells contain the genetic blueprints to make a replica of baby AJ, it’s not enough to just replace the DNA in a fertilized egg with my adult DNA. One of the major hurdles in producing human clones, if it’s possible, is the reprogramming of the human genome that’s necessary to erasing most modifications that have been made in order to sequester or expose segments of DNA, thereby silencing or turning on different genes during the development and differentiation of various cells for different tissues.

These accrued modifications are epigenetic changes, meaning they’re not changes to my primary DNA sequences. Epigenetic changes are dynamic and reversible and involve chemical modifications to DNA and to proteins bound to the DNA (histones) that affect its structure and accessibility. These changes affect how my DNA is read or expressed in different cells and which RNAs (both coding and noncoding) and proteins are made. And that, of course, affects how different cells differentiate and function.

DNA chains are double-stranded, antiparallel, complementary strings of nucleotides, abbreviated A, C, G, and T. The ordered sequence of nucleotides specifies genes, regulatory sequences, and other elements necessary for coordinated development and differentiation of cells and organisms. A frequent epigenetic modification of DNA nucleotides involves the addition of a methyl group (-CH3) to cytosine bases (Cs). Methylation tends to silence DNA, which means the sequence cannot be read (or transcribed) by polymerase complexes.

The recent identification of enzymes that make similar modifications to adenine bases (As) in messenger RNAs and in DNA is adding layers of complexity to the array of epigenetic signals that control development, differentiation, and adaptive changes of highly complex and dynamic cellular systems.1 As we discover more epigenetic marks and learn more about how various epigenetic changes affect our transcriptomes, we are realizing that the level of complexity is staggering.

Epigenetics and Embryogenesis

The complexity at a cellular level in embryogenesis (formation and development of an embryo) and human development is mind-boggling. So much can go wrong even in the transition from insemination to the earliest multicellular blastula stage that it is no exaggeration to think of each pregnancy, let alone a successful birth, as truly miraculous. In fact, transitioning through the steps from insemination to birth is a string of wondrous events, only a few of which are well-characterized molecularly. The overwhelming majority of triggers and signals and coordinating factors that alter epigenetic modifications—erasing some, preserving others, timing and coordinating thousands upon thousands of such events during embryogenesis—are yet to be teased out.

During fertilization, the mother and father each provide one set of human chromosomes for the miracle-to-be offspring (baby). Each set of chromosomes comes from a fully differentiated cell—one an egg, the other a sperm. The genetic material in each cell was programmed, through epigenetic modifications, to be an egg or a sperm. But when the two come together in fertilization, they produce a zygote—the first stage of embryogenesis. The zygote’s DNA must be reprogrammed to a totipotent state—one where all potential outcomes are possible—in order to eventually produce roughly 200 hundred different cell types, through countless cell divisions, en route to becoming a fully developed human being. Reprogramming to totipotency may occur in a single cell cycle from oocyte to zygote. However, additional demethylation and further epigenetic reprogramming may occur in the early blastocyst stage.2

During zygote formation, the egg and sperm are providing not just chromosomes but additional cellular components. No doubt the oocyte (egg) provides the bulk of these as it provides thousands of other RNAs, biomolecules, and nanomachines, in addition to a set of chromosomes. Therefore, many epigenetic modifications passed on to offspring are most likely passed on from the mother. However, scientists know that the father too can pass on epigenetic modifications. Both maternal and paternal DNA are highly methylated (hypermethylated), reflecting the number of genes and regulatory signals that needed to be silenced in terminal differentiation of the gametes (eggs and sperm). Whether maternal or paternal, most epigenetic modifications need to be reset or erased for the embryo to develop properly.

Demethylation (removing the modifications) is absolutely essential for zygotic reprogramming. De novo demethylation occurs in the paternal genome shortly after fertilization. Passive demethylation also occurs as DNA is replicated and cells undergo subsequent divisions. Maternal demethylation occurs after paternal demethylation and by varying mechanisms. Removing epigenetic modifications during de novo demethylation actually damages the DNA when modified bases are cut out.

The mechanisms by which zygotic reprogramming occur are poorly understood, but a recent article in the journal Cell sheds some light on how DNA is repaired after the removal of some modifications.3 Although the triggers for demethylation of the paternal genome are not understood, it appears as though an enzyme responsible for base modification (Tet3) and other proteins involved in DNA repair are provided by the oocyte. The researchers show that the reprogramming of paternal DNA occurs at different times and through shared and unique pathways in comparison to the reprogramming of maternal DNA. Numerous factors, including two different repair pathways (involving base excision repair machinery and cohesin), provide critical functions necessary to restoring and protecting the integrity of reprogrammed DNA. Remarkably, checkpoints exist within the cellular milieu that prevent zygotes from undergoing cell division if the DNA is not properly repaired during reprogramming.

Another recent review article in Reproduction highlights roles for additional oocyte factors in paternal DNA reprogramming.4 The extreme compaction of the transcriptionally silent (quiescent) paternal genome in the sperm involves strong binding to protamines and formation of disulfide bridges within the paternal DNA. This helps sperm motility and provides protection for the paternal genome. But the paternal genome must undergo biochemical remodeling and decondensation through the replacement of protamines with new histones once fertilization takes place. The oocyte provides the endogenous resources needed to accomplish these tasks, too. Sperm also carry and deliver small regulatory RNAs essential for early (preimplantation) embryogenesis.

Fearfully and Wonderfully Complex

As I read through these articles, I began to marvel at how complex the early stages of human development are. I wonder if we will discover that the human being is more finely tuned for life at a molecular level than the universe and Earth are for supporting life. As I read about the DNA repair mechanisms replacing excised bases with unmodified bases coupled with checkpoints, I couldn’t help but think of the scripture in Psalm 139 where David refers to being knit together in his mother’s womb. The checkpoints ensure that persistent DNA lesions (where bases have been cut out) aren’t like dropped stitches, ultimately ruining the final masterpiece. Scientists are just beginning to understand some factors in an amazingly complex and extensive reprogramming of paternal genomes to produce a zygote that is ready to grow and develop. Demethylation of the maternal genome occurs later but is just as critical for embryogenesis. It too uses de novo and passive mechanisms to reprogram epigenetic changes.

How long will it take us to unravel the mysteries of human development, and when will we cross the threshold to the revelation that we are indeed fearfully and wonderfully made! Some of us have been hurled over the threshold already. Others will follow. But will we ever be able to clone a human being? Certainly not before we master the intricacies and complexities of zygotic reprogramming.

Making a Mini-Me?

Even if we were able to take my adult DNA and reprogram it back to a developmentally naive state that would allow successful transition through embryogenesis again, all (or the vast majority) of the controlling and contributing epigenetic factors would be different. If a human life were to come from such an endeavor, she too would be fearfully and wonderfully made, having been knit together in her mother’s womb. But she would be more unlike me than I would have been from an identical twin, had my mother birthed twins.

We are each fearfully and wonderfully made and uniquely different, each made in the image of God, and each God-breathed, living and moving and being in the One who creates and sustains all things. Everywhere we look—to the stars overhead or to the overwhelming complexity of a single cell or into the orchestrated flurries of cellular activities of embryogenesis—since the beginning of creation and now in the modern molecular biological era, it is evident from all that we see that God exists and is all-powerful, so wise, truly good, utterly magnificent, and worthy of praise. And our souls know it full well.

Resources

Endnotes

  1. Yanan Yue, Jianzhao Liu, and Chuan He, “RNA N6-methyladenosine Methylation in Post-transcriptional Gene Expression Regulation,” Genes & Development 29 (July 2015): 1343–55, doi:10.1101/gad.262766.115; Gerd P. Pfeifer, “Epigenetics: An Elusive DNA Base in Mammals,” Nature 532 (April 2016): 319–20, doi:10.1038/nature17315.
  2. Daniel Messerschmidt, Barbara Knowles, and Davor Solter, “DNA Methylation Dynamics during Epigenetic Reprogramming in the Germline and Preimplantation Embryos,” Genes & Development 28 (April 2014): 812–28, doi:10.1101/gad.234294.113.
  3. Sabrina Ladstätter and Kikuë Tachibana-Konwalski, “A Surveillance Mechanism Ensures Repair of DNA Lesions during Zygotic Reprogramming,” Cell 167 (December 2016): 1774–87, doi:10.1016/j.cell.2016.11.009.
  4. Rupsha Fraser and Chih-Jen Lin, “Epigenetic Reprogramming of the Zygote in Mice and Men: On Your Marks, Get Set, Go!,” Reproduction 152 (December 2016): R211–R222, doi:10.1530/REP-16-0376.

Subjects: Design, Fine-Tuning, Genetic Variation, Human Uniqueness, Life