Placement: Promote to Homepage
The McKnight Endowment Fund for Neuroscience has selected Whitehead Institute Member Siniša Hrvatin as one of ten early career scientists to receive a 2024 McKnight Scholar Award, supporting his research on mechanisms underlying certain animals’ capacity to enter states of torpor and hibernation.
Merrill Meadow | Whitehead Institute
June 20, 2024
Mary-Lou Pardue, Professor Emeritus of Biology, dies at 90
Lillian Eden | Department of Biology
June 17, 2024
Known for her rigorous approach to science and pioneering research, Pardue paved the way for women scientists at MIT and beyond
Mary-Lou Pardue, professor emerita in the Department of Biology, died on June 1, 2024. She was 90.
Early in her career, Pardue developed a technique called in situ hybridization with her PhD advisor Joseph Gall, which allows researchers to localize genes on chromosomes. This led to many discoveries, including critical advancements in developmental biology, our understanding of embryonic development, and the structure of chromosomes. She also studied the remarkably complex way organisms respond to stress, such as heat shock, and discovered how telomeres, the ends of chromosomes, in fruit flies differ from those of other eukaryotic organisms during cell division.
“The reason she was a professor at MIT and why she was doing research was first and foremost because she wanted to answer questions and make discoveries,” says longtime colleague and Professor Emerita Terry Orr-Weaver. “She had her feet cemented in a love of biology.”
In 1983, Pardue was the first woman in the School of Science at MIT to be inducted into the National Academy of Sciences. She served as Chairman for the Section of Genetics from 1991 to 1994 and as a Council Member from 1995 to 1998. Among other honors, she was named a Fellow of the American Academy of Arts and Sciences, where she served as a Council Member, and a Fellow of the American Association for the Advancement of Science. She also served on numerous editorial boards and review panels, and as the vice president, president, and chair of the Genetics Society of America and president of the American Society for Cell Biology.
Her graduate students and postdoctoral scholars included Alan Spradling, Matthew Scott, Tom Cech, Paul Lasko, and Joan Ruderman.
In the minority
Pardue was born on Sept. 15, 1933, in Lexington, Kentucky. She received a BS in Biology from the College of William and Mary in 1955, and she was awarded an MS in Radiation Biology from the University of Tennessee in 1959. In 1970, she was awarded a PhD in Biology for her work with Gall at Yale University.
As one of the senior women faculty who co-signed a letter to the Dean of Science at MIT about the bias against women scientists at the institute, Pardue’s career was inextricably linked to the slowly rising number of women with advanced degrees in science. During her early years as a graduate student at Yale, there were a few women with PhDs — but none held faculty positions. Indeed, Pardue assumed she would spend her career as a senior scientist working in someone else’s lab, rather than running her own.
Pardue was an avid hiker and loved to travel and spend time outdoors. She scaled peaks from the White Mountains to the Himalayas and pursued postdoctoral work in Europe at the University of Edinburgh. She was delighted to receive invitations to give faculty search seminars for the opportunity to travel to institutions across the U.S.—including an invitation to visit MIT.
MIT had initially rejected her job application, although the department quickly realized it had erred in missing the opportunity to recruit Pardue. In the end, she spent more than 30 years as a professor in Cambridge.
When Pardue joined, the department had two women faculty members, Lisa Steiner and Annamaria Torriani-Gorini — more women than at any other academic institution Pardue had interviewed. Pardue became an associate professor of Biology in 1972, a professor in 1980, and the Boris Magasanik Professor of Biology in 1995.
The person who made a difference
Pardue was known for her rigorous approach to science as well as her bright smile and support of others.
When Graham Walker, American Cancer Society and HHMI Professor, joined the department in 1976, he recalled an event for meeting graduate students at which he was repeatedly mistaken for a graduate student himself. Pardue parked herself by his side to bear the task of introducing the newest faculty member.
“Mary-Lou had an art for taking care of people,” Walker says. “She was a wonderful colleague and a close friend.”
Troy Littleton, Professor of Biology, Menicon Professor of Neuroscience, and Investigator at the Picower Institute for Learning and Memory — then a young faculty member — had his first experience teaching with Pardue for an undergraduate project lab course.
“Observing how Mary-Lou was able to get the students excited about basic research was instrumental in shaping my teaching skills,” Littleton says. “Her passion for discovery was infectious, and the students loved working on basic research questions under her guidance.”
She was also a mentor for fellow women joining the department, including E.C. Whitehead Professor of Biology and HHMI investigator Tania A. Baker, who joined the department in 1992, and Orr-Weaver, the first female faculty member to join the Whitehead Institute in 1987.
“She was seriously respected as a woman scientist—as a scientist,” recalls Nancy Hopkins, Amgen Professor of Biology Emerita. “For women of our generation, there were no role models ahead of us, and so to see that somebody could do it, and have that kind of respect, was really inspiring.”
Hopkins first encountered Pardue’s work on in situ hybridization as a graduate student. Although it wasn’t Hopkins’ field, she remembers being struck by the implications — a leap in science that today could be compared to the discoveries that are possible because of the applications of gene-editing CRISPR technology.
“The questions were very big, but the technology was small,” Hopkins says. “That you could actually do these kinds of things was kind of a miracle.”
Pardue was the person who called to give Hopkins the news that she had been elected to the National Academy of Sciences. They hadn’t worked together, yet, but Hopkins felt like Pardue had been looking out for her, and was so excited on her behalf.
Later, though, Hopkins was initially hesitant to reach out to Pardue to discuss the discrimination Hopkins had experienced as a faculty member at MIT — Pardue seemed so successful that surely her gender had not held her back. Hopkins found that women, in general, didn’t discuss the ways they had been undervalued; it was humiliating to admit to being treated unfairly.
Hopkins drafted a letter about the systemic and invisible discrimination she had experienced — but Hopkins, ever the scientist, needed a reviewer.
At a table in the corner of Rebecca’s Café, a now-defunct eatery, Pardue read the letter — and declared she’d like to sign it and take it to the Dean of the School of Science.
“I knew the world had changed in that instant,” Hopkins says. “She’s the person who made the difference. She changed my life, and changed, in the end, MIT.”
MIT and the status of women
It was only when some of the tenured women faculty of the School of Science all came together that they discovered their experiences were similar. Hopkins, Pardue, Orr-Weaver, Steiner, Susan Carey, Sylvia Ceyer, Sallie “Penny” Chisholm, Suzanne Corkin, Mildred Dresselhaus, Ann Graybiel, Ruth Lehmann, Marcia McNutt, Molly Potter, Paula Malanotte-Rizzoli, Leigh Royden, and Joanne Stubbe ultimately signed a letter to Robert Birgeneau, then the Dean of Science.
Their efforts led to a Committee on the Status of Women Faculty in 1995, the report for which was made public in 1999. The report captured pervasive bias against women across the School of Science. In response, MIT ultimately worked to improve the working conditions of women scientists across the institute. These efforts reverberated at academic institutions across the country.
Walker notes that creating real change requires a monumental effort of political and societal pressure — but it also requires outstanding individuals whose work surpasses the barriers holding them back.
“When Mary-Lou came to MIT, there weren’t many cracks in the glass ceiling,” he says. “I think she, in many ways, was a leader in helping to change the status of women in science by just being who she was.”
Later years
Kerry Kelley, now a research laboratory operations manager in the Yilmaz Lab at the Koch Institute for Integrative Cancer Research, joined Pardue as a technical lab assistant in 2008, Kelley’s first job at MIT. Pardue, throughout her career, was committed to hands-on work, preparing her own slides whenever possible.
“One of the biggest things I learned from her was mistakes aren’t always mistakes. If you do an experiment, and it doesn’t turn out the way you had hoped, there’s something there that you can learn from,” Kelley says. She recalls a frequent refrain with a smile: “‘It’s research. What do you do? Re-search.’”
Their birthdays were on consecutive days in September; Pardue would mark the occasion for both at Legal Seafoods in Kendall Square with Bluefish, white wine, and lab members and collaborators including Kelley, Karen Traverse, and the late Paul Gregory DeBaryshe.
In the years before her death, Pardue resided at Youville House Assisted Living in Cambridge, where Kelley would often visit.
“I was sad to hear of the passing of Mary-Lou, whose seminal work expanded our understanding of chromosome structure and cellular responses to environmental stresses over more than three decades at MIT. Mary-Lou was an exceptional person who was known as a gracious mentor and a valued teacher and colleague,” says Biology Department Head and Jay A. Stein (1968) Professor of Biology and Professor of Biological Engineering Amy Keating. “She was kind to everyone, and she is missed by our faculty and staff. Women at MIT and beyond, including me, owe a huge debt to Mary-Lou, Nancy Hopkins, and their colleagues who so profoundly advanced opportunities for women in science.”
She is survived by a niece and nephew, Todd Pardue and Sarah Gibson.
Creating the Crossroads
Lillian Eden | Department of Biology
June 13, 2024
From academia to industry, at the intersection of computation, biology, and physics, Gevorg Grigoryan, PhD ’07, says there is no right path–just the path that works for you
A few years ago, Gevorg Grigoryan, PhD ‘07, then a professor at Dartmouth, had been pondering an idea for data-driven protein design for therapeutic applications. Unsure how to move forward with launching that concept into a company, he dug up an old syllabus from an entrepreneurship course he took during his PhD at MIT and decided to email the instructor for the class.
He labored over the email for hours. It went from a few sentences to three pages, then back to a few sentences. Grigoryan finally hit send in the wee hours of the morning.
Just 15 minutes later, he received a response from Noubar Afeyan, PhD ’87, the CEO and co-founder of venture capital company Flagship Pioneering (and the commencement speaker for the 2024 OneMIT Ceremony)
That ultimately led to Grigoryan, Afeyan, and others co-founding Generate:Biomedicines, where Grigoryan now serves as CTO.
“Success is defined by who is evaluating you,” Grigoryan says. “There is no right path—the best path for you is the one that works for you.”
Generalizing Principles and Improving Lives
Generate:Biomedicines is the culmination of decades of advancements in machine learning, biological engineering, and medicine. Until recently, de novo design of a protein was extremely labor intensive, requiring months or years of computational methods and experiments.
“Now, we can just push a button and have a generative model spit out a new protein with close to perfect probability it will actually work. It will fold. It will have the structure you’re intending,” Grigoryan says. “I think we’ve unearthed these generalizable principles for how to approach understanding complex systems, and I think it’s going to keep working.”
Drug development was an obvious application for his work early on. Grigoryan says part of the reason he left academia—at least for now—are the resources available for this cutting-edge work.
“Our space has a rather exciting and noble reason for existing,” he says. “We’re looking to improve human lives.”
Mixing Disciplines
Mixed-discipline STEM majors are increasingly common, but when Grigoryan was an undergraduate at the University of Maryland Baltimore County, little to no infrastructure existed for such an education.
“There was this emerging intersection between physics, biology, and computational sciences,” Grigoryan recalls. “It wasn’t like there was this robust discipline at the intersection of those things—but I felt like there could be, and maybe I could be part of creating one.”
He majored in Biochemistry and Computer Science, much to the confusion of his advisors for each major. This was so unprecedented that there wasn’t even guidance for which group he should walk with at graduation.
Heading to Cambridge
Grigoryan admits his decision to attend MIT in the Department of Biology wasn’t systematic.
“I was like ‘MIT sounds great, strong faculty, good techie school, good city. I’m sure I’ll figure something out,’” he says. “I can’t emphasize enough how important and formative those years at MIT were to who I ultimately became as a scientist.”
He worked with Amy Keating, then a junior faculty member, now Department Head for the Department of Biology, modeling protein-protein interactions. The work involved physics, math, chemistry, and biology. The Computational and Systems Biology PhD program was still a few years away, but the developing field was being recognized as important.
Keating remains an advisor and confidant to this day. Grigoryan also commends her for her commitment to mentoring while balancing the demands of a faculty position—acquiring funding, running a research lab, and teaching.
“It’s hard to make time to truly advise and help your students grow, but Amy is someone who took it very seriously and was very intentional about it,” Grigoryan says. “We spent a lot of time discussing ideas and doing science. The kind of impact that one can have through mentorship is hard to overestimate.”
Grigoryan next pursued a postdoc at UPenn with William “Bill” DeGrado, continuing to focus on protein design while gaining more experience in experimental approaches and exposure to thinking about proteins differently.
Just by examining them, DeGrado had an intuitive understanding of molecules—anticipating their functionality or what mutations would disrupt that functionality. His predictive skill surpassed the abilities of computer modeling at the time.
Grigoryan began to wonder: could computational models use prior observations to be at least as predictive as someone who spent a lot of time considering and observing the structure and function of those molecules?
Grigoryan next went to Dartmouth for a faculty position in computer science with cross-appointments in biology and chemistry to explore that question.
Balancing Industry and Academia
Much of science is about trial and error, but early on, Grigoryan showed that accurate predictions of proteins and how they would bind, bond, and behave didn’t require starting from first principles. Models became more accurate by solving more structures and taking more binding measurements.
Grigoryan credits the leaders at Flagship Pioneering for their initial confidence in the possible applications for this concept—more bullish, at the time, than Grigoryan himself.
He spent four years splitting his time between Dartmouth and Cambridge and ultimately decided to leave academia altogether.
“It was inevitable because I was just so in love with what we had built at Generate,” he says. “It was so exciting for me to see this idea come to fruition.”
Pause or Grow
Grigoryan says the most important thing for a company is to scale at the right time, to balance “hitting the iron while it’s hot” while considering the readiness of the company, the technology, and the market.
But even successful growth creates its own challenges.
When there are fewer than two dozen people, aligning strategies across a company is straightforward: everyone can be in the room. However, growth—say, expanding to 200 employees—requires more deliberate communication and balancing agility while maintaining the company’s culture and identity.
“Growing is tough,” he says. “And it takes a lot of intentional effort, time, and energy to ensure a transparent culture that allows the team to thrive.”
Grigoryan’s time in academia was invaluable for learning that “everything is about people”—but academia and industry require different mindsets.
“Being a PI is about creating a lane for each of your trainees, where they’re essentially somewhat independent scientists,” he says. “In a company, by construction, you are bound by a set of common goals, and you have to value your work by the amount of synergy that it has with others, as opposed to what you can do only by yourself.”
The International Society for Transgenic Technologies recognized Whitehead Institute Founding Member Rudolf Jaenisch for his exceptional contribution to the field of animal transgenesis over the past five decades.
Merrill Meadow | Whitehead Institute
June 11, 2024
Second annual assembly, sponsored by the Department of Biology and Picower Institute, invited postdocs from across the country to meet with faculty, present their work to the MIT community, and build relationships.
Lillian Eden | Department of Biology
June 10, 2024
For science — and the scientists who practice it — to succeed, research must be shared. That’s why members of the MIT community recently gathered to learn about the research of eight postdocs from across the country for the second annual Catalyst Symposium, an event co-sponsored by the Department of Biology and The Picower Institute for Learning and Memory.
The eight Catalyst Fellows came to campus as part of an effort to increase engagement between MIT scholars and postdocs excelling in their respective fields from traditionally underrepresented backgrounds in science. The three-day symposium included panel discussions with faculty and postdocs, one-on-one meetings, social events, and research talks from the Catalyst Fellows.
“I love the name of this symposium because we’re all, of course, eager to catalyze advancements in our professional lives, in science, and to move forward faster by lowering activation barriers,” says MIT biology department head Amy Keating. “I feel we can’t afford to do science with only part of the talent pool, and I don’t think people can do their best work when they are worried about whether they belong.”
The 2024 Catalyst Fellows include Chloé Baron from Boston Children’s Hospital; Maria Cecília Canesso from The Rockefeller University; Kiara Eldred from the University of Washington School of Medicine; Caitlin Kowalski from the University of Oregon; Fabián Morales-Polanco from Stanford University; Kali Pruss from the Washington University School of Medicine in St. Louis; Rodrigo Romero from Memorial Sloan Kettering Cancer Center; and Zuri Sullivan from Harvard University.
Romero, who received his PhD from MIT working in the Jacks Lab at the Koch Institute, said that it was “incredible to see so many familiar faces,” but he spent the symposium lunch chatting with new students in his old lab.
“Especially having been trained to think differently after MIT, I can now reach out to people that I didn’t as a graduate student, and make connections that I didn’t think about before,” Romero says.
He presented his work on lineage plasticity in the tumor microenvironment. Lineage plasticity is a hallmark of tumor progression but also occurs during normal development, such as wound healing.
As for the general mission of the symposium, Romero agrees with Keating.
“Trying to lower the boundary for other people to actually have a chance to do academic research in the future is important,” Romero says.
The Catalyst Symposium is aimed at early-career scientists who foresee a path in academia. Of the 2023 Catalyst Fellows, one has already secured a faculty position. Starting this September, Shan Maltzer will be an assistant professor at Vanderbilt University in the Department of Pharmacology and the Vanderbilt Brain Institute studying mechanisms of somatosensory circuit assembly, development, and function.
Another aim of the Catalyst Symposium is to facilitate collaborations and strengthen existing relationships. Sullivan, an immunologist and molecular neuroscientist who presented on the interactions between the immune system and the brain, is collaborating with Sebastian Lourido, an associate professor of biology and core member of the Whitehead Institute for Biomedical Research. Lourido’s studies include pathogens such as Toxoplasma gondii, which is known to alter the behavior of infected rodents. In the long term, Sullivan hopes to bridge research in immunology and neuroscience — for instance by investigating how infection affects behavior. She has observed that two rodents experiencing illness will huddle together in a cage, whereas an unafflicted rodent and an ill one will generally avoid each other when sharing the same space.
Pruss presented research on the interactions between the gut microbiome and the environment, and how they may affect physiology and fetal development. Kowalski discussed the relationship between fungi residing on our bodies and human health. Beyond the opportunity to deliver talks, both agreed that the small group settings of the three-day event were rewarding.
“The opportunity to meet with faculty throughout the symposium has been invaluable, both for finding familiar faces and for establishing friendly relationships,” Pruss says. “You don’t have to try to catch them when you’re running past them in the hallway.”
Eldred, who studies cell fate in the human retina, says she was excited about the faculty panels because they allowed her to ask faculty about fundamental aspects of recruiting for their labs, like bringing in graduate students.
Kowalski also says she enjoyed interfacing with so many new ideas — the spread of scientific topics from among the cohort of speakers extended beyond those she usually interacts with.
Mike Laub, professor of biology and Howard Hughes Medical Institute investigator, and Yadira Soto-Feliciano, assistant professor of biology and intramural faculty at the Koch Institute for Integrative Cancer Research, were on the symposium’s planning committee, along with Diversity, Equity, and Inclusion Officer Hallie Dowling-Huppert. Laub hopes the symposium will continue to be offered annually; next year’s Catalyst Symposium is already scheduled to take place in early May.
“I thought this year’s Catalyst Symposium was another great success. The talks from the visiting fellows featured some amazing science from a wide range of fields,” Laub says. “I also think it’s fair to say that their interactions with the faculty, postdocs, and students here generated a lot of excitement and energy in our community, which is exactly what we hoped to accomplish with this symposium.”
New camera chip design allows for optimizing each pixel’s timing to maximize signal to noise ratio when tracking real-time visual indicator of neural voltage, described in a new paper from a team in the Wilson Lab published in Nature Communications.
David Orenstein | The Picower Institute for Learning and Memory
June 7, 2024
The Building 68 manager’s leadership, innovation, and laid-back attitude have helped to build a strong culture of community.
Samantha Edelen | Department of Biology
June 6, 2024
When you enter John Fucillo’s office at MIT, you will likely be greeted with an amiable nose boop and wagging tail from Shadow, a 4-year-old black lab, followed by a warm welcome from the office’s human occupant. Fucillo, manager of Building 68 — home to the MIT Department of Biology — is an animal lover, and Shadow is the gentlest of roughly nine dogs and one Siamese cat he’s taken care of throughout his life. Fortunately for the department, Shadow is not the only lab Fucillo cares for.
Fucillo came to MIT Biology in 1989 and says he couldn’t be happier. A Boston-area local, Fucillo previously spent two years working at Revere Beach, then learned skills as an auto mechanic, and later completed an apprenticeship with the International Brotherhood of Electrical Workers. As Building 68’s manager; environment, health, and safety coordinator; and chemical hygiene officer, Fucillo’s goal is to make workflows “easier, less expensive, more desirable, and more comfortable.” According to Mitchell Galanek, MIT radiation protection officer and Fucillo’s colleague for over 30 years, Fucillo was key for the department’s successful move into its new home when Building 68 was completed in 1994.
Throughout his time as a building manager, Fucillo has decreased routine spending and increased sustainability. He lowered the cost of lab coats by a whopping 92 percent — from $2,600 to $200 — with just one phone call to North Star, the building’s uniform/linens provider. Auditing the building’s plastic waste generation inspired the institute-wide MIT Lab Plastics Recycling Program, which now serves over 200 labs across campus. More than 50,000 pounds of plastic have been recycled in the last four years alone.
“John is not a cog in the wheel, but an integral part of the whole system,” says Anthony Fuccione, technical instructor and manager of the Biology Teaching lab.
Connecting and leading
Fucillo says one of his favorite parts of the job is chatting with researchers and helping them achieve their goals. He reportedly clocks about 10,000 steps per day on campus, responding to requests from labs, collaborating with colleagues, and connecting Biology to the Institute’s Environment, Health, and Safety (EHS) office.
“John is called upon — literally and figuratively — morning, noon, and night,” says Whitehead Professor of Molecular Genetics Monty Krieger. “He has had to become an expert in so very many areas to support staff, faculty, and students. His enormous success is due in part to his technical talents, in part to his genuine care for the welfare of his colleagues, and in part to his very special and caring personality.”
When MIT needed to comply with the Environmental Protection Agency’s decree to improve safety standards across campus, Fucillo sat on the committees tasked with meeting those standards while avoiding undue burden on researchers, establishing the Environmental Health and Safety Management system in 2002.
“From a safety perspective, that was one of the most challenging things MIT had to go through — but it came out at the end a better, safer, place,” says John Collins, EHS project technician and friend and colleague to Fucillo for over 20 years.
Fucillo later co-led the initiative for a 2011 overhaul of MIT’s management of regulated medical waste (RMW), such as Petri dishes, blood, and needles. Fucillo volunteered to pilot a new approach in Building 68 — despite a lukewarm response to the proposal from other biology EHS representatives, according to Galanek. This abundantly successful management system is now used by all MIT departments that generate RMW. It’s not only less expensive, but also does a better job at decontaminating waste than the previous management system.
“Anyone who has worked with John during his MIT career understands it is truly a privilege to partner with him,” Galanek says. “Not only does the work get done and done well, but you also gain a friend along the way.”
After consolidating a disparate group of individual lab assistants, Fucillo took on a supervisory role for the centralized staff tasked with cleaning glassware, preparing media, and ensuring consistency and sterility across Building 68 labs.
According to maintenance mechanic James (Jimmy) Carr, “you can’t find a better boss.”
“He’s just an easy-going guy,” says Karen O’Leary, who has worked with Fucillo for over 30 years. “My voice matters — I feel heard and respected by him.”
Looking forward
Although there are still many updates Fucillo hopes to see in Building 68, which will soon celebrate its 30th birthday, he is taking steps to cut back on his workload. He recently began passing on his knowledge to Facilities Manager and EHS Coordinator Cesar Duarte, who joined the department in 2023.
“It’s been a pleasure working alongside John and learning about the substantial role and responsibility he’s had in the biology department for the last three decades,” Duarte says. “Not only is John’s knowledge of Building 68 and the department’s history unparalleled, but his dedication to MIT and continued care and commitment to the health and well-being of the biology community throughout his career are truly remarkable.”
As he winds down his time at MIT, Fucillo hopes to spend more time on music, one of his earliest passions, which began when he picked up an accordion in first grade. He still plays guitar and bass nearly every day. When he rocks out at home more often, he’ll be leaving behind the foundations of innovation, leadership, and respect in Building 68.
By capturing short-lived RNA molecules, scientists can map relationships between genes and the regulatory elements that control them.
Anne Trafton | MIT News
June 5, 2024
The human genome contains about 23,000 genes, but only a fraction of those genes are turned on inside a cell at any given time. The complex network of regulatory elements that controls gene expression includes regions of the genome called enhancers, which are often located far from the genes that they regulate.
This distance can make it difficult to map the complex interactions between genes and enhancers. To overcome that, MIT researchers have invented a new technique that allows them to observe the timing of gene and enhancer activation in a cell. When a gene is turned on around the same time as a particular enhancer, it strongly suggests the enhancer is controlling that gene.
Learning more about which enhancers control which genes, in different types of cells, could help researchers identify potential drug targets for genetic disorders. Genomic studies have identified mutations in many non-protein-coding regions that are linked to a variety of diseases. Could these be unknown enhancers?
“When people start using genetic technology to identify regions of chromosomes that have disease information, most of those sites don’t correspond to genes. We suspect they correspond to these enhancers, which can be quite distant from a promoter, so it’s very important to be able to identify these enhancers,” says Phillip Sharp, an MIT Institute Professor Emeritus and member of MIT’s Koch Institute for Integrative Cancer Research.
Sharp is the senior author of the new study, which appears today in Nature. MIT Research Assistant D.B. Jay Mahat is the lead author of the paper.
Hunting for eRNA
Less than 2 percent of the human genome consists of protein-coding genes. The rest of the genome includes many elements that control when and how those genes are expressed. Enhancers, which are thought to turn genes on by coming into physical contact with gene promoter regions through transiently forming a complex, were discovered about 45 years ago.
More recently, in 2010, researchers discovered that these enhancers are transcribed into RNA molecules, known as enhancer RNA or eRNA. Scientists suspect that this transcription occurs when the enhancers are actively interacting with their target genes. This raised the possibility that measuring eRNA transcription levels could help researchers determine when an enhancer is active, as well as which genes it’s targeting.
“That information is extraordinarily important in understanding how development occurs, and in understanding how cancers change their regulatory programs and activate processes that lead to de-differentiation and metastatic growth,” Mahat says.
However, this kind of mapping has proven difficult to perform because eRNA is produced in very small quantities and does not last long in the cell. Additionally, eRNA lacks a modification known as a poly-A tail, which is the “hook” that most techniques use to pull RNA out of a cell.
One way to capture eRNA is to add a nucleotide to cells that halts transcription when incorporated into RNA. These nucleotides also contain a tag called biotin that can be used to fish the RNA out of a cell. However, this current technique only works on large pools of cells and doesn’t give information about individual cells.
While brainstorming ideas for new ways to capture eRNA, Mahat and Sharp considered using click chemistry, a technique that can be used to join two molecules together if they are each tagged with “click handles” that can react together.
The researchers designed nucleotides labeled with one click handle, and once these nucleotides are incorporated into growing eRNA strands, the strands can be fished out with a tag containing the complementary handle. This allowed the researchers to capture eRNA and then purify, amplify, and sequence it. Some RNA is lost at each step, but Mahat estimates that they can successfully pull out about 10 percent of the eRNA from a given cell.
Using this technique, the researchers obtained a snapshot of the enhancers and genes that are being actively transcribed at a given time in a cell.
“You want to be able to determine, in every cell, the activation of transcription from regulatory elements and from their corresponding gene. And this has to be done in a single cell because that’s where you can detect synchrony or asynchrony between regulatory elements and genes,” Mahat says.
Timing of gene expression
Demonstrating their technique in mouse embryonic stem cells, the researchers found that they could calculate approximately when a particular region starts to be transcribed, based on the length of the RNA strand and the speed of the polymerase (the enzyme responsible for transcription) — that is, how far the polymerase transcribes per second. This allowed them to determine which genes and enhancers were being transcribed around the same time.
The researchers used this approach to determine the timing of the expression of cell cycle genes in more detail than has previously been possible. They were also able to confirm several sets of known gene-enhancer pairs and generated a list of about 50,000 possible enhancer-gene pairs that they can now try to verify.
Learning which enhancers control which genes would prove valuable in developing new treatments for diseases with a genetic basis. Last year, the U.S. Food and Drug Administration approved the first gene therapy treatment for sickle cell anemia, which works by interfering with an enhancer that results in activation of a fetal globin gene, reducing the production of sickled blood cells.
The MIT team is now applying this approach to other types of cells, with a focus on autoimmune diseases. Working with researchers at Boston Children’s Hospital, they are exploring immune cell mutations that have been linked to lupus, many of which are found in non-coding regions of the genome.
“It’s not clear which genes are affected by these mutations, so we are beginning to tease apart the genes these putative enhancers might be regulating, and in what cell types these enhancers are active,” Mahat says. “This is a tool for creating gene-to-enhancer maps, which are fundamental in understanding the biology, and also a foundation for understanding disease.”
The findings of this study also offer evidence for a theory that Sharp has recently developed, along with MIT professors Richard Young and Arup Chakraborty, that gene transcription is controlled by membraneless droplets known as condensates. These condensates are made of large clusters of enzymes and RNA, which Sharp suggests may include eRNA produced at enhancer sites.
“We picture that the communication between an enhancer and a promoter is a condensate-type, transient structure, and RNA is part of that. This is an important piece of work in building the understanding of how RNAs from enhancers could be active,” he says.
The research was funded by the National Cancer Institute, the National Institutes of Health, and the Emerald Foundation Postdoctoral Transition Award.
