{"id":3275,"date":"2016-11-02T20:44:30","date_gmt":"2016-11-02T20:44:30","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/wm-biology1\/?post_type=chapter&#038;p=3275"},"modified":"2023-07-11T17:32:41","modified_gmt":"2023-07-11T17:32:41","slug":"eukaryotic-gene-regulation","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/ivytech-wmopen-nmbiology\/chapter\/eukaryotic-gene-regulation\/","title":{"raw":"Eukaryotic Gene Regulation","rendered":"Eukaryotic Gene Regulation"},"content":{"raw":"<h2>What you'll learn to do: Discuss different components and types of epigenetic gene regulation<\/h2>\r\nYour amazing body contains hundreds of different cell types, from immune cells to skin cells to neurons. Almost all of your cells contain the same set of DNA instructions: so why do they look so different, and do such different jobs? The answer: different gene regulation!\r\n\r\nGene regulation is how a cell controls which genes, out of the many genes in its genome, are \"turned on\" (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes \u2013 despite the fact that almost all the cells of your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell type uniquely specialized to do its job.\r\n\r\nEukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated.\r\n<div class=\"textbox learning-objectives\">\r\n<h3>Learning Outcomes<\/h3>\r\n<ul>\r\n \t<li>Explain the process of epigenetic regulation<\/li>\r\n \t<li>Discuss the role of transcription factors in gene regulation<\/li>\r\n \t<li>Understand RNA splicing and explain its role in regulating gene expression<\/li>\r\n \t<li>Describe the importance of RNA stability in gene regulation<\/li>\r\n<\/ul>\r\n<\/div>\r\n<h2>Eukaryotic Epigenetic Gene Regulation<\/h2>\r\nThe human genome encodes over 20,000 genes; each of the 23 pairs of human chromosomes encodes thousands of genes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type.\r\n\r\nThe first level of organization, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions (Figure 1a). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string (Figure 1b). These beads (histone proteins) can move along the string (DNA) and change the structure of the molecule.\r\n\r\n[caption id=\"attachment_3893\" align=\"aligncenter\" width=\"1024\"]<img class=\"size-large wp-image-3893\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12232927\/Figure_16_03_01ab-1024x423.jpg\" alt=\"Part A depicts a nucleosome composed of spherical histone proteins that are fused together. A double-stranded DNA helix wraps around the nucleosome twice. Free DNA extends from either end of the nucleosome. Part B is an electron micrograph of DNA that is associated with nucleosomes. Each nucleosome looks like a bead. The beads are connected together by free DNA. Nine beads strung together is approximately 150 nm across.\" width=\"1024\" height=\"423\" \/> Figure 1. DNA is folded around histone proteins to create (a) nucleosome complexes. These nucleosomes control the access of proteins to the underlying DNA. When viewed through an electron microscope (b), the nucleosomes look like beads on a string. (credit \u201cmicrograph\u201d: modification of work by Chris Woodcock)[\/caption]\r\n\r\nIf DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription (Figure 2). Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner.\r\n<div class=\"textbox exercises\">\r\n<h3>Practice Question<\/h3>\r\n[caption id=\"attachment_3894\" align=\"aligncenter\" width=\"600\"]<img class=\" wp-image-3894\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12233022\/Figure_16_03_02.png\" alt=\"Nucleosomes are depicted as wheel-like structures. The nucleosomes are made up of histones, and have DNA wrapped around the outside. Each histone has a tail that juts out from the wheel. When DNA and the histone tails are methylated, the nucleosomes pack tightly together so there is no free DNA. Transcription factors cannot bind, and genes are not expressed. Acetylation of histone tails results in a looser packing of the nucleosomes. Free DNA is exposed between the nucleosomes, and transcription factors are able to bind genes on this exposed DNA.\" width=\"600\" height=\"464\" \/> Figure 2. Nucleosomes can slide along DNA. When nucleosomes are spaced closely together (top), transcription factors cannot bind and gene expression is turned off. When the nucleosomes are spaced far apart (bottom), the DNA is exposed. Transcription factors can bind, allowing gene expression to occur. Modifications to the histones and DNA affect nucleosome spacing.[\/caption]\r\n\r\nIn females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing?\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"670204\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"670204\"]The nucleosomes would pack more tightly together.[\/hidden-answer]\r\n\r\n<\/div>\r\nThis type of gene regulation is called epigenetic regulation. Epigenetic means \u201caround genetics.\u201d The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA.\r\n<div class=\"textbox shaded\">\r\n\r\nView this video that describes how epigenetic regulation controls gene expression.\r\n\r\n<script type=\"text\/javascript\" src=\"\/\/static.3playmedia.com\/p\/projects\/20361\/files\/2048739\/plugins\/11118.js\"><\/script>\r\n<script src=\"https:\/\/www.youtube.com\/iframe_api\" type=\"text\/javascript\"><\/script>\r\n<iframe id=\"myytplayer4\" src=\"https:\/\/www.youtube.com\/embed\/eYrQ0EhVCYA?enablejsapi=1\" width=\"440\" height=\"300\" frameborder=\"0\" data-mce-fragment=\"1\"><\/iframe>\r\n\r\n<\/div>\r\n<div class=\"textbox learning-objectives\">\r\n<h3>In Summary: Eukaryotic Epigenetic Gene Regulation<\/h3>\r\nIn eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. 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. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.\r\n\r\n<\/div>\r\n<h2>Eukaryotic Transcription Gene Regulation<\/h2>\r\nLike prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. <strong>Transcription factors<\/strong> are proteins that bind to the <strong>promoter<\/strong> sequence and other regulatory sequences to control the transcription of the target gene. RNA polymerase by itself cannot initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established.\r\n<div class=\"textbox shaded\">\r\n\r\nView the process of transcription\u2014the making of RNA from a DNA template:\r\n\r\nhttps:\/\/youtu.be\/WsofH466lqk\r\n\r\n<\/div>\r\n<h3>The Promoter and the Transcription Machinery<\/h3>\r\n[caption id=\"attachment_3898\" align=\"alignright\" width=\"345\"]<img class=\" wp-image-3898\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12233554\/Figure_16_04_01.jpg\" alt=\"Eukaryotic gene expression is controlled by a promoter immediately adjacent to the gene, and an enhancer far upstream. The DNA folds over itself, bringing the enhancer next to the promoter. Transcription factors and mediator proteins are sandwiched between the promoter and the enhancer. Short DNA sequences within the enhancer called distal control elements bind activators, which in turn bind transcription factors and mediator proteins bound to the promoter. RNA polymerase binds the complex, allowing transcription to begin. Different genes have enhancers with different distal control elements, allowing differential regulation of transcription.\" width=\"345\" height=\"404\" \/> Figure 3. An enhancer is a DNA sequence that promotes transcription. Each enhancer is made up of short DNA sequences called distal control elements. Activators bound to the distal control elements interact with mediator proteins and transcription factors. Two different genes may have the same promoter but different distal control elements, enabling differential gene expression.[\/caption]\r\n\r\nGenes are organized to make the control of gene expression easier. The <strong>promoter region<\/strong> is immediately upstream of the coding sequence. The purpose of the promoter is to bind transcription factors that control the initiation of transcription.\r\n<h3>Enhancers and Transcription<\/h3>\r\nIn some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called <strong>enhancers<\/strong>, are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away.\u00a0 Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes (Figure 3). This shape change allows for the interaction of the <strong>activators<\/strong> bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase.\r\n<h3>Turning Genes Off: Transcriptional Repressors<\/h3>\r\nLike prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional <strong>repressors<\/strong> can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors.\r\n<div class=\"textbox learning-objectives\">\r\n<h3>In Summary: Eukaryotic Transcription Gene Regulation<\/h3>\r\nTo start transcription, transcription factors,\u00a0 must first bind to the promoter and recruit RNA polymerase to that location. \u00a0 In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.\r\n\r\n<\/div>\r\n<div class=\"textbox exercises\">\r\n<h3>Practice Questions<\/h3>\r\nThe binding of ________ is required for transcription to start.\r\n<ol>\r\n \t<li>a protein<\/li>\r\n \t<li>DNA polymerase<\/li>\r\n \t<li>RNA polymerase<\/li>\r\n \t<li>a transcription factor<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"670222\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"670222\"]Answer c.\u00a0The binding of RNA polymerase is required for transcription to start.\r\n\r\n[\/hidden-answer]\r\n\r\nWhat will result from the binding of a transcription factor to an enhancer region?\r\n<ol>\r\n \t<li>decreased transcription of an adjacent gene<\/li>\r\n \t<li>increased transcription of a distant gene<\/li>\r\n \t<li>alteration of the translation of an adjacent gene<\/li>\r\n \t<li>initiation of the recruitment of RNA polymerase<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"829037\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"829037\"]Answer b. Increased transcription of a distant gene\u00a0will result from the binding of a transcription factor to an enhancer region.\r\n\r\n[\/hidden-answer]\r\n\r\nA mutation within the promoter region can alter transcription of a gene. Describe how this can happen.\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"332179\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"332179\"]A mutation in the promoter region can change the binding site for a transcription factor that normally binds to increase transcription. The mutation could either decrease the ability of the transcription factor to bind, thereby decreasing transcription, or it can increase the ability of the transcription factor to bind, thus increasing transcription.\r\n\r\n[\/hidden-answer]\r\n\r\nWhat could happen if a cell had too much of an activating transcription factor present?\r\n\r\n[practice-area rows=\"2\"][\/practice-area]\r\n[reveal-answer q=\"162780\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"162780\"]If too much of an activating transcription factor were present, then transcription would be increased in the cell. This could lead to dramatic alterations in cell function. \u00a0[\/hidden-answer]\r\n\r\n<\/div>\r\n<h2>Post-Translational Control of Gene Expression<\/h2>\r\nRNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized.\r\n<h3>RNA splicing, the first stage of post-transcriptional control<\/h3>\r\nIn eukaryotic cells, the RNA transcript often contains regions, called <strong>introns<\/strong>, that are removed prior to translation. The regions of RNA that code for protein are called <strong>exons<\/strong> (Figure 4). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by <strong>splicing<\/strong>.\r\n\r\n[caption id=\"attachment_3904\" align=\"aligncenter\" width=\"544\"]<img class=\"size-full wp-image-3904\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12234813\/Figure_16_05_03.jpg\" alt=\"A pre-mRNA has four exons separated by three introns. The pre-mRNA can be alternatively spliced to create two different proteins, each with three exons. One protein contains exons one, two, and three. The other protein contains exons one, three and four.\" width=\"544\" height=\"155\" \/> Figure 4. Pre-mRNA can be alternatively spliced to create different proteins.[\/caption]\r\n<h4>Alternative RNA Splicing<\/h4>\r\nAlternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript (Figure 5).\r\n\r\n[caption id=\"attachment_3905\" align=\"aligncenter\" width=\"500\"]<img class=\"wp-image-3905\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12234933\/Figure_15_04_02.jpg\" alt=\"Diagram shows five methods of alternative splicing of pre-mRNA. When exon skipping occurs, an exon is spliced out in one mature mRNA product and retained in another. When mutually exclusive exons are present in the pre-mRNA, only one is retained in the mature mRNA. When an alternative 5\u2032 donor site is present, the location of the 5\u2032 splice site is variable. When an alternative 3\u2032 acceptor site is present, the location of the 3\u2032 splice site is variable. Intron retention results in an intron being retained in one mature mRNA and spliced out in another.\" width=\"500\" height=\"475\" \/> Figure 5. There are five basic modes of alternative splicing.[\/caption]\r\n\r\nThis alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation.\r\n<div class=\"textbox shaded\">\r\n\r\nVisualize how mRNA splicing happens by watching the process in action in this video:\r\n\r\nhttps:\/\/youtu.be\/FVuAwBGw_pQ\r\n\r\n<\/div>\r\n<h3>Control of RNA Stability<\/h3>\r\nBefore the mRNA leaves the nucleus, it is given two protective \"caps\" that prevent the end of the strand from degrading during its journey. The <strong>5\u2032 cap<\/strong>, which is placed on the 5\u2032 end of the mRNA and <strong>poly-A tail<\/strong>, which is attached to the 3\u2032 end. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate.\u00a0 This rate of decay is referred to as the <strong>RNA stability<\/strong>. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm.\r\n<h3>RNA Stability and microRNAs<\/h3>\r\nThe <strong>microRNAs<\/strong>, or miRNAs, are short single-stranded RNA molecules that are only 21\u201324 nucleotides in length.\u00a0 Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA to degrade the target mRNA.\u00a0 They rapidly destroy the RNA molecule.\r\n<div class=\"textbox learning-objectives\">\r\n<h3>In Summary: Post-Translational Control of Gene Expression<\/h3>\r\nPost-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon\/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. RNA stability is controlled by microRNAs (miRNAs). These miRNAs bind to the 5\u2032 CAP or the 3\u2032 Tail of the RNA to decrease RNA stability and promote decay.\r\n\r\n<\/div>\r\n<div class=\"textbox exercises\">\r\n<h3>Practice Questions<\/h3>\r\nWhich of the following are involved in post-transcriptional control?\r\n<ol>\r\n \t<li>control of RNA splicing<\/li>\r\n \t<li>control of RNA shuttling<\/li>\r\n \t<li>control of RNA stability<\/li>\r\n \t<li>all of the above<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"681081\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"681081\"]Answer d. All of the above (control of RNA splicing, RNA shuttling, and RNA stability)\u00a0are involved in post-transcriptional control.\r\n\r\n[\/hidden-answer]\r\n\r\nBinding of a miRNAs will ________ the stability of the RNA molecule.\r\n<ol>\r\n \t<li>increase<\/li>\r\n \t<li>decrease<\/li>\r\n \t<li>neither increase nor decrease<\/li>\r\n \t<li>either increase or decrease<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"464261\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"464261\"]Answer b. Binding of a miRNAs will decrease the stability of the RNA molecule.\r\n\r\n[\/hidden-answer]\r\n\r\n<\/div>\r\n<div class=\"textbox exercises\">\r\n<h3>Check Your Understanding<\/h3>\r\nChanges in gene regulation that are caused by modifications to histones and the DNA, but not the nucleotide sequence itself, are known as ________.\r\n<ul>\r\n \t<li>hypermethylation<\/li>\r\n \t<li>epigenetic<\/li>\r\n \t<li>CpG islands<\/li>\r\n<\/ul>\r\n<details><summary>Show Answer<\/summary>epigenetic\r\n\r\n<\/details><\/div>\r\n","rendered":"<h2>What you&#8217;ll learn to do: Discuss different components and types of epigenetic gene regulation<\/h2>\n<p>Your amazing body contains hundreds of different cell types, from immune cells to skin cells to neurons. Almost all of your cells contain the same set of DNA instructions: so why do they look so different, and do such different jobs? The answer: different gene regulation!<\/p>\n<p>Gene regulation is how a cell controls which genes, out of the many genes in its genome, are &#8220;turned on&#8221; (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes \u2013 despite the fact that almost all the cells of your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell type uniquely specialized to do its job.<\/p>\n<p>Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated.<\/p>\n<div class=\"textbox learning-objectives\">\n<h3>Learning Outcomes<\/h3>\n<ul>\n<li>Explain the process of epigenetic regulation<\/li>\n<li>Discuss the role of transcription factors in gene regulation<\/li>\n<li>Understand RNA splicing and explain its role in regulating gene expression<\/li>\n<li>Describe the importance of RNA stability in gene regulation<\/li>\n<\/ul>\n<\/div>\n<h2>Eukaryotic Epigenetic Gene Regulation<\/h2>\n<p>The human genome encodes over 20,000 genes; each of the 23 pairs of human chromosomes encodes thousands of genes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type.<\/p>\n<p>The first level of organization, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions (Figure 1a). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string (Figure 1b). These beads (histone proteins) can move along the string (DNA) and change the structure of the molecule.<\/p>\n<div id=\"attachment_3893\" style=\"width: 1034px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-3893\" class=\"size-large wp-image-3893\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12232927\/Figure_16_03_01ab-1024x423.jpg\" alt=\"Part A depicts a nucleosome composed of spherical histone proteins that are fused together. A double-stranded DNA helix wraps around the nucleosome twice. Free DNA extends from either end of the nucleosome. Part B is an electron micrograph of DNA that is associated with nucleosomes. Each nucleosome looks like a bead. The beads are connected together by free DNA. Nine beads strung together is approximately 150 nm across.\" width=\"1024\" height=\"423\" \/><\/p>\n<p id=\"caption-attachment-3893\" class=\"wp-caption-text\">Figure 1. DNA is folded around histone proteins to create (a) nucleosome complexes. These nucleosomes control the access of proteins to the underlying DNA. When viewed through an electron microscope (b), the nucleosomes look like beads on a string. (credit \u201cmicrograph\u201d: modification of work by Chris Woodcock)<\/p>\n<\/div>\n<p>If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription (Figure 2). Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner.<\/p>\n<div class=\"textbox exercises\">\n<h3>Practice Question<\/h3>\n<div id=\"attachment_3894\" style=\"width: 610px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-3894\" class=\"wp-image-3894\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12233022\/Figure_16_03_02.png\" alt=\"Nucleosomes are depicted as wheel-like structures. The nucleosomes are made up of histones, and have DNA wrapped around the outside. Each histone has a tail that juts out from the wheel. When DNA and the histone tails are methylated, the nucleosomes pack tightly together so there is no free DNA. Transcription factors cannot bind, and genes are not expressed. Acetylation of histone tails results in a looser packing of the nucleosomes. Free DNA is exposed between the nucleosomes, and transcription factors are able to bind genes on this exposed DNA.\" width=\"600\" height=\"464\" \/><\/p>\n<p id=\"caption-attachment-3894\" class=\"wp-caption-text\">Figure 2. Nucleosomes can slide along DNA. When nucleosomes are spaced closely together (top), transcription factors cannot bind and gene expression is turned off. When the nucleosomes are spaced far apart (bottom), the DNA is exposed. Transcription factors can bind, allowing gene expression to occur. Modifications to the histones and DNA affect nucleosome spacing.<\/p>\n<\/div>\n<p>In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing?<\/p>\n<p><textarea aria-label=\"Your Answer\" rows=\"2\"><\/textarea><\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q670204\">Show Answer<\/span><\/p>\n<div id=\"q670204\" class=\"hidden-answer\" style=\"display: none\">The nucleosomes would pack more tightly together.<\/div>\n<\/div>\n<\/div>\n<p>This type of gene regulation is called epigenetic regulation. Epigenetic means \u201caround genetics.\u201d The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA.<\/p>\n<div class=\"textbox shaded\">\n<p>View this video that describes how epigenetic regulation controls gene expression.<\/p>\n<p><script type=\"text\/javascript\" src=\"\/\/static.3playmedia.com\/p\/projects\/20361\/files\/2048739\/plugins\/11118.js\"><\/script><br \/>\n<script src=\"https:\/\/www.youtube.com\/iframe_api\" type=\"text\/javascript\"><\/script><br \/>\n<iframe loading=\"lazy\" id=\"myytplayer4\" src=\"https:\/\/www.youtube.com\/embed\/eYrQ0EhVCYA?enablejsapi=1\" width=\"440\" height=\"300\" frameborder=\"0\" data-mce-fragment=\"1\"><\/iframe><\/p>\n<\/div>\n<div class=\"textbox learning-objectives\">\n<h3>In Summary: Eukaryotic Epigenetic Gene Regulation<\/h3>\n<p>In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. 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. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.<\/p>\n<\/div>\n<h2>Eukaryotic Transcription Gene Regulation<\/h2>\n<p>Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. <strong>Transcription factors<\/strong> are proteins that bind to the <strong>promoter<\/strong> sequence and other regulatory sequences to control the transcription of the target gene. RNA polymerase by itself cannot initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established.<\/p>\n<div class=\"textbox shaded\">\n<p>View the process of transcription\u2014the making of RNA from a DNA template:<\/p>\n<p><iframe loading=\"lazy\" id=\"oembed-1\" title=\"Transcription\" width=\"500\" height=\"375\" src=\"https:\/\/www.youtube.com\/embed\/WsofH466lqk?feature=oembed&#38;rel=0\" frameborder=\"0\" allowfullscreen=\"allowfullscreen\"><\/iframe><\/p>\n<\/div>\n<h3>The Promoter and the Transcription Machinery<\/h3>\n<div id=\"attachment_3898\" style=\"width: 355px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-3898\" class=\"wp-image-3898\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12233554\/Figure_16_04_01.jpg\" alt=\"Eukaryotic gene expression is controlled by a promoter immediately adjacent to the gene, and an enhancer far upstream. The DNA folds over itself, bringing the enhancer next to the promoter. Transcription factors and mediator proteins are sandwiched between the promoter and the enhancer. Short DNA sequences within the enhancer called distal control elements bind activators, which in turn bind transcription factors and mediator proteins bound to the promoter. RNA polymerase binds the complex, allowing transcription to begin. Different genes have enhancers with different distal control elements, allowing differential regulation of transcription.\" width=\"345\" height=\"404\" \/><\/p>\n<p id=\"caption-attachment-3898\" class=\"wp-caption-text\">Figure 3. An enhancer is a DNA sequence that promotes transcription. Each enhancer is made up of short DNA sequences called distal control elements. Activators bound to the distal control elements interact with mediator proteins and transcription factors. Two different genes may have the same promoter but different distal control elements, enabling differential gene expression.<\/p>\n<\/div>\n<p>Genes are organized to make the control of gene expression easier. The <strong>promoter region<\/strong> is immediately upstream of the coding sequence. The purpose of the promoter is to bind transcription factors that control the initiation of transcription.<\/p>\n<h3>Enhancers and Transcription<\/h3>\n<p>In some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called <strong>enhancers<\/strong>, are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away.\u00a0 Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes (Figure 3). This shape change allows for the interaction of the <strong>activators<\/strong> bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase.<\/p>\n<h3>Turning Genes Off: Transcriptional Repressors<\/h3>\n<p>Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional <strong>repressors<\/strong> can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors.<\/p>\n<div class=\"textbox learning-objectives\">\n<h3>In Summary: Eukaryotic Transcription Gene Regulation<\/h3>\n<p>To start transcription, transcription factors,\u00a0 must first bind to the promoter and recruit RNA polymerase to that location. \u00a0 In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.<\/p>\n<\/div>\n<div class=\"textbox exercises\">\n<h3>Practice Questions<\/h3>\n<p>The binding of ________ is required for transcription to start.<\/p>\n<ol>\n<li>a protein<\/li>\n<li>DNA polymerase<\/li>\n<li>RNA polymerase<\/li>\n<li>a transcription factor<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q670222\">Show Answer<\/span><\/p>\n<div id=\"q670222\" class=\"hidden-answer\" style=\"display: none\">Answer c.\u00a0The binding of RNA polymerase is required for transcription to start.<\/p>\n<\/div>\n<\/div>\n<p>What will result from the binding of a transcription factor to an enhancer region?<\/p>\n<ol>\n<li>decreased transcription of an adjacent gene<\/li>\n<li>increased transcription of a distant gene<\/li>\n<li>alteration of the translation of an adjacent gene<\/li>\n<li>initiation of the recruitment of RNA polymerase<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q829037\">Show Answer<\/span><\/p>\n<div id=\"q829037\" class=\"hidden-answer\" style=\"display: none\">Answer b. Increased transcription of a distant gene\u00a0will result from the binding of a transcription factor to an enhancer region.<\/p>\n<\/div>\n<\/div>\n<p>A mutation within the promoter region can alter transcription of a gene. Describe how this can happen.<\/p>\n<p><textarea aria-label=\"Your Answer\" rows=\"2\"><\/textarea><\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q332179\">Show Answer<\/span><\/p>\n<div id=\"q332179\" class=\"hidden-answer\" style=\"display: none\">A mutation in the promoter region can change the binding site for a transcription factor that normally binds to increase transcription. The mutation could either decrease the ability of the transcription factor to bind, thereby decreasing transcription, or it can increase the ability of the transcription factor to bind, thus increasing transcription.<\/p>\n<\/div>\n<\/div>\n<p>What could happen if a cell had too much of an activating transcription factor present?<\/p>\n<p><textarea aria-label=\"Your Answer\" rows=\"2\"><\/textarea><\/p>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q162780\">Show Answer<\/span><\/p>\n<div id=\"q162780\" class=\"hidden-answer\" style=\"display: none\">If too much of an activating transcription factor were present, then transcription would be increased in the cell. This could lead to dramatic alterations in cell function. \u00a0<\/div>\n<\/div>\n<\/div>\n<h2>Post-Translational Control of Gene Expression<\/h2>\n<p>RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized.<\/p>\n<h3>RNA splicing, the first stage of post-transcriptional control<\/h3>\n<p>In eukaryotic cells, the RNA transcript often contains regions, called <strong>introns<\/strong>, that are removed prior to translation. The regions of RNA that code for protein are called <strong>exons<\/strong> (Figure 4). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by <strong>splicing<\/strong>.<\/p>\n<div id=\"attachment_3904\" style=\"width: 554px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-3904\" class=\"size-full wp-image-3904\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12234813\/Figure_16_05_03.jpg\" alt=\"A pre-mRNA has four exons separated by three introns. The pre-mRNA can be alternatively spliced to create two different proteins, each with three exons. One protein contains exons one, two, and three. The other protein contains exons one, three and four.\" width=\"544\" height=\"155\" \/><\/p>\n<p id=\"caption-attachment-3904\" class=\"wp-caption-text\">Figure 4. Pre-mRNA can be alternatively spliced to create different proteins.<\/p>\n<\/div>\n<h4>Alternative RNA Splicing<\/h4>\n<p>Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript (Figure 5).<\/p>\n<div id=\"attachment_3905\" style=\"width: 510px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-3905\" class=\"wp-image-3905\" src=\"https:\/\/s3-us-west-2.amazonaws.com\/courses-images\/wp-content\/uploads\/sites\/1087\/2016\/12\/12234933\/Figure_15_04_02.jpg\" alt=\"Diagram shows five methods of alternative splicing of pre-mRNA. When exon skipping occurs, an exon is spliced out in one mature mRNA product and retained in another. When mutually exclusive exons are present in the pre-mRNA, only one is retained in the mature mRNA. When an alternative 5\u2032 donor site is present, the location of the 5\u2032 splice site is variable. When an alternative 3\u2032 acceptor site is present, the location of the 3\u2032 splice site is variable. Intron retention results in an intron being retained in one mature mRNA and spliced out in another.\" width=\"500\" height=\"475\" \/><\/p>\n<p id=\"caption-attachment-3905\" class=\"wp-caption-text\">Figure 5. There are five basic modes of alternative splicing.<\/p>\n<\/div>\n<p>This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation.<\/p>\n<div class=\"textbox shaded\">\n<p>Visualize how mRNA splicing happens by watching the process in action in this video:<\/p>\n<p><iframe loading=\"lazy\" id=\"oembed-2\" title=\"mRNA Splicing\" width=\"500\" height=\"375\" src=\"https:\/\/www.youtube.com\/embed\/FVuAwBGw_pQ?feature=oembed&#38;rel=0\" frameborder=\"0\" allowfullscreen=\"allowfullscreen\"><\/iframe><\/p>\n<\/div>\n<h3>Control of RNA Stability<\/h3>\n<p>Before the mRNA leaves the nucleus, it is given two protective &#8220;caps&#8221; that prevent the end of the strand from degrading during its journey. The <strong>5\u2032 cap<\/strong>, which is placed on the 5\u2032 end of the mRNA and <strong>poly-A tail<\/strong>, which is attached to the 3\u2032 end. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate.\u00a0 This rate of decay is referred to as the <strong>RNA stability<\/strong>. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm.<\/p>\n<h3>RNA Stability and microRNAs<\/h3>\n<p>The <strong>microRNAs<\/strong>, or miRNAs, are short single-stranded RNA molecules that are only 21\u201324 nucleotides in length.\u00a0 Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA to degrade the target mRNA.\u00a0 They rapidly destroy the RNA molecule.<\/p>\n<div class=\"textbox learning-objectives\">\n<h3>In Summary: Post-Translational Control of Gene Expression<\/h3>\n<p>Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon\/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. RNA stability is controlled by microRNAs (miRNAs). These miRNAs bind to the 5\u2032 CAP or the 3\u2032 Tail of the RNA to decrease RNA stability and promote decay.<\/p>\n<\/div>\n<div class=\"textbox exercises\">\n<h3>Practice Questions<\/h3>\n<p>Which of the following are involved in post-transcriptional control?<\/p>\n<ol>\n<li>control of RNA splicing<\/li>\n<li>control of RNA shuttling<\/li>\n<li>control of RNA stability<\/li>\n<li>all of the above<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q681081\">Show Answer<\/span><\/p>\n<div id=\"q681081\" class=\"hidden-answer\" style=\"display: none\">Answer d. All of the above (control of RNA splicing, RNA shuttling, and RNA stability)\u00a0are involved in post-transcriptional control.<\/p>\n<\/div>\n<\/div>\n<p>Binding of a miRNAs will ________ the stability of the RNA molecule.<\/p>\n<ol>\n<li>increase<\/li>\n<li>decrease<\/li>\n<li>neither increase nor decrease<\/li>\n<li>either increase or decrease<\/li>\n<\/ol>\n<div class=\"qa-wrapper\" style=\"display: block\"><span class=\"show-answer collapsed\" style=\"cursor: pointer\" data-target=\"q464261\">Show Answer<\/span><\/p>\n<div id=\"q464261\" class=\"hidden-answer\" style=\"display: none\">Answer b. Binding of a miRNAs will decrease the stability of the RNA molecule.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<div class=\"textbox exercises\">\n<h3>Check Your Understanding<\/h3>\n<p>Changes in gene regulation that are caused by modifications to histones and the DNA, but not the nucleotide sequence itself, are known as ________.<\/p>\n<ul>\n<li>hypermethylation<\/li>\n<li>epigenetic<\/li>\n<li>CpG islands<\/li>\n<\/ul>\n<details>\n<summary>Show Answer<\/summary>\n<p>epigenetic<\/p>\n<\/details>\n<\/div>\n\n\t\t\t <section class=\"citations-section\" role=\"contentinfo\">\n\t\t\t <h3>Candela Citations<\/h3>\n\t\t\t\t\t <div>\n\t\t\t\t\t\t <div id=\"citation-list-3275\">\n\t\t\t\t\t\t\t <div class=\"licensing\"><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Original<\/div><ul class=\"citation-list\"><li>Introduction to Eukaryotic Gene Regulation. <strong>Provided by<\/strong>: Lumen Learning. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY: Attribution<\/a><\/em><\/li><\/ul><div class=\"license-attribution-dropdown-subheading\">CC licensed content, Shared previously<\/div><ul class=\"citation-list\"><li>Biology. <strong>Provided by<\/strong>: OpenStax CNX. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\">http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by\/4.0\/\">CC BY: Attribution<\/a><\/em>. <strong>License Terms<\/strong>: Download for free at http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8<\/li><li>Overview: Eukaryotic gene regulation. <strong>Provided by<\/strong>: Khan Academy. <strong>Located at<\/strong>: <a target=\"_blank\" href=\"https:\/\/www.khanacademy.org\/science\/biology\/gene-regulation\/gene-regulation-in-eukaryotes\/a\/overview-of-eukaryotic-gene-regulation\">https:\/\/www.khanacademy.org\/science\/biology\/gene-regulation\/gene-regulation-in-eukaryotes\/a\/overview-of-eukaryotic-gene-regulation<\/a>. <strong>License<\/strong>: <em><a target=\"_blank\" rel=\"license\" href=\"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">CC BY-NC-SA: Attribution-NonCommercial-ShareAlike<\/a><\/em><\/li><\/ul><\/div>\n\t\t\t\t\t\t <\/div>\n\t\t\t\t\t <\/div>\n\t\t\t <\/section>","protected":false},"author":17,"menu_order":3,"template":"","meta":{"_candela_citation":"[{\"type\":\"original\",\"description\":\"Introduction to Eukaryotic Gene Regulation\",\"author\":\"\",\"organization\":\"Lumen Learning\",\"url\":\"\",\"project\":\"\",\"license\":\"cc-by\",\"license_terms\":\"\"},{\"type\":\"cc\",\"description\":\"Biology\",\"author\":\"\",\"organization\":\"OpenStax CNX\",\"url\":\"http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\",\"project\":\"\",\"license\":\"cc-by\",\"license_terms\":\"Download for free at http:\/\/cnx.org\/contents\/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.8\"},{\"type\":\"cc\",\"description\":\"Overview: Eukaryotic gene regulation\",\"author\":\"\",\"organization\":\"Khan 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