16.3 Regulation of Eukaryotic Epigenetic Genes - Biology for AP® Courses | OpenStax (2023)

Learning goals

In this section, you will examine the following question:

  • What is the science of epigenetics and how is this process regulated?

AP connection®Courses

One reason eukaryotic gene expression is more complex than prokaryotic gene expression is that the processes of transcription and translation are physically separate within the eukaryotic cell. Eukaryotic cells also package their genomes in a more sophisticated way than prokaryotic cells. Consequently, eukaryotic cells can regulate gene expression at multiple levels, starting with controlling access to DNA. Because genomic DNA folds around histone proteins to form nucleosome complexes, nucleosomes physically regulate the access of proteins, such as transcription factors and enzymes, to the underlying DNA. DNA and histone methylation causes nucleosomes to pack tightly together, preventing transcription factors from binding to DNA. Methylated nucleosomes contain DNA that is not expressed. On the other hand, histone acetylation results in loose nucleosome packing, allowing transcription factors to bind to DNA. Acetylated nucleosomes contain DNA that can be expressed.

The information presented and highlighted examples in the section support the concepts laid out in Big Idea 3 PA.®Biology Curriculum Framework. The learning objectives described in the curriculum provide a transparent basis for AP.®Biology courses, research-based lab experience, classroom activities, and AP®exam questions. The learning objective combines the necessary content with one or more of the seven scientific practices.

big idea 3Living systems store, retrieve, transmit and respond to information that is essential to life processes.
Permanent Understanding 3.BCellular and molecular mechanisms are involved in the expression of genetic information.
essential knowledge3.B.1Gene regulation results in differential gene expression, which leads to cell specialization.
scientific practice7.1The student can connect phenomena and patterns through spatial and temporal scales.
Learning objective3.19The student can describe the relationship between the regulation of gene expression and observed differences between individuals in a population.

Epigenetic control: regulation of access to genes within chromosomes

As noted above, one of the reasons eukaryotic gene expression is more complex than prokaryotic gene expression is that the processes of transcription and translation are physically separate. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with controlling access to DNA. This form of regulation, called epigenetic regulation, takes place even before transcription begins.

continued support

Introduce epigenetics and have students work on the epigenetics activity found on the University of Utah website.web page.

The human genome encodes more than 20,000 genes; each of the 23 pairs of human chromosomes codes for thousands of genes. The DNA in the nucleus is precisely coiled, folded, and compressed into chromosomes that fit inside the nucleus. It is also organized so that specific segments can be accessed by a specific cell type when needed.

The first level of organization, or packaging, is the wrapping of DNA strands around histone proteins. Histones package and arrange DNA into structural units called nucleosome complexes that can control protein access to regions of DNA.Figure 16.6A). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes resembles small beads attached to a thread (Figure 16.6B). These balls (histone proteins) can move along the strand (DNA) and change the structure of the molecule.

(Video) Epigenetics

16.3 Regulation of Eukaryotic Epigenetic Genes - Biology for AP® Courses | OpenStax (1)

Code16.6 DNA folds around histone proteins to (a) form nucleosome complexes. These nucleosomes control the access of proteins to the DNA below. When viewed through an electron microscope (b), nucleosomes look like beads on a string. (credit "micrograph": adapted work by Chris Woodcock)

If the DNA encoding a particular gene needs to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down to open up that specific chromosomal region and allow the transcription machinery (RNA polymerase) to begin transcription.Figure 16.7). Nucleosomes can move to open up the chromosome structure and expose a piece of DNA, but they do so in a very controlled way.

visual connection

16.3 Regulation of Eukaryotic Epigenetic Genes - Biology for AP® Courses | OpenStax (2)

Code16.7 Nucleosomes can slide along DNA. When nucleosomes are close together (above), transcription factors cannot bind and gene expression is turned off. When the nucleosomes are far apart (bottom), the DNA is exposed. Transcription factors can bind, allowing gene expression. Histone and DNA modifications affect nucleosome spacing.

Refers toFigure 16.7

(Video) Gene Regulation and the Order of the Operon

The X chromosome is very large compared to the Y chromosome. Expressing both copies of most of these genes would cause developmental problems. How is this challenge overcome in female mammals?

  1. DNA methylation and histone hypoacetylation cause a dense accumulation of nucleosomes, randomly deactivating one of the X chromosomes in each cell.

  2. DNA methylation and histone hypoacetylation cause tight nucleosome packing, inactivating the top half of the paternal chromosome and the bottom half of the maternal chromosome.

  3. DNA acetylation and histone hypermethylation cause the nucleosome to unwind, randomly deactivating one of the X chromosomes in each cell.

  4. DNA acetylation and histone hypermethylation cause the nucleosome to unwind, deactivating only the paternal chromosome.

How histone proteins move depends on signals found on both histone proteins and DNA. These signals are markers added to histone proteins and DNA that tell the histones whether a chromosomal region should be open or closed.Figure 16.8represents modifications in histone proteins and DNA). These tags are not permanent, but can be added or removed as needed. These are chemical modifications (phosphate, methyl or acetyl groups) attached to specific amino acids of proteins or to DNA nucleotides. The tags do not change the base sequence of the DNA, but they do change the tightness with which the DNA is wrapped around the histone proteins. DNA is a negatively charged molecule; therefore, changes in the histone charge will alter the density to which the DNA molecule will be coiled. When unmodified, histone proteins have a large positive charge; By adding chemical modifications, such as acetyl groups, the charge becomes less positive.

The DNA molecule itself can also be modified. This happens within very specific regions called CpG islands. These are high-frequency sections of DNA pairs (CG) of cytosine and guanine dinucleotides located in the promoter regions of genes. When this configuration exists, the cytosine member of the pair can be methylated (a methyl group is added). This alteration changes the way DNA interacts with proteins, including histone proteins that control access to the region. Highly methylated (hypermethylated) DNA regions with deacetylated histones are tightly coiled and transcriptionally inactive.

16.3 Regulation of Eukaryotic Epigenetic Genes - Biology for AP® Courses | OpenStax (3)

Code16.8 Histone proteins and DNA nucleotides can be chemically modified. Modifications affect nucleosome spacing and gene expression. (credit: NIH custom paper)

This type of gene regulation is called epigenetic regulation. Epigenetic means "around genetics". Changes that occur in histone proteins and DNA do not change the nucleotide sequence and are not permanent. Instead, these changes are temporary (although often lasting several rounds of cell division) and alter chromosome structure (open or closed) as needed. A gene can be turned on or off depending on its location and changes to histone proteins and DNA. If a gene is to be transcribed, histone proteins and DNA are modified around the chromosomal region that codes for that gene. This opens up the chromosomal region to access RNA polymerase and other so-called proteinstranscription factors, to bind to the promoter region, located upstream of the gene, and initiate transcription. If a gene is to remain turned off or shut down, the histone proteins and DNA have various modifications that indicate a closed chromosome configuration. In this closed configuration, RNA polymerase and transcription factors cannot access the DNA and transcription cannot take place.Figure 16.7).

(Video) AP Bio: 16.3 DNA Packaging

Science Practice Link for AP® courses

Think about it

In females, one of the two X chromosomes is inactivated during embryonic development due to epigenetic changes in the chromatin. What impact do you think these changes will have on nucleosome packing and consequently on gene expression?

continued support

The question is an application of Learning Objective 3.19 and Science Practice 7.1, where students are asked to describe how epigenetic changes in chromatin during development can result in differential gene expression and, consequently, differences between cells and organisms.


Nucleosomes will move closer together.

(Video) DNA Replication (Updated)

connection to learning

Aspectit's a moviedescribes how epigenetic regulation controls gene expression.

Refers to[link]

Explain how the study of epigenetics can lead to better cancer treatment.

  1. Epigenetics would make it possible to synthesize new body parts that could replace those damaged by cancer.

    (Video) AP Biology #65 - Ras and p53 genes

  2. Epigenetics could change the genetic code of all cells in the body to prevent them from becoming cancerous.

  3. New therapies may be developed that alter the genetic code of harmful cancer genes.

  4. New therapies can be developed that do not require changing the DNA of cancer cells.


What is epigenetic gene regulation in eukaryotes? ›

In Summary: Eukaryotic Epigenetic Gene Regulation

Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins.

What is epigenetics AP Biology? ›

As an organism grows and develops, carefully orchestrated chemical reactions activate and deactivate parts of the genome at strategic times and in specific locations. Epigenetics is the study of these chemical reactions and the factors that influence them. The Epigenome at a Glance.

What is epigenetic regulation in biology? ›

Epigenetics is the study of how cells control gene activity without changing the DNA sequence. "Epi-"means on or above in Greek,and "epigenetic" describes factors beyond the genetic code. Epigenetic changes are modifications to DNA that regulate whether genes are turned on or off.

What is the role of epigenetic gene regulation? ›

In the past few decades, many investigations have shown that the epigenetic mechanisms are involved in regulation of all biological process in the body from conception to death. These functional mechanisms are involved in genome reorganization, early embryogenesis and gametogenesis, as well as cell differentiation.

What are examples of eukaryotic gene regulation? ›

An example is the TATA box, so named because it has a core sequence of TATAAA. This is a regulatory element that is part of the promoter of most eukaryotic genes. A number of regulatory proteins bind to the TATA box, forming a multi-protein complex.

What are the 3 types of epigenetics? ›

Epigenetics refers to heritable traits that are not a consequence of DNA sequence. Three classes of epigenetic regulation exist: DNA methylation, histone modification, and noncoding RNA action.

What is the relationship between DNA and epigenetics? ›

Epigenetics looks at the extra layer of instructions that lie over or on top of DNA that control the way genes are expressed. All cells in the body contain the same genetic code. Yet each of these cells have different structures and functions.


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