{"id":10,"date":"2019-10-03T21:38:44","date_gmt":"2019-10-03T20:38:44","guid":{"rendered":"http:\/\/theakaylab.com\/?page_id=10"},"modified":"2023-05-25T10:46:48","modified_gmt":"2023-05-25T09:46:48","slug":"science","status":"publish","type":"page","link":"https:\/\/theakaylab.com\/?page_id=10","title":{"rendered":"Science"},"content":{"rendered":"\n<p>We study <strong>RNA modifications<\/strong>, <strong>RNA splicing<\/strong>, <strong>long non-coding RNAs<\/strong> and <strong>regulation of gene expression<\/strong> during germline development in animals.<\/p>\n\n\n\n<p>During development, cells constantly face a decision between cell division and differentiation. Regulation of gene expression is key to this decision-making process. RNA is at the centre of many gene regulatory processes. We try to understand how different RNA-mediated mechanisms regulate gene expression during germ cell proliferation and differentiation.<\/p>\n\n\n\n<p>There are more than 150 distinct chemical modifications found on RNA. RNA modifications control the processing, stability, expression and function of diverse types of RNAs. <\/p>\n\n\n\n<p><strong>RNA modifications<\/strong><\/p>\n\n\n\n<p>For the majority of RNA modifications, we don&#8217;t know their biological role in multicellular organisms. We use a combination of genetic and biochemical tools to study the function of RNA-modifying enzymes and RNA modifications during animal development.<\/p>\n\n\n\n<p><strong>RNA splicing<\/strong><\/p>\n\n\n\n<p> RNA splicing is generally known to remove intronic sequences and ligate exons to preserve accurate expression of both coding and non-coding genes. In addition, many organisms change the 5&#8242; end of their mRNAs using SL trans-splicing. We study how RNA modifications and splicing factors regulate both cis- and trans-splicing mechanisms during germline development.<\/p>\n\n\n\n<p><strong>Metabolic regulation of gene expression<\/strong><\/p>\n\n\n\n<p>Dietary metabolites are required for a large number of cellular processes. Among these, vitamin B12 is essential for the cellular regeneration of S-adenosyl methionine (SAM). All methyltransferase enzymes use SAM during methylation reactions. We are studying how changing SAM levels in an organism affects gene expression and cellular methylations.<\/p>\n\n\n\n<p>In the lab, we use a wide range of techniques<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMs) to quantify RNA modifications<\/li>\n\n\n\n<li>Oxford Nanopore Direct RNA Sequencing to detect modified RNAs<\/li>\n\n\n\n<li>Genetics and CRISPR\/Cas9 genome editing to generate mutants and transgenes<\/li>\n\n\n\n<li>In vivo and in vitro assays to analyse RNA splicing. modification and gene expression<\/li>\n\n\n\n<li>Confocal microscopy for co-localisation and gene expression<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<p>We use the nematode Caenorhabditis elegans as a discovery organism. The germline development of <em>C. elegans<\/em> provides an ideal model system to study the role of RNA modifications and RNA modifying enzymes, RNA splicing and gene expression during cell proliferation and differentiation. In addition to <em>C. elegans<\/em>, we use bacteria and yeast for various techniques.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>We study RNA modifications, RNA splicing, long non-coding RNAs and regulation of gene expression during germline development in animals. During development, cells constantly face a decision between cell division and differentiation. Regulation of gene expression is key to this decision-making process. RNA is at the centre of many gene regulatory processes. We try to understand [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-10","page","type-page","status-publish","hentry"],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false},"uagb_author_info":{"display_name":"aalper","author_link":"https:\/\/theakaylab.com\/?author=1"},"uagb_comment_info":0,"uagb_excerpt":"We study RNA modifications, RNA splicing, long non-coding RNAs and regulation of gene expression during germline development in animals. During development, cells constantly face a decision between cell division and differentiation. Regulation of gene expression is key to this decision-making process. RNA is at the centre of many gene regulatory processes. We try to understand&hellip;","_links":{"self":[{"href":"https:\/\/theakaylab.com\/index.php?rest_route=\/wp\/v2\/pages\/10","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/theakaylab.com\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/theakaylab.com\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/theakaylab.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/theakaylab.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=10"}],"version-history":[{"count":3,"href":"https:\/\/theakaylab.com\/index.php?rest_route=\/wp\/v2\/pages\/10\/revisions"}],"predecessor-version":[{"id":296,"href":"https:\/\/theakaylab.com\/index.php?rest_route=\/wp\/v2\/pages\/10\/revisions\/296"}],"wp:attachment":[{"href":"https:\/\/theakaylab.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}