4D Nucleome - Funded Research | NIH Common Fund

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**Real-Time Chromatin Dynamics and Function (U01 Clinical Trial Not Allowed) RFA-RM-20-003**
PI Name	Institution Name	Title
BELMONT, ANDREW STEVEN (contact) HAN, KYU YOUNG	UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN	Identification of the active nuclear niche(s) using novel proteomic, genomic, transgenic, and live-cell microscopy technologies
BINTU, LACRAMIOARA (contact) BOETTIGER, ALISTAIR	STANFORD UNIVERSITY	Live-cell multiplex super-resolution imaging of chromatin state transitions
CAI, LONG (contact) ELOWITZ, MICHAEL B GUTTMAN, MITCHELL	CALIFORNIA INSTITUTE OF TECHNOLOGY	Dynamics of chromosome organization and chromatin states in single cells
GREGOR, THOMAS (contact) LEVINE, MICHAEL STEVEN TOETTCHER, JARED E	PRINCETON UNIVERSITY	Control of the 4D chromatin landscape underlying gene activity during development
HA, TAEKJIP (contact) JOHNSON, MARGARET ELLEN WU, CARL	JOHNS HOPKINS UNIVERSITY	Chromatin Function During Transcription and DNA Repair at Single Molecule Resolution in Living Cells
HUANG, BO (contact) NARLIKAR, GEETA J SHU, XIAOKUN	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	Modulation and functional characterization of protein condensation in chromatin organization
PHILLIPS-CREMINS, JENNIFER ELIZABETH (contact) BLOBEL, GERD A QI, LEI STANLEY RAJ, ARJUN	UNIVERSITY OF PENNSYLVANIA	Engineering and Imaging 3D genome structure-function dynamics across time scales
TORRES PADILLA, MARIA ELENA	HELMHOLTZ ZENTRUM MUENCHEN - GMBH	Establishment and visualization of nuclear architecture at the onset of mammalian development

**4DN Centers for Data Integration, Modeling and Visualization (UM1 Clinical Trial Not Allowed) RFA-RM-20-004**
PI Name	Institution Name	Title
DEKKER, JOB (contact) MIRNY, LEONID A	UNIV OF MASSACHUSETTS MED SCH WORCESTER	Center for 3D Structure and Physics of the Genome
MA, JIAN (contact) ALBER, FRANK BELMONT, ANDREW STEVEN WU, CHAO-TING	CARNEGIE-MELLON UNIVERSITY	Multiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data Integration
NOBLE, WILLIAM STAFFORD (contact) DISTECHE, CHRISTINE M. SHENDURE, JAY ASHOK	UNIVERSITY OF WASHINGTON	UW 4-Dimensional Genomic Organization of Mammalian Embryogenesis Center
REN, BING (contact) DULAC, CATHERINE G LEIN, ED NICODEMI, MARIO POMBO, ANA WANG, TING ZHUANG, XIAOWEI	UNIVERSITY OF CALIFORNIA, SAN DIEGO	Center for Integrated Multi-modal and Multi-scale Nucleome Research

**4DN Organization and Function in Human Health and Disease (U01 Clinical Trial Not Allowed) RFA-RM-20-005**
PI Name	Institution Name	Title
BRUNEAU, BENOIT GAETAN (contact) POLLARD, KATHERINE S.	J. DAVID GLADSTONE INSTITUTES	Genetic determinants of 4D genome folding in human cardiac development
DIXON, JESSE R	SALK INSTITUTE FOR BIOLOGICAL STUDIES	Investigating the effects of structural variants on 3D genome organization and gene regulation in cancer genomes
HAWKINS, RAYMOND DAVID	UNIVERSITY OF WASHINGTON	Three-dimensional conformation changes associated with T cell memory and autoimmunity
HUANGFU, DANWEI (contact) APOSTOLOU, EFFIE LESLIE, CHRISTINA S	SLOAN-KETTERING INST CAN RESEARCH	Discovery of diabetes-relevant β cell enhancers through 4D enhancer mapping, integrative analysis, and large-scale CRISPRi perturbation screens
KAUFMAN, PAUL D. (contact) FOLTZ, DANIEL RICHARD HUANG, SUI	UNIV OF MASSACHUSETTS MED SCH WORCESTER	The role of the nucleolus in human genome organization in normal and disease states
LOMVARDAS, STAVROS	COLUMBIA UNIVERSITY HEALTH SCIENCES	Interrogating genome folding trajectories in health and disease
PHILLIPS-CREMINS, JENNIFER ELIZABETH (contact) JAIN, RAJAN JOYCE, ERIC F. LAKADAMYALI, MELIKE VAHEDI, GOLNAZ	UNIVERSITY OF PENNSYLVANIA	Single-cell dissection of chromatin architecture mechanisms connecting pathologic instability and transcriptional silencing
SCHATZ, DAVID G. (contact) WANG, SIYUAN	YALE UNIVERSITY	Genome Architecture in Human Germinal Center B Cell Development, Malignancy, and Somatic Hypermutation
SHEN, YIN (contact) KRIEGSTEIN, ARNOLD	UNIVERSITY OF CALIFORNIA, SAN FRANCISCO	Charting the 3D epigenome in human brain development and diseases
XU, XIANGMIN (contact) COTMAN, CARL WAYNE REN, BING	UNIVERSITY OF CALIFORNIA-IRVINE	Single-Cell Analysis of Aging-Associated 4D Nucleome in the Human Hippocampus

**New Investigator Projects on 4DN Organization and Function in Human Health and Disease (U01 Clinical Trial Not Allowed) RFA-RM-20-006**
PI Name	Institution Name	Title
DIAO, YARUI	DUKE UNIVERSITY	The 4D nucleome of muscle regeneration in ischemia-induced tissue damage and repair
KALHOR, REZA	JOHNS HOPKINS UNIVERSITY	Dynamics of lineage-specific genome reorganization in gastrulation and their response to disease-associated epigenetic perturbations
LI, WENBO	UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON	Beyond Gene Dosage: Understanding Down Syndrome via 4D Genome Organization
SATPATHY, ANSUMAN	STANFORD UNIVERSITY	4DN Interrogation of T Cell Exhaustion in Cancer
YAMADA, TOMOKO	NORTHWESTERN UNIVERSITY	Mechanisms of Genome Organization in Brain Development and Behavior
ZHANG, HUAIYING	CARNEGIE-MELLON UNIVERSITY	Phase separation-induced nuclear organization in ALT Cancer

**Limited Competition: 4DN Organizational Hub (U01 Clinical Trial Not Allowed) RFA-RM-20-007**
PI Name	Institution Name	Title
ZHONG, SHENG	UNIVERSITY OF CALIFORNIA, SAN DIEGO	The second phase of NIH Common Fund 4D Nucleome Network Organizational Hub

**Limited Competition 4DN Data Coordination & Integration Center (U01 Clinical Trial Not Allowed) RFA-RM-20-008**
PI Name	Institution Name	Title
PARK, PETER J	HARVARD MEDICAL SCHOOL	4D Nucleome Network Data Coordination and Integration Center

**NIH Support for Conferences and Scientific Meetings (Parent R13 Clinical Trial Not Allowed) PA-18-648**
PI Name	Institution Name	Title
JARVIS, THALE CROSS	KEYSTONE SYMPOSIA	3D Genome: Gene Regulation and Disease

**Nuclear Organization and Function Interdisciplinary Consortium (NOFIC) (U54) RFA-RM-14-030**
PI Name	Institution Name	Title
ALBER, FRANK (contact) CHEN, LIN	UNIVERSITY OF SOUTHERN CALIFORNIA	Mapping the 3D Genome Landscape
BELMONT, ANDREW STEVEN	UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN	Combined Cytological, Genomic, and Functional Mapping of Nuclear Genome Organization
DEKKER, JOB (contact) MIRNY, LEONID A	UNIV OF MASSACHUSETTS MED SCH WORCESTER	Center for 3D Structure and Physics of the Genome
REN, BING (contact) MURRE, CORNELIS	LUDWIG INSTITUTE FOR CANCER RESEARCH LTD	San Diego Center for 4D Nucleome Research
RUAN, YIJUN	JACKSON LABORATORY	Nucleome Positioning System for Spatiotemporal Genome Organization and Regulation
SHENDURE, JAY ASHOK (contact) NOBLE, WILLIAM STAFFORD	UNIVERSITY OF WASHINGTON	University of Washington Center for Nuclear Organization and Function

**4D Nucleome Imaging Tools (U01) RFA-RM-14-009**
PI Name	Institution Name	Title
BEWERSDORF, JOERG (contact) BADDELEY, DAVID	YALE UNIVERSITY	An Integrated Imaging System for High-throughput Nanoscopy of the 4D Nucleome
CAI, LONG (contact) QI, LEI STANLEY	CALIFORNIA INSTITUTE OF TECHNOLOGY	Hi-resolution dynamic imaging of chromosomes in single cells by combined CRISPR imaging and sequential FISH
ELLENBERG, JAN	EUROPEAN MOLECULAR BIOLOGY LABORATORY	Reconstructing the dynamic 3D architecture of the human genome by superresolution microscopy and DNA sequence modelling
GREGOR, THOMAS (contact) LEVINE, MICHAEL S.	PRINCETON UNIVERSITY	Imaging chromosome dynamics and measuring its impact on transcriptional activity
GRUNWALD, DAVID	UNIV OF MASSACHUSETTS MED SCH WORCESTER	Visualizing local and global chromatin architecture, and gene expression in the individual cell by structural (SUSHI) and temporal (3D-SMRT) single molecule imaging
LAM, KIT S (contact) CHENG, R.HOLLAND IZUMIYA, YOSHIHIRO	UNIVERSITY OF CALIFORNIA AT DAVIS	Genetically Encoded Small Illuminants for 4D nucleome imaging
LIPHARDT, JAN T.	STANFORD UNIVERSITY	Deep Super-localization Microscopy and Effectively Unbleachable Labeling for 4D Nucleomics
O'SHEA, CLODAGH (contact) ELLISMAN, MARK H	SALK INSTITUTE FOR BIOLOGICAL STUDIES	Imaging local and global chromatin structure as a 3D continuum within the nucleus
SINGER, ROBERT H. (contact) DARZACQ, XAVIER	ALBERT EINSTEIN COLLEGE OF MEDICINE	Tools For Imaging the Functional Genome in Living Cells and Tissues

**4D Nucleome Network Data Coordination and Integration Center (U01) RFA-RM-14-011**
PI Name	Institution Name	Title
PARK, PETER J	HARVARD MEDICAL SCHOOL	4D Nucleome Network Data Coordination and Integration Center
WANG, TING (contact)	WASHINGTON UNIVERSITY	The WashU 4DN Network Data Coordination and Integration Center

**4D Nucleome Network Organizational Hub (U01) RFA-RM-14-010**
PI Name	Institution Name	Title
ZHONG, SHENG (contact) CHIEN, SHU REN, BING SUBRAMANIAM, SHANKAR	UNIVERSITY OF CALIFORNIA SAN DIEGO	The Organizational Hub and Web Portal for the 4D Nucleome Network

**Study of Nuclear Bodies and Compartments (U01) RFA-RM-14-008**
PI Name	Institution Name	Title
BRANGWYNNE, CLIFFORD P	PRINCETON UNIVERSITY	Optogenetic Droplets: Using Light to Control Nucleoplasmic Phase Separation
GERACE, LARRY R.	SCRIPPS RESEARCH INSTITUTE	Mapping the organization of the peripheral nuclear compartment
GROUDINE, MARK T	FRED HUTCHINSON CANCER RES CENTER	A toolkit to reversibly disrupt nuclear bodies and move genes among compartments
GUTTMAN, MITCHELL (contact) HESS, SONJA RINN, JOHN LOUIS	CALIFORNIA INSTITUTE OF TECHNOLOGY	Deciphering the function and mechanisms of lncRNA-mediated organization of nuclear compartments
KAUFMAN, PAUL D. (contact) DEKKER, JOB PEDERSON, THORU	UNIV OF MASSACHUSETTS MED SCH WORCESTER	Nucleolar Genomics During Early Mammalian Development
LOMVARDAS, STAVROS (contact) BROWN, LEWIS M.	COLUMBIA UNIVERSITY HEALTH SCIENCES	Deciphering nuclear bodies and compartments that govern singular olfactory receptor expression

**Nucleomics Tools (U01) RFA-RM-14-007**
PI Name	Institution Name	Title
FRASER, PETER J (contact) TANAY, AMOS	THE BABRAHAM INSTITUTE	New automated experimental and computational pipeline for high coverage single-cell Hi-C and its integration with single cell RNA-seq: enabling 4D Nucleomics at single cell resolution
GUTTMAN, MITCHELL (contact) ISMAGILOV, RUSTEM F	CALIFORNIA INSTITUTE OF TECHNOLOGY	Novel tools to comprehensively map dynamic organization of RNA and DNA in higher-order nuclear structures within single cells
LIEBERMAN-AIDEN, EREZ	BAYLOR COLLEGE OF MEDICINE	Beyond pairwise DNA contacts: exploring higher-order genome structure using proximity ligation and split pool barcoding
LIS, JOHN T (contact) LIN, HENING ZIPFEL, WARREN R	CORNELL UNIVERSITY	Distance-Hi-C: Creating Photo Activated X-linkers To Define Nuclear Architecture
RAJ, ARJUN (contact) BLOBEL, GERD A PHILLIPS-CREMINS, JENNIFER	UNIVERSITY OF PENNSYLVANIA	Engineering and visualizing genome folding at high spatiotemporal resolution

This page last reviewed on September 12, 2023

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