Stem cell genomics

Key takeaways

Stem cell genomics belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Stem cell genomics to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Stem cell genomics from memory before moving on to harder problems.

Reference excerpt

In biology and medicine, stem cell genomics is the analysis of the genomes of stem cells. Currently, this field is rapidly expanding due to the dramatic decrease in the cost of sequencing genomes. The study of stem cell genomics has wide reaching implications in the study of stem cell biology and possible therapeutic usages of stem cells.

Applications Application of research in this field could lead to drug discovery and information on diseases by the molecular characterization of the pluripotent stem cell through DNA and transcriptome sequencing and looking at the epigenetic changes of stem cells and subsequent products.

Single cell phenotypic analysis One step in that process is single cell phenotypic analysis, and the connection between the phenotype and genotype of specific stem cells. While current genomic screens are done with entire populations of cells, focusing in on a single stem cell will help determine specific signaling activity associated with varying degrees of stem cell differentiation and limit background due to heterogeneous populations.

Alzheimer's disease Single cell analysis of induced pluripotent stem cells (iPSCs), or stem cells able to differentiate into many different cell types, is a suggested method for treating such diseases like Alzheimer's disease (AD). This includes for understanding the differences between sporadic AD and familial AD. By first taking a skin sample from the patient and are transformed by transducing cells using retroviruses to encode such stem cell genes as Oct4, Sox2, KLF4 and cMYC. This allows for skin cells to be reprogrammed into patient-specific stem cell lines. Taking genomic sequences of these individual cells would allow for patient-specific treatments and furthering understanding of AD disease models.

Other diseases This technique would be used for similar diseases, like amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). These stem cells developed from a singular patient would also be able to be used to produce cells affected in the above-mentioned diseases. As mentioned, it will also lead to patient specific phenotypes of each disease. Further chemical analyses to develop safer drugs can be done through sequence information and cell-culture tests on iPSCs. After development on a specific drug, it can be transferred to other patient diseased cells while also being safety tested.

Methods Included in the study of stem cell genomics, is epigenomics, genomic-scale studies on chromatin regulatory variation. These studies also hope to expand research into regenerative medicine models and stem cell differentiation. Cell-type specific gene expression patterns during development occur as the result of interactions the chromatin level. Stem cell epigenomics focuses in on the epigenetic plasticity of human embryonic stem cells (hESCs).

Bivalent domains This includes investigation into bivalent domains as promoters or chromatin regions that are modified by transcriptional initiation and related to gene silencing.

Active enhancers They are also looking at the differences between active versus poised enhancers or enhancers that specifically control signaling-dependent gene regulation. Active enhancers are marked by acetylation of histone H3-H3K27ac and while poised are instead methylated at H3K27me3.

Methylation Stem cell epigenomic studies are also looking into DNA methylation patterns, specifically characteristics of hydroxy methylation versus overall methylation and the difference between methylation of CpG-island rich and CpG poor promoters. It has been found in mouse embryonic stem cells (mESC) that implanted mESC took up similar characteristics of histone methylation of the embryos where they transplanted into, indicating that methylation may be indicative of environment. This will guide studies into the differences between induced pluripotent and embryonic stem cells. These studies hope to produce information on iPSC differentiation capacity by first needing to enhance chromatin signature reading.

Regulatory factors It also hopes to produce to look into regulatory factors that control human embryonic development. Using drug therapy techniques as mentioned earlier, epigenomics would also allow for more information on drug activity.

Worked examples

Example 1 — a first encounter with Stem cell genomics

Start with the simplest possible case. Write down what Stem cell genomics claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Stem cell genomics before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Stem cell genomics ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Stem cell genomics

In research: Stem cell genomics appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Stem cell genomics in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Stem cell genomics is common in secondary-school and first-year university syllabi. It links to neighbouring topics Stem cells, so understanding it makes those chapters shorter.
In everyday life: Look for Stem cell genomics outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study Stem cell genomics in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Stem cell genomics means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Stem cell genomics out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Stem cell genomics in simple terms?

In biology and medicine, stem cell genomics is the analysis of the genomes of stem cells. Currently, this field is rapidly expanding due to the dramatic decrease in the cost of sequencing genomes.

Why does Stem cell genomics matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Stem cell genomics?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Stem cell genomics.