{"id":329,"date":"2023-03-15T16:43:21","date_gmt":"2023-03-15T16:43:21","guid":{"rendered":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/?post_type=chapter&#038;p=329"},"modified":"2023-05-10T18:21:24","modified_gmt":"2023-05-10T18:21:24","slug":"eukaryotic-transcription-initiation","status":"publish","type":"chapter","link":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/chapter\/eukaryotic-transcription-initiation\/","title":{"raw":"Initiation of Transcription by RNA Polymerase","rendered":"Initiation of Transcription by RNA Polymerase"},"content":{"raw":"<h1 style=\"text-align: center\">Transcription Factors<\/h1>\r\n<p style=\"text-align: justify\"><span>\u00a0RNA polymerase II requires specific proteins <\/span><span>called<strong> transcription factors <\/strong><\/span><span>to initiate transcription <\/span>.<span>\u00a0<\/span><\/p>\r\n<p style=\"text-align: justify\"><span>Two general types of transcription factors have been defined\u00a0 namely ;<\/span><\/p>\r\n\r\n<ul>\r\n \t<li style=\"text-align: justify\"><span><strong>General transcription factors<\/strong>\u00a0 : These are involved in transcription from all polymerase II promoters and\u00a0 part of the basic transcription machinery.<\/span><\/li>\r\n \t<li style=\"text-align: justify\"><span><strong> Additional transcription factors\u00a0 :<\/strong> These bind to DNA\u00a0 <\/span><span>sequences that control the expression of individual genes and\u00a0 regulate gene<\/span><span> expression.<\/span><\/li>\r\n<\/ul>\r\n<h1 style=\"text-align: center\">Enhancers<\/h1>\r\n<p style=\"text-align: justify\"><span>Enhancer regions are binding sequences,\u00a0 for specific transcription factors. [pb_glossary id=\"934\"]Enhancers[\/pb_glossary] may be located upstream or downstream of transcription start site. Each enhancer is made up of short DNA sequences called <strong>distal control elements<\/strong> . <\/span><\/p>\r\n<p style=\"text-align: justify\"><span>Proteins called <strong>Activators\u00a0 , mediator proteins and transcription factors <\/strong>bind to the enhancers .When a transcription factor binds to its enhancer sequence, the shape of the\u00a0 transcription factor protein changes. This enables the transcription factor to\u00a0 \u00a0interact with proteins at the promoter site. <\/span><\/p>\r\n<p style=\"text-align: justify\"><span>As the enhancer region may be distant from the promoter, the DNA must bend to allow the proteins at the two sites to come into contact. DNA bending proteins help to bend the DNA and bring the enhancer and promoter regions together.<\/span><\/p>\r\n<p style=\"text-align: justify\"><span>\u00a0Two different genes may have the same promoter but different distal control elements, enabling differential gene expression.<\/span><\/p>\r\n<img src=\"http:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer.jpg\" alt=\"Figure depicting the binding of activators,mediators and transcription factors binding to the enhancers sites\" width=\"388\" height=\"454\" class=\"aligncenter wp-image-358\" \/>\r\n<p style=\"text-align: center\"><span style=\"color: #993366;background-color: #ffffff\"><a style=\"color: #993366;background-color: #ffffff\">\"Enhancers\" image<\/a> from <a href=\"https:\/\/openstax.org\/books\/biology\/pages\/16-4-eukaryotic-transcription-gene-regulation\" style=\"background-color: #ffffff\"><em data-effect=\"italics\">Biology<\/em>, an OpenStax resource <\/a>is licensed under\u00a0<a href=\"http:\/\/creativecommons.org\/licenses\/by\/4.0\" target=\"_blank\" rel=\"noopener\" style=\"color: #993366;background-color: #ffffff\">CC BY 4.0<\/a><\/span><\/p>\r\n\r\n<h1 style=\"text-align: center\">The promoters of RNA polymerase II<\/h1>\r\n<p style=\"text-align: justify\"><span>\u00a0<strong>The TATA box :<\/strong> This resembles the the -10 sequence element of bacterial promoters. This region contain the sequence TATAA\u00a0 and is located 25 to 30 nucleotides upstream of the transcription start site. <\/span><\/p>\r\n<p style=\"text-align: justify\"><strong>Initiator, or Inr, sequence : <\/strong><span>In addition to the TATA box ,<\/span><span> the promoters of many gene contain a second important sequence element called initiator, or Inr, sequence. Some RNA polymerase II promoters contain only an Inr element, with no TATA box.\u00a0<\/span><\/p>\r\n<p style=\"text-align: justify\"><strong>The promoter -proximal elements : The CAAT box<\/strong>, with the consensus sequence <strong>5\u2019-CCAAT-3\u2019<\/strong> and <strong>the GC box,<\/strong> with the consensus sequence <strong>5\u2019-GGGCGG-3\u2019. <\/strong>These\u00a0 promoter-proximal elements\u00a0 regulate gene transcription.<\/p>\r\n\r\n<h1 style=\"text-align: justify\"><span>Initiation-Formation of the Transcription complex <\/span><\/h1>\r\n<ul>\r\n \t<li style=\"text-align: justify\"><span>The first step in formation of a transcription complex is the binding of a general transcription factors<\/span><span>\u00a0called TFIID to the TATA box.TFIID is itself composed of multiple subunits,\u00a0 including the TATA binding protein . This binds specifically to the TATAA consensus sequence .and 10-12 other polypeptides, called <b>TBP-associated factors<\/b>\u00a0(<b>TAFs<\/b>). <\/span><\/li>\r\n \t<li style=\"text-align: justify\"><span>TBP then binds a second general transcription factor (TFIIB) forming a TBP-TFIIB complex at the along with TF II F at the promoter<\/span><\/li>\r\n \t<li style=\"text-align: justify\">Then RNA polymerase II binds<\/li>\r\n \t<li style=\"text-align: justify\">This is followed by the binding of <span>TFIIE and TFIIH. <\/span><\/li>\r\n \t<li style=\"text-align: justify\"><span>TFIIH is a multi subunit factor. It plays\u00a0 two important roles. First, two subunits of TFIIH are helicases, which unwind DNA\u00a0 around the initiation site. These subunits of TFIIH are also required for Nucleotide excision repair .Another subunit of TFIIH is a\u00a0 Protein kinase . This phosphorylates repeated sequences present in the C-terminal domain of the largest subunit of RNA polymerase II.\u00a0<\/span><\/li>\r\n<\/ul>\r\n<img src=\"http:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Tanscritio-complex-assembly-and-binding-RNA-polymerase-II.jpeg\" alt=\"Transcription complex assembly and binding of RNA polymerase assembly\" width=\"544\" height=\"724\" class=\"aligncenter size-full wp-image-349\" \/>\r\n<p style=\"text-align: center\"><span style=\"color: #993366;background-color: #ffffff\">\"Eukaryotic Transcription Initiation\" image from the book <a href=\"https:\/\/bio.libretexts.org\/Bookshelves\/Introductory_and_General_Biology\/Book%3A_General_Biology_%28Boundless%29\/15%3A_Genes_and_Proteins\/15.06%3A_Eukaryotic_Transcription_-_Initiation_of_Transcription_in_Eukaryotes\" style=\"background-color: #ffffff\">General Biology (Boundless) <\/a>licensed under\u00a0<a href=\"http:\/\/creativecommons.org\/licenses\/by-sa\/4.0\" target=\"_blank\" rel=\"noopener\" style=\"color: #993366;background-color: #ffffff\">CC BY-SA 4.0<\/a><\/span><\/p>\r\n\r\n<ul>\r\n \t<li style=\"text-align: justify\"><span>Once the complex is assembled, RNA polymerase can bind to its upstream sequence. <\/span><\/li>\r\n \t<li style=\"text-align: justify\"><span>When bound along with the transcription factors, RNA polymerase is phosphorylated. This releases part of the protein from the DNA .\u00a0 The transcription initiation complex\u00a0 gets activated and places RNA polymerase in the correct orientation to begin transcription.<\/span><\/li>\r\n \t<li style=\"text-align: justify\"><span>Then the double-stranded DNA in the transcription start region\u00a0 is unwound . The RNA Polymerase II is then\u00a0 positioned at the +1 initiation nucleotide and starts new RNA strand synthesis.<\/span><\/li>\r\n<\/ul>","rendered":"<h1 style=\"text-align: center\">Transcription Factors<\/h1>\n<p style=\"text-align: justify\"><span>\u00a0RNA polymerase II requires specific proteins <\/span><span>called<strong> transcription factors <\/strong><\/span><span>to initiate transcription <\/span>.<span>\u00a0<\/span><\/p>\n<p style=\"text-align: justify\"><span>Two general types of transcription factors have been defined\u00a0 namely ;<\/span><\/p>\n<ul>\n<li style=\"text-align: justify\"><span><strong>General transcription factors<\/strong>\u00a0 : These are involved in transcription from all polymerase II promoters and\u00a0 part of the basic transcription machinery.<\/span><\/li>\n<li style=\"text-align: justify\"><span><strong> Additional transcription factors\u00a0 :<\/strong> These bind to DNA\u00a0 <\/span><span>sequences that control the expression of individual genes and\u00a0 regulate gene<\/span><span> expression.<\/span><\/li>\n<\/ul>\n<h1 style=\"text-align: center\">Enhancers<\/h1>\n<p style=\"text-align: justify\"><span>Enhancer regions are binding sequences,\u00a0 for specific transcription factors. <a class=\"glossary-term\" aria-haspopup=\"dialog\" aria-describedby=\"definition\" href=\"#term_329_934\">Enhancers<\/a> may be located upstream or downstream of transcription start site. Each enhancer is made up of short DNA sequences called <strong>distal control elements<\/strong> . <\/span><\/p>\n<p style=\"text-align: justify\"><span>Proteins called <strong>Activators\u00a0 , mediator proteins and transcription factors <\/strong>bind to the enhancers .When a transcription factor binds to its enhancer sequence, the shape of the\u00a0 transcription factor protein changes. This enables the transcription factor to\u00a0 \u00a0interact with proteins at the promoter site. <\/span><\/p>\n<p style=\"text-align: justify\"><span>As the enhancer region may be distant from the promoter, the DNA must bend to allow the proteins at the two sites to come into contact. DNA bending proteins help to bend the DNA and bring the enhancer and promoter regions together.<\/span><\/p>\n<p style=\"text-align: justify\"><span>\u00a0Two different genes may have the same promoter but different distal control elements, enabling differential gene expression.<\/span><\/p>\n<p><img decoding=\"async\" src=\"http:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer.jpg\" alt=\"Figure depicting the binding of activators,mediators and transcription factors binding to the enhancers sites\" width=\"388\" height=\"454\" class=\"aligncenter wp-image-358\" srcset=\"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer.jpg 544w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer-256x300.jpg 256w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer-65x76.jpg 65w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer-225x263.jpg 225w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Enhancer-350x410.jpg 350w\" sizes=\"(max-width: 388px) 100vw, 388px\" \/><\/p>\n<p style=\"text-align: center\"><span style=\"color: #993366;background-color: #ffffff\"><a style=\"color: #993366;background-color: #ffffff\">&#8220;Enhancers&#8221; image<\/a> from <a href=\"https:\/\/openstax.org\/books\/biology\/pages\/16-4-eukaryotic-transcription-gene-regulation\" style=\"background-color: #ffffff\"><em data-effect=\"italics\">Biology<\/em>, an OpenStax resource <\/a>is licensed under\u00a0<a href=\"http:\/\/creativecommons.org\/licenses\/by\/4.0\" target=\"_blank\" rel=\"noopener\" style=\"color: #993366;background-color: #ffffff\">CC BY 4.0<\/a><\/span><\/p>\n<h1 style=\"text-align: center\">The promoters of RNA polymerase II<\/h1>\n<p style=\"text-align: justify\"><span>\u00a0<strong>The TATA box :<\/strong> This resembles the the -10 sequence element of bacterial promoters. This region contain the sequence TATAA\u00a0 and is located 25 to 30 nucleotides upstream of the transcription start site. <\/span><\/p>\n<p style=\"text-align: justify\"><strong>Initiator, or Inr, sequence : <\/strong><span>In addition to the TATA box ,<\/span><span> the promoters of many gene contain a second important sequence element called initiator, or Inr, sequence. Some RNA polymerase II promoters contain only an Inr element, with no TATA box.\u00a0<\/span><\/p>\n<p style=\"text-align: justify\"><strong>The promoter -proximal elements : The CAAT box<\/strong>, with the consensus sequence <strong>5\u2019-CCAAT-3\u2019<\/strong> and <strong>the GC box,<\/strong> with the consensus sequence <strong>5\u2019-GGGCGG-3\u2019. <\/strong>These\u00a0 promoter-proximal elements\u00a0 regulate gene transcription.<\/p>\n<h1 style=\"text-align: justify\"><span>Initiation-Formation of the Transcription complex <\/span><\/h1>\n<ul>\n<li style=\"text-align: justify\"><span>The first step in formation of a transcription complex is the binding of a general transcription factors<\/span><span>\u00a0called TFIID to the TATA box.TFIID is itself composed of multiple subunits,\u00a0 including the TATA binding protein . This binds specifically to the TATAA consensus sequence .and 10-12 other polypeptides, called <b>TBP-associated factors<\/b>\u00a0(<b>TAFs<\/b>). <\/span><\/li>\n<li style=\"text-align: justify\"><span>TBP then binds a second general transcription factor (TFIIB) forming a TBP-TFIIB complex at the along with TF II F at the promoter<\/span><\/li>\n<li style=\"text-align: justify\">Then RNA polymerase II binds<\/li>\n<li style=\"text-align: justify\">This is followed by the binding of <span>TFIIE and TFIIH. <\/span><\/li>\n<li style=\"text-align: justify\"><span>TFIIH is a multi subunit factor. It plays\u00a0 two important roles. First, two subunits of TFIIH are helicases, which unwind DNA\u00a0 around the initiation site. These subunits of TFIIH are also required for Nucleotide excision repair .Another subunit of TFIIH is a\u00a0 Protein kinase . This phosphorylates repeated sequences present in the C-terminal domain of the largest subunit of RNA polymerase II.\u00a0<\/span><\/li>\n<\/ul>\n<p><img decoding=\"async\" src=\"http:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Tanscritio-complex-assembly-and-binding-RNA-polymerase-II.jpeg\" alt=\"Transcription complex assembly and binding of RNA polymerase assembly\" width=\"544\" height=\"724\" class=\"aligncenter size-full wp-image-349\" srcset=\"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Tanscritio-complex-assembly-and-binding-RNA-polymerase-II.jpeg 544w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Tanscritio-complex-assembly-and-binding-RNA-polymerase-II-225x299.jpeg 225w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Tanscritio-complex-assembly-and-binding-RNA-polymerase-II-65x87.jpeg 65w, https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-content\/uploads\/sites\/17\/2023\/03\/Tanscritio-complex-assembly-and-binding-RNA-polymerase-II-350x466.jpeg 350w\" sizes=\"(max-width: 544px) 100vw, 544px\" \/><\/p>\n<p style=\"text-align: center\"><span style=\"color: #993366;background-color: #ffffff\">&#8220;Eukaryotic Transcription Initiation&#8221; image from the book <a href=\"https:\/\/bio.libretexts.org\/Bookshelves\/Introductory_and_General_Biology\/Book%3A_General_Biology_%28Boundless%29\/15%3A_Genes_and_Proteins\/15.06%3A_Eukaryotic_Transcription_-_Initiation_of_Transcription_in_Eukaryotes\" style=\"background-color: #ffffff\">General Biology (Boundless) <\/a>licensed under\u00a0<a href=\"http:\/\/creativecommons.org\/licenses\/by-sa\/4.0\" target=\"_blank\" rel=\"noopener\" style=\"color: #993366;background-color: #ffffff\">CC BY-SA 4.0<\/a><\/span><\/p>\n<ul>\n<li style=\"text-align: justify\"><span>Once the complex is assembled, RNA polymerase can bind to its upstream sequence. <\/span><\/li>\n<li style=\"text-align: justify\"><span>When bound along with the transcription factors, RNA polymerase is phosphorylated. This releases part of the protein from the DNA .\u00a0 The transcription initiation complex\u00a0 gets activated and places RNA polymerase in the correct orientation to begin transcription.<\/span><\/li>\n<li style=\"text-align: justify\"><span>Then the double-stranded DNA in the transcription start region\u00a0 is unwound . The RNA Polymerase II is then\u00a0 positioned at the +1 initiation nucleotide and starts new RNA strand synthesis.<\/span><\/li>\n<\/ul>\n<div class=\"glossary\"><span class=\"screen-reader-text\" id=\"definition\">definition<\/span><template id=\"term_329_934\"><div class=\"glossary__definition\" role=\"dialog\" data-id=\"term_329_934\"><div tabindex=\"-1\"><p>These are binding sequences for transcription factors and may be located upstream or down stream of transcription start site <\/p>\n<\/div><button><span aria-hidden=\"true\">&times;<\/span><span class=\"screen-reader-text\">Close definition<\/span><\/button><\/div><\/template><\/div>","protected":false},"author":5,"menu_order":15,"template":"","meta":{"om_disable_all_campaigns":false,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"pb_show_title":"on","pb_short_title":"Initiation of Transcription by RNA Polymerase II","pb_subtitle":"Initiation of Transcription by RNA Polymerase II","pb_authors":["dr-v-malathi"],"pb_section_license":"cc-by-sa"},"chapter-type":[],"contributor":[61],"license":[54],"class_list":["post-329","chapter","type-chapter","status-publish","hentry","contributor-dr-v-malathi","license-cc-by-sa"],"aioseo_notices":[],"part":3,"_links":{"self":[{"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/chapters\/329","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/chapters"}],"about":[{"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/wp\/v2\/types\/chapter"}],"author":[{"embeddable":true,"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/wp\/v2\/users\/5"}],"version-history":[{"count":46,"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/chapters\/329\/revisions"}],"predecessor-version":[{"id":1102,"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/chapters\/329\/revisions\/1102"}],"part":[{"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/parts\/3"}],"metadata":[{"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/chapters\/329\/metadata\/"}],"wp:attachment":[{"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/wp\/v2\/media?parent=329"}],"wp:term":[{"taxonomy":"chapter-type","embeddable":true,"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/pressbooks\/v2\/chapter-type?post=329"},{"taxonomy":"contributor","embeddable":true,"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/wp\/v2\/contributor?post=329"},{"taxonomy":"license","embeddable":true,"href":"https:\/\/pressbooks.justwrite.in\/understanding-gene-regulation\/wp-json\/wp\/v2\/license?post=329"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}