Discussion Topics 3
Gene Editing
CRISPR is the immune mechanism that allows bacteria to defend against viruses through adaptive viral resistance. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, and this name is derived from the structure of the CRISPR-Cas9 locus. This locus includes three operons: the tracrRNA operon, the Cas operon, and the CRISPR locus, which includes the CRISPR repeat-spacer array. The CRISPR locus has repeats of identical sequences, and in between these repeats, there are spacer regions, which are not identical. The spacers are the DNA sequences derived from the virus, which are stitched into the bacterial genome. When viral DNA enters the bacteria, a segment of the DNA is cut out via a Cas1-Cas2 complex and integrated into the CRISPR locus as a spacer, creating a ‘memory’ of the virus in the bacteria. Then, when the virus is reintroduced into the bacteria, crRNA is formed from the CRISPR locus, and along with tracrRNA, acts as a guide RNA that guides Cas9, a DNA endonuclease, to a target viral DNA sequence that matches the spacer DNA (complementary to the guide RNA). From here, the Cas9 cleaves the viral DNA by making a double stranded cut, thus defending the bacteria against the virus. This process in bacteria can be applied to the treatment of diseases, such as Sickle Cell disease, through CRISPR-Cas9 based genome editing. Sickle cell disease is commonly caused by a mutation in the hemoglobin-beta subunit (HBB) gene, and the CRISPR-Cas9 method can be used to correct the defect in the hemoglobin-Beta (HBB) gene in a process called ‘knock-in’. In knock in, guide RNA guides the Cas9 endonuclease to a specific, complementary region of the DNA (the defective HBB gene in this case) and the guide RNA binds to this sequence. Then, the Cas9 is able to cleave the DNA, creating a double stranded break. From here, homology-directed repair (HDR) is used to repair the double stranded break by inserting a repair DNA, which in this case, is a functional version of the HBB gene. The repair DNA must have sequences, called homology regions, at both ends that are identical to the regions adjacent to the double stranded cut on the mutated DNA. From here, a form of recombination involving base pairing occurs with the repair DNA and the genomic DNA, and the repair DNA is used as a template for the synthesis of DNA. Therefore, the repair DNA is copied into the genomic DNA, and a functional gene is made. Another treatment of Sickle cell disease involves mutating the BCL11A repressor-type transcription factor gene through a process called ‘knock-out’. In this process, Cas9 makes a double stranded break just as described in knock-in, however, instead of homology-directed repair, non-homologous End Joining (NHEJ) is used to repair the break. NHEJ involves joining the broken DNA back together, however, this results in a mutated BCL11A repressor-type transcription factor gene because NHEJ is error prone and this process often results in insertions and deletions, which results in gene knock-out. In our conversation, my group discussed the difference between knock-in and knock-out, and we concluded that the knock-in process results in the introduction of a functional gene through homology-directed repair while knock-out results in making a gene non-functional.
Genome editing is a way of altering the DNA sequence in order to cause a deletion or correction of mutated nucleotide sequences. Genome editing is commonly used in vitro in order to explore treatments of disorders. The “knock-in” method of genome editing can be done by a process of repairing double-stranded breaks known as homology directed repair (HDR). Double-stranded breaks in the genome of the mutated HBB gene can be caused by the CRISPR/Cas 9 process in which a guide RNA and Cas 9 endonuclease come together and cut the double-stranded DNA, causing a double-stranded break to occur. In HDR, double-stranded breaks not repaired by non-homologous end joining (NHEJ) can use a template strand of DNA to synthesize a new section of genes (repair DNA) that matches the broken ends of the DNA, with another set or a singular gene in between them, to repair the double-stranded break. This new gene between the ends of the repair DNA is known as a “knock-in” gene. This “knock-in” gene effectively repairs the double-stranded break and also repairs the mutation in the HBB gene, allowing for less sickle cells. (HDR → “knock-ins”). The CRISPR/Cas 9 complex can be used in another form of genome editing known as “kock-out.” Like previously mentioned, guide RNA gets together with the Cas 9 endonuclease and the complex cuts the double-stranded DNA of the BCL11A repressive transcription factor which renders it not able to repress, that is, until NHEJ comes along with its ku dimer proteins and repairs the double-stranded break. However, although NHEJ is an efficient process, it is very error prone and can lead to deletions, known as “knock-outs” which again, makes the repressive transcription factors unable to function properly, thereby decreasing sickle cell disease. (NHEJ → “knock-outs”).
iPSCs
Researchers are now transforming the cells of an affected person (ie. fibroblasts obtained via skin biopsy) into chemically induced pluripotent stem cells (CiPSCs) and from here chemically inducing them into various differentiated cells. In traditional cell culture, many cell lines are adherent, but in suspension cells these patient derived cell lines can create small organoids. Since these organoids are made from the cells of the affected person, there is an insight to the various medications that would be the most effective for the person. A pluripotent stem cell is in reference to a cell that has the potential to differentiate into any cell type, these are the original stem cells in embryo before they differentiate to form the fetus.
However, in order to create organoids, the cells must first be prepared from the patient derived sample and then once being propagated, introducing a series of abiotic chemicals will chemically induce pluripotent stem cells (CiPSCs). These chemicals induce the expression of 4 specific transcription factors, called pioneer transcription factors (Myc, KlF4, SOX2, Oct4) that are required to act as a pluripotent stem cell. We discussed the various roles of each pioneer transcription factor: SOX2 & Oct 4: activating genes required for maintaining stem cell properties, Klf4: remodels the chromatin structure and controls target gene accessibility, and Myc: boosts cellular proliferation and enhances efficiency of reprogramming. Pioneer transcription factors are unique in that they can function even if their DNA binding domain is wrapped around a nucleosome. After the fibroblasts are introduced to the first round of chemicals, they become de-differentiated cells as a regeneration phenotype. Following this, they are introduced to another round of chemicals and from here they are now CiPSCs. In suspension cells, these CiPSCs have potential to form organoids as they continue to differentiate. In the case of neurons, the differentiation is due to a series of growth factors and signaling molecules to artificially create neural development. The cells will begin to organize themselves to form an organized structure that resembles that of the human brain with a cerebral cortex and electrical activity present. We also briefly discussed the idea of trans-differentiation where differentiated cells could become a differentiated somatic cell via lineage specific transcription factors in the absence of intermediate steps. For example, the fibroblast would utilize lineage specific transcription factors and immediately form a neuron to structure a brain organoid.
The process of creating brain organoids starts with harvesting differentiated skin cells,
such as fibroblasts. These fibroblasts can then be undifferentiated and reprogrammed into iPSCs
(induced pluripotent stem cells) using genetic factors called pioneer transcription factors. Some
of the pioneer transcription factors mentioned in our discussion were OCT4, SOX2, KLF4, and
c-MYC, which are expressed by the cell and work to reorganize the differentiated somatic cells
into a pluripotent state. While normal transcription factors usually can not bind to
heterochromatin which is tightly packed and inactive, pioneer TFs bind to the cis-acting elements of the nucleosome on heterochromatin. This allows them to open up previously closed off parts of the DNA genome, allowing the regions to become available and grant other transcription factors access to bind and coordinate gene expression.
After the fibroblasts have lost their definitive characteristics they enter into a pluripotent
state where they are analogous to embryonic stem cells. Once transformed into induced
pluripotent stem cells (iPSCs), the cells can be directed to differentiate into various other cell
types, such as neurons. In order to create cerebral organoids, the iPSCs are placed in specific
cultures that mimic the developmental environment of the brain. With time, the cells
self-organize themselves into competent structures that resemble the early developmental stages
of the brain. The final results of this process are 3-D brain organoids that could range in sizes
from less than the width of a hair to about 5 mm.
Nevertheless, even as some research groups work to make more complex organoids, the
current models we can create using iPSCs have benefits.
Our group also discussed the process of trans-differentiation wherein a mature cell
transforms into another mature cell without becoming a pluripotent cell. Some benefits of this
process are reduced risk of mutations since the process does not require cell division, and a shortened time interval for the process because it does not require the transition into the
pluripotent state. We also discussed chemically induced pluripotent stem cells (CiPSCs) wherein
different abiotic chemicals are used instead of TFs to mimic TF behaviors and processes to
produce brain organoids.
During our discussion, we discussed how fibroblasts are converted into stem cells, and from there, into nerve cells and organoids, a miniature, lab grown version of an organ. Fertilized eggs are totipotent cells that make extraembryonic and embryonic stem cells. The embryonic cells are pluripotent, meaning they can make any adult tissue. Pluripotent stem cells can be used to create organoids. Pluripotent stem cells, however, do not need to be acquired from a fertilized egg, but can be synthesized from fibroblasts.
Fibroblasts are taken from skin cells to be converted into an induced pluripotent stem cell (iPSC). Fibroblasts cannot be turned directly into organoids, but need to be converted into iPSCs first. To get from fibroblasts to an iPSC, the heterochromatin in the fibroblast needs to be converted into euchromatin. The transformation of the chromatin from heterochromatin to euchromatin occurs as a result of the pioneer transcription factors, which are Klf4, Sox2, Oct4, and Myc. The pioneer transcription factors are able to bind to the nucleosomes in heterochromatin, which are usually inaccessible to regular transcription factors. By binding to the nucleosomes in heterochromatin, the pioneer transcription factors open up the nucleosomes for more transcription factors to bind, unwinding the heterochromatin effectively into euchromatin. Once the pioneer transcription factors are expressed in the fibroblast, it is induced to be a pluripotent stem cell. The fibroblast already has all of the pioneer transcription factor genes, but they are not expressed until they are induced to turn the fibroblast into a pluripotent stem cell.
The induced pluripotent stem cells that are produced can either go through the process of self-renewal or differentiation. Through self-renewal, the iPSC creates a copy of itself. The process of differentiation creates a different type of cell, such as a nerve cell. It is through the differentiation of the iPSC that organoids are created. By creating organoids from fibroblasts, experiments can be done on the organoid instead of the person the cells are from. Depending on the organoid, differentiated stem cells will group together to form the organoid.
An alternate form of creating pluripotent stem cells is through inducing their creation chemically, creating chemically induced pluripotent stem cells. Fibroblasts are treated with three rounds of chemical mixtures, which are abiotic chemicals. The first round of treatments creates dedifferentiated cells, which are then turned into extraembryonic cells with another round of chemical treatments. The third, and final, treatment transforms the extraembryonic cells into pluripotent stem cells, which can create organoids.
PCR
DNA sequencing and PCR sequencing are two main ways to form primers. During DNA replication in the S phase, DNA synthesis by DNA polymerases needs an RNA primer to get started. This RNA primer is created by an RNA polymerase and doesn’t need a specific template sequence. DNA polymerase then adds deoxyribonucleotides to the 3’ end of the RNA primer, following the template DNA strand to determine the correct sequence. Later on, the RNA primer, which is still attached to the new DNA, is removed, and DNA polymerase fills in the gap with new DNA. PCR uses two DNA primers that bind to complementary sequences on opposite strands of a double-stranded DNA template. In contrast, PCR for cloning into a recombinant plasmid also requires two primers, but these are designed with a 3’ end complementary to the DNA template and a 5’ extension matching the plasmid. After amplification, the PCR product is processed with restriction enzymes to create sticky ends that match those of the plasmid. These ends are annealed and ligated using DNA ligase to insert the DNA fragment into the plasmid. For short-read deep sequencing, DNA fragments are first ligated to adapters at both ends. These adapter-ligated fragments are denatured to form single-stranded DNA, allowing a universal primer to bind to the adapter sequence near the template. In metagenomics, DNA is extracted from a complex sample, fragmented, sequenced, and assembled to reconstruct multiple genomes. For comparing gene expression in skin fibroblasts treated with radiation versus untreated controls, mRNA is purified, converted to DNA, fragmented, and sequenced. The resulting short reads are mapped to a reference genome, and the read count per gene quantifies mRNA expression.
Retrotransposons
In this discussion, we started by discussing retrotransposons, which are mobile genetic elements that can move to new locations within the genome using a "copy-and-paste" mechanism. This process begins when the retrotransposon’s DNA is transcribed into RNA. Then, through the action of reverse transcriptase, the RNA is converted back into double-stranded DNA (dsDNA). Finally, this dsDNA is inserted into a new site in the genome with the help of integrase, an enzyme that facilitates integration into chromosomal DNA. This movement is a key characteristic of retrotransposons and a significant source of genetic variation. Then, we talked about the two primary types of retrotransposons in the human genome: LINE-1 and Alu elements. LINE-1 is autonomous, meaning it encodes the enzymes, such as reverse transcriptase and integrase, needed for its own mobility. We mentioned that LINE-1 accounts for roughly 20% of the human genome, though only about 100 LINE-1 elements remain active. These elements are often referred to as "selfish DNA" because they exist primarily to propagate themselves, often at the expense of the host genome. We brought up how LINE-1 activity can be harmful to the genome. When LINE-1 inserts itself into active gene-coding regions, it can disrupt the sequences, resulting in nonfunctional proteins and mutations. To counteract this, we explained that cells employ regulatory mechanisms using piRNAs and Argonaute proteins. These molecules work together to suppress LINE-1 activity by degrading its transcripts, effectively reducing the number of active retrotransposons in the genome. After that, we discussed Alu elements, another major type of retrotransposon. Like LINE-1, Alu elements also take up about 20% of the genome, but unlike LINE-1, they are non-autonomous. This means they cannot encode the necessary enzymes for their mobility and must rely on those produced by LINE-1 elements to move within the genome. While Alu elements do not encode proteins, their presence can still influence the genome by promoting recombination events, which we talked about next. Then, we brought up how retrotransposons like LINE-1 and Alu elements contribute to genetic variation. Their presence allows for non-sister chromatids to undergo crossover events with other chromosomes. These recombination events can lead to gene duplications, which are important for creating new genetic material. We explained the process of exon shuffling, where exons, or coding regions of genes, are rearranged between different genes. This shuffling can create new protein domains and functions, significantly contributing to the evolutionary diversity of organisms. Finally, we talked about how retrotransposons may play a role in the central nervous system. Specifically, we discussed how retrotransposon insertion events can occur within nerve cells, leading to variability in their genetic makeup. This variability can affect the "fitness" of individual neurons, with some cells potentially adapting better to their environment than others.
Retrotransposons, also known as selfish elements, are genetic elements able to copy themselves to different parts of the genome through reverse transcription. In total, there are two types of retrotransposons: long terminal repeats (LTRs) and non long terminal repeats (non-LTRs). While active LTRs can be found in other species, they are considered an ancient form in human genomes and are not considered. Within the retrotransposons active in modern genomes can be divided into two main categories: long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). The SINEs, such as Alu elements, and LINEs occur in both germ cells and several somatic cells such as neurons. In fact, at least 60% of brain cells have unique transposition events during brain development, mostly due to LINEs. LINEs are considered autonomous, since they contain the necessary machinery to create the enzymes needed to copy themselves into other sections of the genome. Alu elements are not autonomous, as they rely on the enzymes synthesized by LINEs to facilitate their own movement. LINEs from the DNA are transcribed by RNA polymerase into LINE mRNA, which contains the genetic code for the enzymes needed for transposition, including the endonuclease and the reverse transcriptase. Once these proteins are synthesized, the entire complex enters the nucleus of the cell to aid in transposition. First, the endonuclease makes a single stranded cut at the target site of the DNA; then, the reverse transcriptase synthesizes a complementary DNA strand from the LINE mRNA. Afterwards, this new LINE DNA may be inserted into the genome at the cleaved target site. For SINEs/Alu elements, the process is similar in the beginning, where RNA polymerase translates it into SINE mRNA. However, SINEs cannot encode their own enzymes, so they use the endonuclease and reverse transcriptase synthesized by the LINEs to make their single stranded cut and insert themselves into a target site. In the end of both processes, DNA repair finalized integration. While the insertion location of a retrotransposon is relatively random, they have a preference for the enhancer and promoter regions of a target gene. The development of our central nervous system regarding its retrotransposons occurs with a Darwinism type of evolution; that is to say, neurons vary in fitness, with some having more productive connection to each other. The genetic mosaicism that allows for this type of evolution can be attributed to the increased frequency of transposition events in nerve cells compared to other somatic cells. With more transposable elements inserting themselves to different parts of the genome, there is more variation in nerve cell gene expression, allowing for enhanced brain development.
Transposable elements are mobile DNA elements that can “jump” within the genome. Retrotransposons are a class of transposable elements that use a “copy and paste” mechanism where they make a copy of themselves to be inserted back into the genome. They can cause mutations in the genome with no regard for the host organism’s wellbeing. The two classes of retrotransposons are Long Terminal Repeat (LTR) retrotransposons and Non-LTR Retrotransposons. LTR retrotransposons contain reverse transcriptase and are generally all autonomous. Their ends contain long terminal repeats which have promoter elements for transcription, and binding sites for reverse transcriptase. LTR retrotransposons transcribe their DNA into RNA using RNA polymerase and then back into DNA via a reverse transcriptase, synthesizing a complementary cDNA. They encode reverse transcriptase and integrase enzymes to facilitate the insertion of the new cDNA into a different random location in the genome. Non-LTR retrotransposons don’t have long terminal repeats which means they have to use target-primed reverse transcription since they don’t have the primer binding sites for reverse transcription. The 3’ and 5’ ends of LTRs also have integration signals that tell the retrotransposon where they should integrate their cDNA whereas non-LTR retrotransposons don’t have this mechanism. Non-LTR retrotransposons include LINEs (long interspersed retrotransposable elements) and SINEs (short interspersed retrotransposable elements). LINEs are autonomous and encode their own machinery including the RNA chaperone, reverse transcriptase, and integrase. They have internal promoters that drive their transcription into RNA. This RNA is transported into the cytoplasm and it encodes two proteins, ORF1p and ORF2p which facilitate its transportation back into the nucleus and work as an endonuclease and reverse transcriptase. Once the RNA template is transported back to the nucleus, ORF2p makes a single-stranded nick in the target DNA and an end of the nicked DNA is used as a primer. Then, the ORF2p protein works as a reverse transcriptase to turn it into cDNA using the RNA template. Then it is completely integrated into the genome. SINEs are non-autonomous retrotransposons since they do not encode their own reverse transcriptase. SINEs like Alu elements have to use the machinery of other retrotransposons like LINE-1. RNA polymerase will transcribe the Alu DNA into a complementary RNA strand. Then they hijack LINE-1’s ORF1p and ORF2p which allow them to insert their cDNA into the genome. Germline retrotransposition can occur with sperm and in the process of brain-making. If a retrotransposon inserts itself into the coding part of the gene, this can lead to dysfunction. It can cause harmful mutations but it can also create genetic variety. With the brain, inserting into active genes isn’t necessarily bad but it can increase or decrease gene expression. LTR retrotransposons contain promoters and enhancers so insertions near a gene can increase expression. Research also shows that Alu insertions can also cause neurodevelopmental disorders like autism or schizophrenia.
Fertilization
Fertilization occurs when a sperm membrane fuses with an egg membrane, releasing its nucleic contents into the egg. However, the sperm has a long journey ahead of it. There are three layers it must bypass; the cumulus, the zona pellucida, and the plasma membrane. The sperm has receptors embedded in its membrane that are able to form weak bonds with cells in the cumulus, allowing it to navigate its way towards the inner layers. It also has receptors for the zona pellucida. When bound, the acrosome reaction is initiated, exposing receptors for the egg’s plasma membrane (such as Izumo) and degrading some zona pellucida glycoproteins, allowing the sperm to pass. Lastly, Izumo binds to Juno receptors on the egg plasma membrane. The membranes fuse, allowing the haploid DNA of the sperm to pour into the egg. Further, a calcium wave passes through the cell, unfreezing the egg’s polar bodies from meiosis II. The egg’s chromosomes complete their second round of anaphase. One of the polar bodies pinches off in a vesicle and exits, leaving a haploid set of DNA. To prevent polyspermy, cortical vesicles lined along the inside of the plasma membrane release enzymes into the extracellular space. These enzymes form covalent cross-links with the zona pellucida, hardening the outer shell. They also degrade remaining Juno receptors in the membrane. These adjustments block other sperm from binding to the egg. Meanwhile, the sperm and egg haploid chromosomes complete mitosis, each nucleus ending up with one set of paternal and one set of maternal genetic blueprints. Despite the care the cells take to prevent mistakes, errors in early embryonic stages still occur. One of the most common errors is aneuploidy, present in roughly a third of embryos. In the mitotic divisions transforming the single-cell zygote into a multicellular embryo, sometimes the proteins connecting sister chromatids at the centromeres don’t fully degrade. This causes both chromatids to be pulled towards one cell. One cell has an extra copy of the chromosome, while the other is missing one. This mismatch is called aneuploidy.
Neural Crest Cells
Gastrulation is the process where the embryo/blastula begins to rearrange itself into a gastrula, with multiple layers and cell types. This process is important in setting up the body and the three axes—dorsal-ventral, anterior-posterior, and left-right. The embryo/blastula cells begin to commit to a specific fate, becoming three germ layers—the ectoderm, mesoderm, and endoderm. There are three different stages in which these embryonic cells begin to specialize. Commitment is first—cells “choose” a fate based on their location in the blastula, but are free to move between fates given the right chemical signaling. Then, determination occurs when the blastula begins to fold inward and form a gastrula. During this process, cells are fully committed to their fates as endoderm, ectoderm, or mesoderm. To form the gastrula, the blastula creates an invagination, or a depression/fold in the embryo. Endoderm cells are the first to fold into this invagination, followed by the mesoderm cells. Differentiation occurs after the gastrula has fully formed and the embryo has gone through multiple invaginations, causing the different cells to give rise to different body structures. The ectoderm gives rise to the skin and nervous system, the mesoderm muscles and cartilage, and the endoderm gives rise to the internal organs and GI tract. The process of neurulation occurs during the second invagination as the gastrula matures. Neural crest cells, which are ectodermal, begin to migrate based on chemical signals from the dorsal end of the gastrula to other parts of the embryo’s surface. Facial structure is determined by neural crest cells, as they give rise to the bone, cartilage, and connective tissue of the face and skull. If there are specific variations in chemicals and signals, variations in facial structure can occur, such as having a more youthful or rounder face, or having a wider or flatter nose. Neural crest cells also form the peripheral nervous system, which connects to the spinal cord formed by the neural tube from the neural ectoderm. The peripheral nervous system connects the internal organs and muscles formed by the mesoderm and ectoderm to the central nervous system formed by the endoderm. Hiccups in neural crest cell chemical signaling or mutations in the cells themselves can cause facial defects, such as cleft palate. We can also examine the gastrula through the three axes created during gastrulation. From top to bottom, we have the dorsal side (back) and the ventral side (stomach). We also have the anterior (where the head forms) to the posterior side (where the tail end of the spinal cord forms). There are different concentration gradients between morphogen proteins and their antagonists that determine which cells belong to which axis. In the dorsal-ventral axis, the morphogen BMP acts on the ventral side and its antagonist chordin acts on the dorsal side. The concentration of BMP is highest on the ventral side because it can bind to receptors there more easily. Chordin acts directly on the morphogen BMP and inhibits it from binding to the dorsal side cell receptors, so BMP concentration is low and chordin concentration is high toward the dorsal side. However, not all antagonists act directly on the morphogen. The Wnt morphogen, responsible for the creation of the posterior side, can also act on the anterior side. However, it competes with the antagonist Dickkopf to bind to the LRP5 and LRP6 receptors necessary to create the posterior axis. Therefore, Dickkopf concentration is highest near the anterior end, and Wnt concentration is highest toward the posterior.
Cell divisions form blastula which have a fate map with three locations for determination: the ectoderm, endoderm and mesoderm. During gastrulation, the embryo undergoes significant reorganization into a multilayered structure, preparing for further developmental processes. The ectoderm thickens along the dorsal side of the embryo to form the neural plate, which will eventually give rise to the neural tube. As neurulation begins, the neural plate folds inward, creating neural folds at its edges. The neural folds represent the areas where the cells start to pinch off and form the neural tube. This process is critical for the formation of the central nervous system. As the neural folds continue to fold in a process called invagination where the edges undergo delamination, a mechanism where they separate from the neural tube and become neural crest cells. These cells undergo an epithelial-to-mesenchymal transition (EMT), in which they lose their epithelial properties (such as cell-to-cell adhesion) and acquire mesenchymal characteristics, giving them greater migratory potential. Once formed, neural crest cells migrate extensively throughout the developing embryo. Their migration is guided by chemical gradients of morphogens and their antagonists, which provide positional information. For example, WNT and its antagonist, Dickkopf, establish the anterior-posterior axis, with higher Dickkopf concentrations at the anterior and higher WNT concentrations at the posterior. Similarly, the dorsal-ventral axis is patterned by the antagonistic relationship between Chordin (a BMP antagonist) and BMP, where Chordin is more concentrated at the dorsal side and BMP at the ventral side. These gradients of signaling molecules direct the neural crest cells to specific regions of the embryo, including the face, teeth, and eyes, particularly guiding them to the anterior and ventral parts of the embryo. This precise spatial arrangement and guidance are crucial for the proper formation of these structures during embryonic development.
Gastrulation and neurulation are fundamental developmental processes characterized by large-scale cellular rearrangements that establish the foundation for the gastrointestinal tract and central nervous system, respectively. Neurulation involves the folding of the neural plate into the neural tube, a structure that gives rise to the central nervous system. During this process, neural crest cells emerge from the edges of the folding neural plate. These cells are unique in their ability to undergo an epithelial-to-mesenchymal transition (EMT), enabling them to detach and migrate extensively throughout the developing embryo. In our discussion section, we talked about how the migration of neural crest cells is guided by chemical gradients of signaling molecules such as Wnt, BMP, Dickkopf, and Chordin. These gradients provide directional cues that drive neural crest cells toward different regions of the embryo. For example, Wnt signaling primarily directs neural cells towards a posterior fate, influencing the development of structures like the midbrain, hindbrain, and spinal cord, while BMPs primarily direct neural cells in the dorsal region of the developing neural tube, influencing their differentiation into specific neuronal subtypes and contributing to the establishment of the dorsal-ventral axis within the spinal cord. This migration is essential for the formation of craniofacial structures, including the nose, jaw, and palate. Errors in chemical signaling or cell responsiveness can disrupt neural crest cell migration and differentiation, leading to developmental disorders such as cleft palate.