Selected

Convergence of coronary artery disease genes onto endothelial cell programs

Gavin R Schnitzler*, Helen Kang*, Shi Fang, Ramcharan S Angom, Vivian S Lee-Kim, X Rosa Ma, Tony Zeng, Ronghao Zhou, Katherine Guo, Martin S. Taylor, Shamsudheen Karuthedath Vellarikkal, Aurelie E. Barry, Oscar Sias-Garcia, Alex Bloemendal, Glen Munson, Philine Guckelberger, Tung H Nguyen, Drew T Bergman, Stephen Hinshaw, Nathan Cheng, Brian Cleary, Krishna Aragam, Eric S Lander, Hilary K Finucane, Debabrata Mukhopadhyay, Rajat M Gupta†, and Jesse M. Engreitz†. *co-first authors. †co-corresponding authors.
Nature (2024) | Free article

Rewriting regulatory DNA to dissect and reprogram gene expression

Gabriella E Martyn*, Michael T Montgomery*, Hank Jones, Katherine Guo, Benjamin R Doughty, Johannes Linder, Ziwei Chen, Kelly Cochran, Kathryn A Lawrence, Glen Munson, Anusri Pampari, Charles P Fulco, David R Kelley, Eric S Lander, Anshul Kundaje, Jesse M Engreitz. *co-first authors.
bioRxiv (2023)

An encyclopedia of enhancer-gene regulatory interactions in the human genome

Andreas R. Gschwind*, Kristy S. Mualim*, Alireza Karbalayghareh*, Maya U. Sheth*, Kushal K. Dey*, Evelyn Jagoda*, Ramil N. Nurtdinov*, Wang Xi*, Anthony S. Tan, Hank Jones, X. Rosa Ma, David Yao, Joseph Nasser, Žiga Avsec, Benjamin T. James, Muhammad S. Shamim, Neva C. Durand, Suhas S. P. Rao, Ragini Mahajan, Benjamin R. Doughty, Kalina Andreeva, Jacob C. Ulirsch, Kaili Fan, Elizabeth M. Perez, Tri C. Nguyen, David R. Kelley, Hilary K. Finucane, Jill E. Moore, Zhiping Weng, Manolis Kellis, Michael C. Bassik, Alkes L. Price†, Michael A. Beer†, Roderic Guigó†, John A. Stamatoyannopoulos†, Erez Lieberman Aiden†, William J. Greenleaf†, Christina S. Leslie†, Lars M. Steinmetz†, Anshul Kundaje†, Jesse M. Engreitz†. *co-first authors. †co-last authors.
bioRxiv (2023)

Compatibility rules of human enhancer and promoter sequences

Drew T. Bergman*, Thouis R. Jones*, Vincent Liu, Judhajeet Ray, Evelyn Jagoda, Layla Siraj, Helen Y Kang, Joseph Nasser, Michael Kane, Antonio Rios, Tung H Nguyen, Sharon R Grossman, Charles P Fulco, Eric S Lander, and Jesse M Engreitz. *co-first authors.
Nature (2022)

Genome-wide enhancer maps link risk variants to disease genes

Joseph Nasser*, Drew T. Bergman*, Charles P. Fulco*, Philine Guckelberger*, Benjamin R. Doughty*, Tejal A. Patwardhan, Thouis R. Jones, Tung H. Nguyen, Jacob C. Ulirsch, Fritz Lekschas, Kristy Mualim, Heini M. Natri, Elle M. Weeks, Glen Munson, Michael Kane, Helen Y. Kang, Ang Cui, John P. Ray, Tom M. Eisenhaure, Ryan L. Collins, Kushal Dey, Hanspeter Pfister, Alkes L. Price, Charles B. Epstein, Anshul Kundaje, Ramnik J. Xavier, Mark J. Daly, Hailiang Huang, Hilary K. Finucane, Nir Hacohen, Eric S. Lander†, and Jesse M. Engreitz†. *co-first authors. †co-corresponding authors.
Nature (2021) | Free Article | Resources

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

Jamie L. Marshall*, Benjamin R. Doughty*, Vidya Subramanian, Philine Guckelberger, Qingbo Wang, Linlin M. Chen, Samuel G. Rodriques, Kaite Zhang, Charles P. Fulco, Joseph Nasser, Elizabeth J. Grinkevich, Teia Noel, Sarah Mangiameli, Anna Greka, Eric S. Lander†, Fei Chen†, and Jesse M. Engreitz†. *co-first authors. †co-corresponding authors.
PNAS (2020)

Activity-by-Contact model of enhancer regulation from thousands of CRISPR perturbations

Fulco CP*, Nasser J*, Jones TJ, Munson G, Bergman DT, Subramanian V, Grossman SR, Anyoha R, Patwardhan TA, Nguyen TH, Kane M, Doughty BR, Perez EM, Durand NC, Stamenova EK, Aiden EL, Lander ES†, and Engreitz JM†. *co-first authors. †co-corresponding authors.
Nature Genetics (2019) | Resources | Blog | Perspective

Systematic mapping of functional enhancer-promoter connections with CRISPR interference

Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, and Lander ES*, Engreitz JM*. *co-corresponding authors.
Science (2016) | Resources | News

Local regulation of gene expression by lncRNA promoters, transcription, and splicing

Engreitz JM, Haines JE, Munson G, Chen J, Perez EM, Kane M, McDonel PE, Guttman M, and Lander ES.
Nature (2016).

RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites

Engreitz JM, Sirokman K, McDonel P, Shishkin A, Surka C, Russell P, Grossman SR, Chow AY, Guttman M*, and Lander ES*. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites.
Cell (2014) | Protocols | Perspective

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Surka C, Sirokman K, Kadri S, Xing J, Goren A, Lander ES*, Plath K*, and Guttman M*.
Science (2013) | Protocols | Perspective

CRISPR Tools for Systematic Studies of RNA Regulation

Engreitz J*, Abudayyeh O*, Gootenberg J*, and Zhang F.
In RNA Worlds: New Tools for Deep Exploration. Eds. Cech TR and Steitz JA.
CSHL Press (2019)

Long non-coding RNAs (lncRNAs) as spatial amplifiers that control nuclear architecture and gene expression

Engreitz JM*, Ollikainen N*, and Guttman M.
Nat Rev Mol Cell Biol (2016)

2023

Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

Elle M Weeks, Jacob C Ulirsch, Nathan Y Cheng, Brian L Trippe, Rebecca S Fine, Jenkai Miao, Tejal A Patwardhan, Masahiro Kanai, Joseph Nasser, Charles P Fulco, Katherine C Tashman, Francois Aguet, Taibo Li, Jose Ordovas-Montanes, Christopher S Smillie, Moshe Biton, Alex K Shalek, Ashwin N Ananthakrishnan, Ramnik J Xavier, Aviv Regev, Rajat M Gupta, Kasper Lage, Kristin G Ardlie, Joel N Hirschhorn, Eric S Lander, Jesse M Engreitz, Hilary K Finucane.
Nature Genetics (2023). medRxiv (2020).

Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes

Mengyao Yu, Matthew Aguirre, Meiwen Jia, Ketrin Gjoni, Aldo Cordova-Palomera, Chad Munger, Dulguun Amgalan, X. Rosa Ma, Alexandre Pereira, Catherine Tcheandjieu, Christine Seidman, Jonathan Seidman, Martin Tristani-Firouzi, Wendy Chung, Elizabeth Goldmuntz, Deepak Srivastava, Ruth J.F. Loos, Nathalie Chami, Heather Cordell, Martina Dreßen, Bertram Mueller-Myhsok, Harald Lahm, Markus Krane, Katherine S. Pollard, Jesse M. Engreitz, Sarah A. Gagliano Taliun, Bruce D. Gelb and James R. Priest.
Circulation: Genomic and Precision Medicine (2023).

Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy

Mengyao Yu, Andrew R Harper, Matthew Aguirre, Maureen Pittman, Catherine Tcheandjieu, Dulguun Amgalan, Christopher Grace, Anuj Goel, Martin Farrall, Ke Xiao, Jesse Engreitz, Katherine S Pollard, Hugh Watkins, James R Priest
Circulation: Genomic and Precision Medicine (2023).

2022

Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease

Mohamed Ameen*, Laksshman Sundaram*, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D. Wilson, Avyay Varadarajan, Nirmal Vadgama, Akshay Balsubramani, Joseph C. Wu, Jesse M. Engreitz, Kyle Farh, Ioannis Karakikes†, Kevin C. Wang†, Thomas Quertermous†, William Greenleaf†, Anshul Kundaje†
Cell (2022).

SNP-to-gene linking strategies reveal contributions of enhancer-related and candidate master-regulator genes to autoimmune disease

Kushal K. Dey, Steven Gazal, Bryce van de Geijn, Samuel Sungil Kim, Joseph Nasser, Jesse M. Engreitz, Alkes L. Price.
Cell Genomics (2022).

Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity.

Steven Gazal, Omer Weissbrod, Farhad Hormozdiari, Kushal K Dey, Joseph Nasser, Karthik A Jagadeesh, Daniel J Weiner, Huwenbo Shi, Charles P Fulco, Luke J O'Connor, Bogdan Pasaniuc, Jesse M Engreitz, Price AL.
Nature Genetics (2022).

Computational estimates of annular diameter reveal genetic determinants of mitral valve function and disease

Mengyao Yu , Catherine Tcheandjieu, Adrien Georges, Ke Xiao, Helio Tejeda , Christian Dina, Thierry Le Tourneau, Madalina Fiterau, Renae Judy, Noah L Tsao, Dulguun Amgalan, Chad J Munger, Jesse M Engreitz, Scott M Damrauer, Nabila Bouatia-Naji, James R Priest
JCI Insight (2022).

Identifying disease-critical cell types and cellular processes across the human body by integration of single-cell profiles and human genetics

Karthik A. Jagadeesh*, Kushal K. Dey*, Daniel T. Montoro, Rahul Mohan, Steven Gazal, Jesse M. Engreitz, Ramnik J. Xavier, Alkes L. Price†, Aviv Regev†.
Nature Genetics (2022).

KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress

Jan-Renier Moonen, James Chappell, Minyi Shi, Tsutomu Shinohara, Dan Li, Maxwell R Mumbach, Fan Zhang, Ramesh V Nair, Joseph Nasser, Daniel H Mai, Shalina Taylor, Lingli Wang, Ross J Metzger, Howard Y Chang, Jesse M Engreitz, Michael P Snyder, Marlene Rabinovitch
Nature Communications (2022).

Multi-center integrated analysis of non-coding CRISPR screens

David Yao*, Josh Tycko*, Woo Oh†, Lexi R Bounds†, Sager J Gosai†, Lazaros Lataniotis†, Ava Mackay-Smith†, Benjamin R Doughty†, Idan Gabdank†, Henri Schmidt, Ingrid Youngworth, Kalina Andreeva, Xingjie Ren, Alejandro Barrera, Yunahi Luo, Keith Siklenka, Galip Gurkan Yardimci, ENCODE4 Consortium, Ryan Tewhey+, Anshul Kundaje+, William J Greenleaf+, Pardis C Sabeti+, Christina Leslie+, Yuri Pritykin+, Jill E Moore+, Michael A Beer+, Charles Gersbach+, Timothy E Reddy+, Yin Shen+, Jesse M Engreitz+, Michael C Bassik+, Steven K Reilly
bioRxiv (2022).

2021

Activity-dependent regulome of human GABAergic neurons reveals new patterns of gene regulation and neurological disease heritability

Gabriella L Boulting, Ershela Durresi, Bulent Ataman, Maxwell A Sherman, Kevin Mei, David A Harmin, Ava C Carter, Daniel R Hochbaum, Adam J Granger, Jesse M Engreitz, Sinisa Hrvatin, Michael R Blanchard, Marty G Yang, Eric C Griffith, Michael E Greenberg.
Nature Neuroscience (2021).

Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease

Johanna Dahlqvist, Charles P Fulco, John P Ray, Thomas Liechti, Carl G de Boer, David J Lieb, Thomas M Eisenhaure, Jesse M Engreitz, Mario Roederer, Nir Hacohen
Human Molecular Genetics (2021).

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Toni M. Delorey, Carly G. K. Ziegler, Graham Heimberg, Rachelly Normand, Yiming Yang, Asa Segerstolpe, Domenic Abbondanza, Stephen J. Fleming, Ayshwarya Subramanian, …, Orr Ashenberg, Caroline B.M. Porter, Bo Li, Alex K. Shalek, Alexandra-Chloé Villani, Orit Rozenblatt-Rosen, Aviv Regev
Nature (2021).

2020

Integrative approaches to improve the informativeness of deep learning models for human complex diseases

Kushal K. Dey, Samuel S. Kim, Steven Gazal, Joseph Nasser, Jesse M. Engreitz, Alkes L. Price.
bioRxiv (2020).

Inherited causes of clonal haematopoiesis in 97,691 whole genomes

Alexander G Bick*, Joshua S Weinstock*, Satish K Nandakumar, Charles P Fulco, Erik L Bao, Seyedeh M Zekavat, Mindy D Szeto, Xiaotian Liao, Matthew J Leventhal, Joseph Nasser, …, Eric S Lander, Jesse M Engreitz, Benjamin L Ebert, Alexander P Reiner, Siddhartha Jaiswal, Goncalo Abecasis, Vijay G Sankaran, Pradeep Natarajan, and Sekar Kathiresan, on behalf of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium.
Nature (2020).

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

John P Ray, Carl G de Boer, Charles P Fulco, Caleb A Lareau, Masahiro Kanai, Jacob C Ulirsch, Ryan Tewhey, Leif S Ludwig, Steven K Reilly, Drew T Bergman, Jesse M Engreitz, Robbyn Issner, Hilary K Finucane, Eric S Lander, Aviv Regev, and Nir Hacohen.
Nature Communications (2020).

2019

Discovering metabolic disease gene interactions by correlated effects on cellular morphology

Jiao Y, Ahmed U, Sim MFM, Bejar A, Zhang X, Malukder MMU, Rice R, Flannick J, Podgornaia AI, Reilly DF, Engreitz JM, Kost-Alimova M, Hartland K, Mercader JM, Georges S, Wagh V, Tadin-Strapps M, Doench JG, Edwardson JM, Rochford JJ, Rosen ED, and Majithia AR.
Mol Metab (2019).

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis.

Nandakumar SK, McFarland SK, Mateyka LM, Lareau CA, Ulirsch JC, Ludwig LS, Agarwal G, Engreitz JM, Przychodzen B, McConkey M, Cowley GS, Doench JG, Maciejewski J, Ebert BL, Root DE, and Sankaran VG.
eLife (2019).

Functional disease architectures reveal unique biological role of transposable elements.

Hormozdiari FI, van de Geijn B, Nasser J, Weissbrod O, Gazal S, Ju C, O'Connor L, Hujoel MLA, Engreitz JM, Hormozdiari F, and Price A.
Nat Commun (2019).

2018

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, and Pinello L.
Nat Methods (2018).

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, and Lander ES.
Nature (2018).

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

Natarajan P, Peloso GM, Zekavat SM, Montasser M, Ganna A, Chaffin M, Khera AV, Zhou W, Bloom JM, Engreitz JM, Ernst J, O'Connell JR, Ruotsalainen SE, Alver M, Manichaikul A, Johnson WC, Perry JA, Poterba T, Seed C, Surakka IL, Esko T, Ripatti S, Salomaa V, Correa A, Vasan RS, Kellis M, Neale BM, Lander ES, Abecasis G, Mitchell B, Rich SS, Wilson JG, Cupples LA, Rotter JI, Willer CJ, Kathiresan S; NHLBI TOPMed Lipids Working Group.
Nat Commun (2018).

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

Zekavat SM, Ruotsalainen S, Handsaker RE, Alver M, Bloom J, Poterba T, Seed C, Ernst J, Chaffin M, Engreitz J, Peloso GM, Manichaikul A, Yang C, Ryan KA, Fu M, Johnson WC, Tsai M, Budoff M, Vasan RS, Cupples LA, Rotter JI, Rich SS, Post W, Mitchell BD, Correa A, Metspalu A, Wilson JG, Salomaa V, Kellis M, Daly MJ, Neale BM, McCarroll S, Surakka I, Esko T, Ganna A, Ripatti S, Kathiresan S, Natarajan P; NHLBI TOPMed Lipids Working Group.
Nat Commun (2018).

Positional specificity of different transcription factor classes within enhancers.

Grossman SR, Engreitz J, Ray JP, Nguyen TH, Hacohen N, and Lander ES.
PNAS (2018).

Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis

Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, Jovanovic M, Ellis SR, Fulco CP, Engreitz JM, Schütz S, Lian J, Gripp KW, Weinberg OK, Pinkus GS, Gehrke L, Regev A, Lander ES, Gazda HT, Lee WY, Panse VG, Carr SA, and Sankaran VG.
Cell (2018).

2017

Cohesin loss eliminates all loop domains

Rao SSP, Huang SC, St. Hilaire BT, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, and Aiden EL.
Cell (2017).

A genetic variant associated with five vascular diseases is a distal regulator of Endothelin-1 gene expression

Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, Emdin C, Hilvering CRE, Bianchi V, Mueller C, Khera AV, Ryan RJH, Engreitz JM, Issner R, Epstein C, Brown J, Bernstein BE, de Laat W, Katherisan S.
Cell (2017).

Recurrent and functional regulatory mutations in breast cancer

Rheinbay E, Parasuraman P, Grimsb J, Tiao G, Engreitz JM, Kim J, Lawrence MS, Taylor-Weiner A, Rodriguez-Cuevas S, Rosenberg M, Hess J, Stewart C, Maruvka YE, Stojanov P, Cortes ML, Seepo S, Cibulskis C, Tracy A, Pugh TJ, Lee J, Zheng Z, Ellisen LW, Iafrate AJ, Boehm JA, Gabriel SB, Meyerson ML, Golub TR, Baselga J, Hidalgo-Miranda A, Shioda T, Bernards A, Lander ES, and Getz G.
Nature (2017).

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

Joung J, Engreitz JM, Konermann S, Abudayyeh OA, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, and Zhang F.
Nature (2017).

Systematic dissection of genomic features determining transcription factor binding and enhancer function

Grossman SR, Zhang X, Wang L, Engreitz JM, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Regev A, Mikkelsen TS, and Lander ES.
Proc Nat Acad Sci (2017).

2010-
2016

Eradication of large established tumors by combination immunotherapy engaging innate and adaptive immunity

Moynihan KD*, Opel CF*, Szeto GL, Tzeng A, Zhu ER, Engreitz JM, Williams RT, Rakhra K, Zhang MH, Rothschilds AM, Kumari S, Kelly RL, Kwan BH, Abraham W, Hu K, Mehta NK, Kauke MJ, Suh H, Cochran JR, Lauffenburger DA, Wittrup KD, and Irvine DJ.
Nat Med (2016).

Publications