{"id":11914,"date":"2019-07-03T21:34:49","date_gmt":"2019-07-04T01:34:49","guid":{"rendered":"https:\/\/biology.mit.edu\/?page_id=11914"},"modified":"2022-02-25T15:09:01","modified_gmt":"2022-02-25T20:09:01","slug":"profile-emma-kowal","status":"publish","type":"page","link":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/","title":{"rendered":"Profile: Emma Kowal"},"content":{"rendered":"

Junk DNA makes a comeback<\/strong><\/h2>\n

\"\"<\/p>\n

Third-year graduate student Emma Kowal is searching DNA for sequences that regulate gene expression.<\/h3>\n

Saima Sidik<\/h4>\n

 <\/p>\n

\u201cI went into science because of a certain obsession with the romance of it,\u201d says Emma Kowal<\/a>, a third-year graduate student in Chris Burge\u2019s<\/a> lab in the MIT Department of Biology. \u201cI loved the idea of the scientist as an adventurer exploring the frontiers of knowledge and the universe. And I haven\u2019t let go of that yet.\u201d<\/p>\n

Kowal has always been an avid science fiction reader, and now she\u2019s living out a real-life scientific odyssey. The quest she\u2019s taken on for her PhD research involves an understudied type of DNA sequence called an intron, and the roles that introns might play in regulating gene expression.<\/p>\n

Introns lie between the DNA sequences that cells use for protein production, and are initially incorporated into the messenger RNA, or mRNA, that cells produce as an intermediate step in synthesizing proteins from DNA. But before they complete protein synthesis, cells remove introns from mRNA through a process called splicing, which has led many people to view introns as junk DNA with splicing acting like a garbage disposal.<\/p>\n

\u201cIntrons appeal to me as the underdog genomic region,\u201d Kowal says. Although they\u2019re often seen as unimportant, introns are ubiquitous and plentiful, collectively making up 24% of the human genome. All eukaryotes have them, and, on average, each human gene encodes eight<\/a>. Many researchers, including Kowal, think that introns have been underestimated, and that they may play an important role in regulating gene expression.<\/p>\n

Introns are only the latest chapter in Kowal\u2019s RNA story. She began her research career as a Harvard University undergraduate student working in the Szostak Lab<\/a> at Massachusetts General Hospital, where she studied how RNA catalyzed the evolution of cells on the early earth. Although studying primordial life was intellectually stimulating, Kowal wanted to work on something more applied, and so she joined the Church Lab<\/a> in the Harvard Department of Genetics. There she developed methods<\/a> for purifying and imaging<\/a> enigmatic RNA-containing lipid compartments called extracellular vesicles, which cells release into their surrounding environments possibly to communicate with one another.<\/p>\n

\"Person<\/p>\n

For the sequel to her bachelor\u2019s degree, Kowal chose to attend MIT Biology because she\u2019d heard that, \u201cat MIT, everyone is one standard deviation nerdier, on average, than they are at other schools.\u201d In this sense, she has not been disappointed. Kowal calls the energy at MIT \u201cunparalleled,\u201d and she says, \u201cpeople are jazzed about what they\u2019re doing, and the whole campus reflects that.\u201d<\/p>\n

In some ways, these reflections are physical. Much of the artwork around MIT pays homage to major scientific discoveries, and Kowal says this reverence for science is one factor that attracted her to MIT. From the mural of DNA in the Biology Department to the golden neurons that descend alongside the staircase in the McGovern Institute for Brain Research, it\u2019s as if the community is saying, \u201clook at how awesome the universe is!\u201d as Kowal puts it.<\/p>\n

In other ways, this energy is reflected in the people she converses with daily. \u201cI really like the students here,\u201d Kowal says. \u201cEveryone is enthusiastic, but also down to earth.\u201d When she\u2019s not exploring the realms of science, Kowal sometimes has more fanciful adventures with the Dungeons and Dragons group that she\u2019s formed with some of her classmates.<\/p>\n

Kowal didn\u2019t necessarily intend to continue working on RNA at MIT Biology, but when she heard about Chris Burge\u2019s lab<\/a>, which focuses on RNA and the proteins that mediate its production and stability, she felt a call to action.<\/p>\n

The Burge Lab combines high throughput experimental techniques with bioinformatics, and Kowal wants to develop expertise in both these fields. \u201cIf you\u2019re skilled in generating and analyzing big data sets, you can ask questions that other people can\u2019t,\u201d she says. The Burge lab seemed like the perfect setting for her PhD.<\/p>\n

\"Illustration
Adding an intron to a gene can boost its expression in many different ways. Credit: Emma Kowal.<\/figcaption><\/figure>\n

Burge asks his students to begin their degrees with a month-long reading period during which they sift through the literature to find a topic that they want to study. \u201cYou\u2019re not allowed to pick up a pipette or do any analysis during your reading period,\u201d Kowal says. \u201cYou just read and discuss your ideas and let things percolate.\u201d As she read, Kowal came across a number of studies that discussed the influence that introns have on gene expression levels.<\/p>\n

Over and over, scientists have noticed that cells produce more protein from genes that contain introns than when those same introns are removed. Intron mediated enhancement<\/a> (IME), as this effect is called, is a \u201cstunningly broad phenomenon,\u201d Kowal says, and scientists have observed it in a wide range of organisms, from yeast to plants to humans.<\/p>\n

Splicing machinery, which removes introns from mRNA, likely plays a role in IME. This machinery binds mRNA as it\u2019s being produced from DNA, then interacts with, and influences, the RNA production machinery. However, researchers have created mutant introns that can\u2019t be recognized by splicing machinery, and sometimes these introns still enhance gene expression, so splicing isn\u2019t the only factor that drives IME. Moreover, replacing one intron with another of the same size containing a different DNA sequence can change its effect, implying that the exact DNA sequences within introns may dictate their effects on gene expression. Kowal is intrigued by this last point, and wants to find these intronic sequences and figure out which have the largest effects on gene expression and why.<\/p>\n

\u201cThis is an old mystery that\u2019s ripe for new tools,\u201d Kowal says. Over the last decade, researchers have begun using a technique called RNAseq to count the copies of mRNA that are made from each gene in a population of cells. Instead of replacing an intron with a single alternative DNA sequence, Kowal plans to replace an intron with a myriad of random DNA sequences, then use RNAseq to count how many copies of mRNA cells make when they encode each of these random introns.<\/p>\n

Preparing to test these random sequences has been an odyssey in and of itself, and Kowal has spent the last year building the system that she\u2019ll use. First, she needed to decide which intron to replace. She chose one from a gene called UbC<\/em><\/a>. Removing this intron reduces expression of UbC<\/em> by ten-fold.<\/p>\n

Besides contributing strongly to IME, the UbC<\/em> intron is a great candidate for Kowal\u2019s experiment because it lies in a regulatory region of the UbC<\/em> mRNA that precedes the portion that\u2019s translated into protein. This let her replace the UbC<\/em> protein coding region with a fluorescent protein that she\u2019ll use to visualize how much protein cells make when they encode each random intron sequence.<\/p>\n

\"Person
Kowal on a climbing trip in Red River Gorge, Kentucky. Credit: Max Lenail.<\/figcaption><\/figure>\n

Kowal has spent the last year meticulously incorporating a library of random introns into this synthetic version of the UbC<\/em> gene. She anticipates being able to introduce them into cells soon, to see which random introns result in the highest levels of mRNA and protein production. Thanks to RNAseq, she\u2019ll be able to monitor how much each random intron contributes to mRNA expression. Because she can measure how brightly the fluorescent protein glows, she can correlate these mRNA levels with protein levels. From this, she\u2019ll learn which intron sequences enhance gene expression most strongly, and she\u2019ll also know whether these introns lead to higher levels of mRNA production, or if the same amount of mRNA is made into more protein. This distinction will offer her clues about the mechanism that introns use to enhance gene expression.<\/p>\n

Once Kowal knows which intron sequences promote gene expression most effectively, she\u2019ll take advantage of the Burge lab\u2019s bioinformatics expertise to analyze the distribution of these sequences throughout genomes and predict how they affect global gene expression. Kowal suspects certain intron sequences are bound by proteins that mediate mRNA production and stability, and she thinks her work will identify these protein-intron pairs.<\/p>\n

Kowal balances her scientific adventures with outdoor adventures. Specifically, she\u2019s recently fallen in love with rock climbing. \u201cClimbing is a great counterpart to science because it\u2019s something you can chip away at, and then there\u2019s this huge satisfaction when you finally achieve a climb,\u201d she says. \u201cAnd also, between climbing and pipetting, I have really strong fingers.\u201d<\/p>\n

As for her love of science fiction, Kowal hopes to one day pen a science-based adventure of her own, but not before she\u2019s made her mark as a scientist, either as a professor or in industry. \u201dIt makes sense for me to focus most of my energy on science right now,\u201d she says. \u201cBut after I\u2019ve led a spectacular, adventurous life in science, maybe I\u2019ll use my reflections to write a novel.\u201d<\/p>\n

Photo credit: Raleigh McElvery (top photo); Saima Sidik (second photo)
\nPosted 7.8.19<\/h5>\n

Why MIT Biology?<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Junk DNA makes a comeback Third-year graduate student Emma Kowal is searching DNA for sequences that regulate gene expression. Saima Sidik   \u201cI went into science because of a certain obsession with the romance of it,\u201d says Emma Kowal, a third-year graduate student in Chris Burge\u2019s lab in the MIT Department of Biology. \u201cI loved […]<\/p>\n","protected":false},"author":16,"featured_media":0,"parent":1247,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-11914","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"\nProfile: Emma Kowal - MIT Department of Biology<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Profile: Emma Kowal\" \/>\n<meta property=\"og:description\" content=\"Junk DNA makes a comeback Third-year graduate student Emma Kowal is searching DNA for sequences that regulate gene expression. Saima Sidik   \u201cI went into science because of a certain obsession with the romance of it,\u201d says Emma Kowal, a third-year graduate student in Chris Burge\u2019s lab in the MIT Department of Biology. \u201cI loved […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/\" \/>\n<meta property=\"og:site_name\" content=\"MIT Department of Biology\" \/>\n<meta property=\"article:modified_time\" content=\"2022-02-25T20:09:01+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A-300x150.jpg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"8 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/\",\"url\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/\",\"name\":\"Profile: Emma Kowal - MIT Department of Biology\",\"isPartOf\":{\"@id\":\"https:\/\/biology.mit.edu\/#website\"},\"primaryImageOfPage\":{\"@id\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#primaryimage\"},\"image\":{\"@id\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A-300x150.jpg\",\"datePublished\":\"2019-07-04T01:34:49+00:00\",\"dateModified\":\"2022-02-25T20:09:01+00:00\",\"breadcrumb\":{\"@id\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#breadcrumb\"},\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"ReadAction\",\"target\":[\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/\"]}]},{\"@type\":\"ImageObject\",\"inLanguage\":\"en-US\",\"@id\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#primaryimage\",\"url\":\"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A.jpg\",\"contentUrl\":\"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A.jpg\",\"width\":1400,\"height\":701,\"caption\":\"Person smiling and leaning on wall\"},{\"@type\":\"BreadcrumbList\",\"@id\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#breadcrumb\",\"itemListElement\":[{\"@type\":\"ListItem\",\"position\":1,\"name\":\"Home\",\"item\":\"https:\/\/biology.mit.edu\/\"},{\"@type\":\"ListItem\",\"position\":2,\"name\":\"Graduate\",\"item\":\"https:\/\/biology.mit.edu\/graduate\/\"},{\"@type\":\"ListItem\",\"position\":3,\"name\":\"Why MIT Biology?\",\"item\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/\"},{\"@type\":\"ListItem\",\"position\":4,\"name\":\"Graduate Testimonials\",\"item\":\"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/\"},{\"@type\":\"ListItem\",\"position\":5,\"name\":\"Profile: Emma Kowal\"}]},{\"@type\":\"WebSite\",\"@id\":\"https:\/\/biology.mit.edu\/#website\",\"url\":\"https:\/\/biology.mit.edu\/\",\"name\":\"MIT Department of Biology\",\"description\":\"\",\"potentialAction\":[{\"@type\":\"SearchAction\",\"target\":{\"@type\":\"EntryPoint\",\"urlTemplate\":\"https:\/\/biology.mit.edu\/?s={search_term_string}\"},\"query-input\":\"required name=search_term_string\"}],\"inLanguage\":\"en-US\"}]}<\/script>\n","yoast_head_json":{"title":"Profile: Emma Kowal - MIT Department of Biology","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/","og_locale":"en_US","og_type":"article","og_title":"Profile: Emma Kowal","og_description":"Junk DNA makes a comeback Third-year graduate student Emma Kowal is searching DNA for sequences that regulate gene expression. Saima Sidik   \u201cI went into science because of a certain obsession with the romance of it,\u201d says Emma Kowal, a third-year graduate student in Chris Burge\u2019s lab in the MIT Department of Biology. \u201cI loved […]","og_url":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/","og_site_name":"MIT Department of Biology","article_modified_time":"2022-02-25T20:09:01+00:00","og_image":[{"url":"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A-300x150.jpg"}],"twitter_card":"summary_large_image","twitter_misc":{"Est. reading time":"8 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/","url":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/","name":"Profile: Emma Kowal - MIT Department of Biology","isPartOf":{"@id":"https:\/\/biology.mit.edu\/#website"},"primaryImageOfPage":{"@id":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#primaryimage"},"image":{"@id":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#primaryimage"},"thumbnailUrl":"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A-300x150.jpg","datePublished":"2019-07-04T01:34:49+00:00","dateModified":"2022-02-25T20:09:01+00:00","breadcrumb":{"@id":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/"]}]},{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#primaryimage","url":"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A.jpg","contentUrl":"https:\/\/biology.mit.edu\/wp-content\/uploads\/2019\/07\/Emma_Kowal_A.jpg","width":1400,"height":701,"caption":"Person smiling and leaning on wall"},{"@type":"BreadcrumbList","@id":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/profile-emma-kowal\/#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/biology.mit.edu\/"},{"@type":"ListItem","position":2,"name":"Graduate","item":"https:\/\/biology.mit.edu\/graduate\/"},{"@type":"ListItem","position":3,"name":"Why MIT Biology?","item":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/"},{"@type":"ListItem","position":4,"name":"Graduate Testimonials","item":"https:\/\/biology.mit.edu\/graduate\/why-mit-biology\/graduate-testimonials\/"},{"@type":"ListItem","position":5,"name":"Profile: Emma Kowal"}]},{"@type":"WebSite","@id":"https:\/\/biology.mit.edu\/#website","url":"https:\/\/biology.mit.edu\/","name":"MIT Department of Biology","description":"","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/biology.mit.edu\/?s={search_term_string}"},"query-input":"required name=search_term_string"}],"inLanguage":"en-US"}]}},"_links":{"self":[{"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/pages\/11914"}],"collection":[{"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/users\/16"}],"replies":[{"embeddable":true,"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/comments?post=11914"}],"version-history":[{"count":44,"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/pages\/11914\/revisions"}],"predecessor-version":[{"id":23458,"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/pages\/11914\/revisions\/23458"}],"up":[{"embeddable":true,"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/pages\/1247"}],"wp:attachment":[{"href":"https:\/\/biology.mit.edu\/wp-json\/wp\/v2\/media?parent=11914"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}