18 results on '"Munson, Glen"'
Search Results
2. Massively parallel base editing to map variant effects in human hematopoiesis
- Author
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Martin-Rufino, Jorge D., Castano, Nicole, Pang, Michael, Grody, Emanuelle I., Joubran, Samantha, Caulier, Alexis, Wahlster, Lara, Li, Tongqing, Qiu, Xiaojie, Riera-Escandell, Anna Maria, Newby, Gregory A., Al’Khafaji, Aziz, Chaudhary, Santosh, Black, Susan, Weng, Chen, Munson, Glen, Liu, David R., Wlodarski, Marcin W., Sims, Kacie, Oakley, Jamie H., Fasano, Ross M., Xavier, Ramnik J., Lander, Eric S., Klein, Daryl E., and Sankaran, Vijay G.
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- 2023
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3. Abstract 14675: High-Throughput CRISPR Screening Links CAD Loci to Endothelial Cell Programs and Causal Pathways
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Gupta, Rajat M, Schnitzler, Gavin R, Kang, Helen, Ma, Rosa R, Lee-Kim, Vivian, Zeng, Anthony, Zhou, Ronghao, Vellarikkal, Shamsudheen K, Sias, Oscar, Munson, Glen, Guo, Katherine, Cleary, Brian, Lander, Eric, and Engreitz, Jesse M
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- 2022
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4. Genome-wide enhancer maps link risk variants to disease genes
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Nasser, Joseph, Bergman, Drew T., Fulco, Charles P., Guckelberger, Philine, Doughty, Benjamin R., Patwardhan, Tejal A., Jones, Thouis R., Nguyen, Tung H., Ulirsch, Jacob C., Lekschas, Fritz, Mualim, Kristy, Natri, Heini M., Weeks, Elle M., Munson, Glen, Kane, Michael, Kang, Helen Y., Cui, Ang, Ray, John P., Eisenhaure, Thomas M., Collins, Ryan L., Dey, Kushal, Pfister, Hanspeter, Price, Alkes L., Epstein, Charles B., Kundaje, Anshul, Xavier, Ramnik J., Daly, Mark J., Huang, Hailiang, Finucane, Hilary K., Hacohen, Nir, Lander, Eric S., and Engreitz, Jesse M.
- Published
- 2021
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5. Rewriting regulatory DNA to dissect and reprogram gene expression
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Martyn, Gabriella E, primary, Montgomery, Michael T, additional, Jones, Hank, additional, Guo, Katherine, additional, Doughty, Benjamin R, additional, Linder, Johannes, additional, Chen, Ziwei, additional, Cochran, Kelly, additional, Lawrence, Kathryn A, additional, Munson, Glen, additional, Pampari, Anusri, additional, Fulco, Charles P, additional, Kelley, David R, additional, Lander, Eric S, additional, Kundaje, Anshul, additional, and Engreitz, Jesse M, additional
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- 2023
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6. Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
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Fulco, Charles P., Nasser, Joseph, Jones, Thouis R., Munson, Glen, Bergman, Drew T., Subramanian, Vidya, Grossman, Sharon R., Anyoha, Rockwell, Doughty, Benjamin R., Patwardhan, Tejal A., Nguyen, Tung H., Kane, Michael, Perez, Elizabeth M., Durand, Neva C., Lareau, Caleb A., Stamenova, Elena K., Aiden, Erez Lieberman, Lander, Eric S., and Engreitz, Jesse M.
- Published
- 2019
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7. Systematic mapping of functional enhancer-promoter connections with CRISPR interference
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Fulco, Charles P., Munschauer, Mathias, Anyoha, Rockwell, Munson, Glen, Grossman, Sharon R., Perez, Elizabeth M., Kane, Michael, Cleary, Brian, Lander, Eric S., and Engreitz, Jesse M.
- Published
- 2016
8. Abstract B016: Quantifying and dissecting pancreatic cancer cell phenotypic plasticity using lineage tracing, single-cell multiomics and CRISPR perturbations reveals novel regulators of plastic states
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Mehta, Arnav, primary, Bi, Lynn, additional, Al'Khafaji, Aziz, additional, Jankowiak, Martin, additional, Parikh, Milan, additional, Babadi, Mehrtash, additional, Bloemendal, Alex, additional, Schwartz, Marc, additional, Munson, Glen, additional, Chan, Joeseph, additional, Burdziak, Cassandra, additional, Donnard, Elisa, additional, Park, Ryan, additional, Lu, Chen, additional, Rigollet, Philippe, additional, Aguirre, Andrew, additional, Subramanian, Vidya, additional, Jones, Ray, additional, Lander, Eric S., additional, Ting, David T., additional, Pe'er, Dana, additional, and Hacohen, Nir, additional
- Published
- 2022
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9. Mapping the convergence of genes for coronary artery disease onto endothelial cell programs
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Schnitzler, Gavin R, primary, Kang, Helen, additional, Lee-Kim, Vivian S, additional, Ma, Rosa X, additional, Zeng, Tony, additional, Angom, Ramcharan S, additional, Fang, Shi, additional, Vellarikkal, Shamsudheen Karuthedath, additional, Zhou, Ronghao, additional, Guo, Katherine, additional, Sias-Garcia, Oscar, additional, Bloemendal, Alex, additional, Munson, Glen, additional, Guckelberger, Philine, additional, Nguyen, Tung H, additional, Bergman, Drew T, additional, Cheng, Nathan, additional, Cleary, Brian, additional, Aragam, Krishna, additional, Mukhopadhyay, Debabrata, additional, Lander, Eric S, additional, Finucane, Hilary K, additional, Gupta, Rajat M, additional, and Engreitz, Jesse M, additional
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- 2022
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10. lincRNAs act in the circuitry controlling pluripotency and differentiation
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Guttman, Mitchell, Donaghey, Julie, Carey, Bryce W., Garber, Manuel, Grenier, Jennifer K., Munson, Glen, Young, Geneva, Lucas, Anne Bergstrom, Ach, Robert, Bruhn, Laurakay, Yang, Xiaoping, Amit, Ido, Meissner, Alexander, Regev, Aviv, Rinn, John L., Root, David E., and Lander, Eric S.
- Subjects
Gene expression -- Models ,RNA -- Physiological aspects -- Electric properties ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of- function studies on most lincRNAs expressed in mouse embryonic stem (ES) cells and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ES cell regulators. Notably, lincRNAs primarily affect gene expression in trans. Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ES cells and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state., The mammalian genome encodes many thousands of large noncoding transcripts1 including a class of ~3,500 lincRNAs identified using a chromatin signature of actively transcribed genes2-4. These lincRNA genes have been [...]
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- 2011
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11. Local regulation of gene expression by lncRNA promoters, transcription and splicing
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Engreitz, Jesse M., Haines, Jenna E., Perez, Elizabeth M., Munson, Glen, Chen, Jenny, Kane, Michael, McDonel, Patrick E., Guttman, Mitchell, and Lander, Eric S.
- Subjects
Genetic research ,Transcription (Genetics) -- Research ,Gene expression -- Research ,RNA -- Physiological aspects ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Jesse M. Engreitz [1, 2]; Jenna E. Haines [1]; Elizabeth M. Perez [1]; Glen Munson [1]; Jenny Chen [1, 2]; Michael Kane [1]; Patrick E. McDonel [1]; Mitchell Guttman [...]
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- 2016
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12. Analysis of the DNA sequence and duplication history of human chromosome 15
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Zody, Michael C., Garber, Manuel, Sharpe, Ted, Young, Sarah K., Rowen, Lee, O'Neill, Keith, Whittaker, Charles A., Kamal, Michael, Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Kodira, Chinnappa D., Madan, Anup, Qin, Shizhen, Yang, Xiaoping, Abbasi, Nissa, Abouelleil, Amr, Arachchi, Harindra M., Baradarani, Lida, Birditt, Brian, Bloom, Scott, Bloom, Toby, Borowsky, Mark L., Burke, Jeremy, Butler, Jonathan, Cook, April, DeArellano, Kurt, DeCaprio, David, Dorris, III, Lester, Dors, Monica, Eichler, Evan E., Engels, Reinhard, Fahey, Jessica, Fleetwood, Peter, Friedman, Cynthia, Gearin, Gary, Hall, Jennifer L., Hensley, Grace, Johnson, Ericka, Jones, Charlien, Kamat, Asha, Kaur, Amardeep, Locke, Devin P., Madan, Anuradha, Munson, Glen, Jaffe, David B., Lui, Annie, Macdonald, Pendexter, Mauceli, Evan, Naylor, Jerome W., Nesbitt, Ryan, Nicol, Robert, O'Leary, Sinead B., Ratcliffe, Amber, Rounsley, Steven, She, Xinwei, Sneddon, Katherine M. B., Stewart, Sandra, Sougnez, Carrie, Stone, Sabrina M., Topham, Kerri, Vincent, Dascena, Wang, Shunguang, Zimmer, Andrew R., Birren, Bruce W., Hood, Leroy, Lander, Eric S., and Nusbaum, Chad
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Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Michael C. Zody (corresponding author) [1]; Manuel Garber [1]; Ted Sharpe [1]; Sarah K. Young [1]; Lee Rowen [2]; Keith O'Neill [1]; Charles A. Whittaker [1, 6]; Michael Kamal [...]
- Published
- 2006
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13. Genome sequence, comparative analysis and haplotype structure of the domestic dog
- Author
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Lindblad-Toh, Kerstin, Wade, Claire M., Mikkelsen, Tarjei S., Karlsson, Elinor K., Jaffe, David B., Kamal, Michael, Clamp, Michele, Chang, Jean L., Kulbokas, III, Edward J., Zody, Michael C., Mauceli, Evan, Xie, Xiaohui, Breen, Matthew, Wayne, Robert K., Ostrander, Elaine A., Ponting, Chris P., Galibert, Francis, Smith, Douglas R., deJong, Pieter J., Kirkness, Ewen, Alvarez, Pablo, Biagi, Tara, Brockman, William, Butler, Jonathan, Chin, Chee-Wye, Cook, April, Cuff, James, Daly, Mark J., DeCaprio, David, Gnerre, Sante, Grabherr, Manfred, Kellis, Manolis, Kleber, Michael, Bardeleben, Carolyne, Goodstadt, Leo, Heger, Andreas, Hitte, Christophe, Kim, Lisa, Koepfli, Klaus-Peter, Parker, Heidi G., Pollinger, John P., Searle, Stephen M. J., Sutter, Nathan B., Thomas, Rachael, Webber, Caleb, Baldwin, Jennifer, Abebe, Adal, Abouelleil, Amr, Aftuck, Lynne, Ait-zahra, Mostafa, Aldredge, Tyler, Allen, Nicole, An, Peter, Anderson, Scott, Antoine, Claudel, Arachchi, Harindra, Aslam, Ali, Ayotte, Laura, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Benamara, Mostafa, Berlin, Aaron, Bessette, Daniel, Blitshteyn, Berta, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Brown, Adam, Cahill, Patrick, Calixte, Nadia, Camarata, Jody, Cheshatsang, Yama, Chu, Jeffrey, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Dawoe, Tenzin, Daza, Riza, Decktor, Karin, DeGray, Stuart, Dhargay, Norbu, Dooley, Kimberly, Dooley, Kathleen, Dorje, Passang, Dorjee, Kunsang, Dorris, Lester, Duffey, Noah, Dupes, Alan, Egbiremolen, Osebhajajeme, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Ferreira, Patricia, Fisher, Sheila, FitzGerald, Mike, Foley, Karen, Foley, Chelsea, Franke, Alicia, Friedrich, Dennis, Gage, Diane, Garber, Manuel, Gearin, Gary, Giannoukos, Georgia, Goode, Tina, Goyette, Audra, Graham, Joseph, Grandbois, Edward, Gyaltsen, Kunsang, Hafez, Nabil, Hagopian, Daniel, Hagos, Birhane, Hall, Jennifer, Healy, Claire, Hegarty, Ryan, Honan, Tracey, Horn, Andrea, Houde, Nathan, Hughes, Leanne, Hunnicutt, Leigh, Husby, M., Jester, Benjamin, Jones, Charlien, Kamat, Asha, Kanga, Ben, Kells, Cristyn, Khazanovich, Dmitry, Kieu, Alix Chinh, Kisner, Peter, Kumar, Mayank, Lance, Krista, Landers, Thomas, Lara, Marcia, Lee, William, Leger, Jean-Pierre, Lennon, Niall, Leuper, Lisa, LeVine, Sarah, Liu, Jinlei, Liu, Xiaohong, Lokyitsang, Yeshi, Lokyitsang, Tashi, Lui, Annie, Macdonald, Jan, Major, John, Marabella, Richard, Maru, Kebede, Matthews, Charles, McDonough, Susan, Mehta, Teena, Meldrim, James, Melnikov, Alexandre, Meneus, Louis, Mihalev, Atanas, Mihova, Tanya, Miller, Karen, Mittelman, Rachel, Mlenga, Valentine, Mulrain, Leonidas, Munson, Glen, Navidi, Adam, Naylor, Jerome, Nguyen, Tuyen, Nguyen, Nga, Nguyen, Cindy, Nguyen, Thu, Nicol, Robert, Norbu, Nyima, Norbu, Choe, Novod, Nathaniel, Nyima, Tenchoe, Olandt, Peter, O'Neill, Barry, O'Neill, Keith, Osman, Sahal, Oyono, Lucien, Patti, Christopher, Perrin, Danielle, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Rachupka, Anthony, Raghuraman, Sujaa, Rameau, Rayale, Ray, Verneda, Raymond, Christina, Rege, Filip, Rise, Cecil, Rogers, Julie, Rogov, Peter, Sahalie, Julie, Settipalli, Sampath, Sharpe, Theodore, Shea, Terrance, Sheehan, Mechele, Sherpa, Ngawang, Shi, Jianying, Shih, Diana, Sloan, Jessie, Smith, Cherylyn, Sparrow, Todd, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Stone, Sabrina, Sykes, Sean, Tchuinga, Pierre, Tenzing, Pema, Tesfaye, Senait, Thoulutsang, Dawa, Thoulutsang, Yama, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Venkataraman, Vijay, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Yang, Shuli, Yang, Xiaoping, Young, Geneva, Yu, Qing, Zainoun, Joanne, Zembek, Lisa, Zimmer, Andrew, and Lander, Eric S.
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Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Author(s): Kerstin Lindblad-Toh (corresponding author) [1]; Claire M Wade [1, 2]; Tarjei S. Mikkelsen [1, 3]; Elinor K. Karlsson [1, 4]; David B. Jaffe [1]; Michael Kamal [1]; Michele Clamp [...]
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- 2005
- Full Text
- View/download PDF
14. Genome-wide maps of enhancer regulation connect risk variants to disease genes
- Author
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Nasser, Joseph, primary, Bergman, Drew T., additional, Fulco, Charles P., additional, Guckelberger, Philine, additional, Doughty, Benjamin R., additional, Patwardhan, Tejal A., additional, Jones, Thouis R., additional, Nguyen, Tung H., additional, Ulirsch, Jacob C., additional, Natri, Heini M., additional, Weeks, Elle M., additional, Munson, Glen, additional, Kane, Michael, additional, Kang, Helen Y., additional, Cui, Ang, additional, Ray, John P., additional, Eisenhaure, Tom M., additional, Mualim, Kristy, additional, Collins, Ryan L., additional, Dey, Kushal, additional, Price, Alkes L., additional, Epstein, Charles B., additional, Kundaje, Anshul, additional, Xavier, Ramnik J., additional, Daly, Mark J., additional, Huang, Hailiang, additional, Finucane, Hilary K., additional, Hacohen, Nir, additional, Lander, Eric S., additional, and Engreitz, Jesse M., additional
- Published
- 2020
- Full Text
- View/download PDF
15. Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations
- Author
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Fulco, Charles P., primary, Nasser, Joseph, additional, Jones, Thouis R., additional, Munson, Glen, additional, Bergman, Drew T., additional, Subramanian, Vidya, additional, Grossman, Sharon R., additional, Anyoha, Rockwell, additional, Patwardhan, Tejal A., additional, Nguyen, Tung H., additional, Kane, Michael, additional, Doughty, Benjamin, additional, Perez, Elizabeth M., additional, Durand, Neva C., additional, Stamenova, Elena K., additional, Aiden, Erez Lieberman, additional, Lander, Eric S., additional, and Engreitz, Jesse M., additional
- Published
- 2019
- Full Text
- View/download PDF
16. Neighborhood regulation by lncRNA promoters, transcription, and splicing
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Engreitz, Jesse M., primary, Haines, Jenna E., additional, Munson, Glen, additional, Chen, Jenny, additional, Perez, Elizabeth M., additional, Kane, Michael, additional, McDonel, Patrick E., additional, Guttman, Mitchell, additional, and Lander, Eric S., additional
- Published
- 2016
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17. Cohesin-mediated 3D contacts tune enhancer-promoter regulation.
- Author
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Guckelberger P, Doughty BR, Munson G, Rao SSP, Tan Y, Cai XS, Fulco CP, Nasser J, Mualim KS, Bergman DT, Ray J, Jagoda E, Munger CJ, Gschwind AR, Sheth MU, Tan AS, Pulido SG, Mitra N, Weisz D, Shamim MS, Durand NC, Mahajan R, Khan R, Steinmetz LM, Kanemaki MT, Lander ES, Meissner A, Aiden EL, and Engreitz JM
- Abstract
Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin result in only limited changes in gene expression, despite a loss of contact domains and loops. Consequently, the role of cohesin and 3D contacts in enhancer function remains debated. Here, we developed CRISPRi of regulatory elements upon degron operation (CRUDO), a novel approach to measure how changes in contact frequency impact enhancer effects on target genes by perturbing enhancers with CRISPRi and measuring gene expression in the presence or absence of cohesin. We systematically perturbed all 1,039 candidate enhancers near five cohesin-dependent genes and identified 34 enhancer-gene regulatory interactions. Of 26 regulatory interactions with sufficient statistical power to evaluate cohesin dependence, 18 show cohesin-dependent effects. A decrease in enhancer-promoter contact frequency upon removal of cohesin is frequently accompanied by a decrease in the regulatory effect of the enhancer on gene expression, consistent with a contact-based model for enhancer function. However, changes in contact frequency and regulatory effects on gene expression vary as a function of distance, with distal enhancers (e.g., >50Kb) experiencing much larger changes than proximal ones (e.g., <50Kb). Because most enhancers are located close to their target genes, these observations can explain how only a small subset of genes - those with strong distal enhancers - are sensitive to cohesin. Together, our results illuminate how 3D contacts, influenced by both cohesin and genomic distance, tune enhancer effects on gene expression.
- Published
- 2024
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18. Rewriting regulatory DNA to dissect and reprogram gene expression.
- Author
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Martyn GE, Montgomery MT, Jones H, Guo K, Doughty BR, Linder J, Chen Z, Cochran K, Lawrence KA, Munson G, Pampari A, Fulco CP, Kelley DR, Lander ES, Kundaje A, and Engreitz JM
- Abstract
Regulatory DNA sequences within enhancers and promoters bind transcription factors to encode cell type-specific patterns of gene expression. However, the regulatory effects and programmability of such DNA sequences remain difficult to map or predict because we have lacked scalable methods to precisely edit regulatory DNA and quantify the effects in an endogenous genomic context. Here we present an approach to measure the quantitative effects of hundreds of designed DNA sequence variants on gene expression, by combining pooled CRISPR prime editing with RNA fluorescence in situ hybridization and cell sorting (Variant-FlowFISH). We apply this method to mutagenize and rewrite regulatory DNA sequences in an enhancer and the promoter of PPIF in two immune cell lines. Of 672 variant-cell type pairs, we identify 497 that affect PPIF expression. These variants appear to act through a variety of mechanisms including disruption or optimization of existing transcription factor binding sites, as well as creation of de novo sites. Disrupting a single endogenous transcription factor binding site often led to large changes in expression (up to -40% in the enhancer, and -50% in the promoter). The same variant often had different effects across cell types and states, demonstrating a highly tunable regulatory landscape. We use these data to benchmark performance of sequence-based predictive models of gene regulation, and find that certain types of variants are not accurately predicted by existing models. Finally, we computationally design 185 small sequence variants (≤10 bp) and optimize them for specific effects on expression in silico . 84% of these rationally designed edits showed the intended direction of effect, and some had dramatic effects on expression (-100% to +202%). Variant-FlowFISH thus provides a powerful tool to map the effects of variants and transcription factor binding sites on gene expression, test and improve computational models of gene regulation, and reprogram regulatory DNA., Competing Interests: Competing Interests J.M.E. is a consultant and equity holder in Martingale Labs, Inc., has received materials from 10x Genomics unrelated to this study, and has received speaking honoraria from GSK plc. J.L. and D.R.K. are employed by Calico Life Sciences LLC. C.P.F. is employed by Sanofi. A.K. is on the scientific advisory board of PatchBio, SerImmune and OpenTargets, was a consultant with Illumina, and owns shares in DeepGenomics, ImmunAI and Freenome. M.T.M., G.E.M., B.R.D., H.J., K.G., and J.M.E. are inventors on a provisional patent application related to this work.
- Published
- 2023
- Full Text
- View/download PDF
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