Frequently Asked Questions


1. What is the goal of the NIH Common Fund program on the 4D Nucleome?
2. What consortial agreements are expected in the 4DN Program?
3. Who should I contact regarding organ/cell/disease-questions?
4. What kind of research and technologies fall under this initiative?
5. What role does the NIH have in this cooperative agreement?
6. Will these FOAs be reissued?
7. How many meetings will project PIs/co-PIs be required to attend each year?
8. Will site visits be conducted?
9. Do I have to submit a detailed budget for the competing and noncompeting awards or can I use the modular format?
10. Can work be performed outside the US?
11. Can additional PIs be added during the course of the Project Period?
12. Can changes be made to the Research Plan during the Project period as new information is obtained?
13. What are the plans for data and resource sharing for this program?

 

 1. What is the goal of the NIH Common Fund program on the 4D Nucleome?

The Common Fund¹s 4D Nucleome program (http://commonfund.nih.gov/4Dnucleome/index) aims to understand the principles underlying nuclear organization in space and time, the role nuclear organization plays in gene expression and cellular function, and how changes in nuclear organization affect normal development as well as various diseases. To achieve these goals, the program recently released six new Funding Opportunity Announcements (FOAs):

•  Nuclear Organization and Function Interdisciplinary Consortium (NOFIC)(U54) - RFA-RM-14-006:

This FOA seeks to establish technology-development and data-production centers whose mission will be to develop, benchmark, standardize, and validate the next generation of high-throughput technologies that can produce three dimensional physical and functional maps of mammalian genomes, develop predictive models of mammalian genome structure-function relationships, and test the relevance of new nuclear organizational principles within the context of specific biological paradigms and systems.

•   Nucleomics Tools (U01) - RFA-RM-14-007:

The purpose of this Funding Opportunity Announcement (FOA) is to solicit applications that propose to develop and validate physical, chemical and biochemical approaches for measuring properties and dynamics of the three-dimensional organization of the genome that cannot be measured adequately using existing methodologies.

•   Study of Nuclear Bodies and Compartments (U01) - RFA-RM-14-008:

The purpose of this FOA is to support projects to develop tools and strategies for studying: 1. the three dimensional architecture of the nucleus in relationship to the topography of nuclear bodies and transcriptional machineries, 2. the structure and function of poorly characterized nuclear structures, or 3. the role of specialized proteins and RNAs in the assembly, organization, and function of nuclear bodies, nuclear structures, and specialized subnuclear domains.

•   4D Nucleome Imaging Tools (U01) - RFA-RM-14-009:

The purpose of this FOA is to solicit applications that will accelerate the development and validation of imaging technologies for visualizing the structural and functional organization of the mammalian genome and its spatiotemporal dynamics. Projects must propose innovative, high resolution, high throughput, quantitative technologies that can be used to study a statistically significant number of single cells to address critical unmet needs in our understanding of nuclear organization.

•   4D Nucleome Network Organizational Hub (U01) - RFA-RM-14-010:

The purpose of this FOA is to identify and support an Organizational Hub (OH) that will provide the administrative infrastructure for the 4D Nucleome Network, a collaborative research network being launched by the NIH Common Fund to support innovative research and tool development for further understanding the nuclear organization of mammalian genomes in space and time.

•    4D Nucleome Network Data Coordination and Integration Center (U01) - RFA-RM-14-011:
The purpose of this Funding Opportunity Announcement (FOA) is to identify and support a Four-Dimensional Nucleome (4DN) Network Data Coordination and Integration Center (DCIC). The overarching mission of 4DN-DCIC will be to collect, store, curate, and display all data, metadata, and analysis tools generated by the 4DN Network. The DCIC will also assist in the development and dissemination of metadata and standards to be adopted by the community at large, approaches for integrative analysis of a wide-range of data types, and visualization and analysis tools to facilitate access and understanding of complex datasets to non-expert users.

Please visit the Funding Opportunities page for more information on these announcements.

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2. What consortial agreements are expected in the 4DN Program?

Awards funded under RFA-RM-14-006 (NOFIC) are anticipated to involve activities conducted by multidisciplinary teams of investigators. NOFIC awardees will form a consortium, with the overarching mission to develop, benchmark, standardize, and validate the next generation of high-throughput technologies with the potential to produce three dimensional (3D) physical and functional maps of mammalian genomes. Projects funded under RFA-RM-14-007, RFA-RM-14-008 and RFA-RM-14-009 can be single-laboratory projects or multidisciplinary team projects of various sizes, based on the proposed scope of work. All investigators and teams funded under at least one of the six 4DN FOAs will be part of the 4DN Program Research Network that will encourage consortium-type partnership amongst all 4DN Network awardees. In addition to completing the research goals outlined in their applications, successful applicants will be expected to work collaboratively with all members of the 4D Nucleome Network, including the 4DN Network Organizational Hub (RFA-RM-14-010) and the 4DN Network Data Coordination & Integration Center (RFA-RM-14-011), to help develop common standards, metrics for data generation and storage, and data analysis and visualization tools that can be used by the broader scientific community. The 4DN Network will encourage the initiation of new collaborative research projects across the entire network. Some of these interactions could be facilitated by an Opportunity Pool of funds that will be managed by the 4DN Organizational Hub and NIH Program Staff. All 4DN Network investigators will be required to attend the initial 4DN Kickoff meeting, as well as annual 4DN investigator meetings and regular teleconferences with Network members and NIH Staff for the duration of the funding cycle.

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3. Who should I contact regarding organ/cell/disease-questions?

The Scientific and Research contacts are indicated in each of the Funding Opportunity Announcements (FOAs) and these individuals should be your first contact for a specific FOA.  In addition, the Common Fund 4DN Program is administered via a team of NIH program experts.  The NIH 4DN Program working group members and their affiliations are listed below and at the 4DN Program URL: http://commonfund.nih.gov/4DNucleome/members.

Working Group Coordinators:

Olivier Blondel, Ph.D.
Program Director, Endocrine Systems Biology Program
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) blondelol@niddk.nih.gov

Judy Mietz, Ph.D.
Program Director and Chief, DNA and Chromosome Aberrations Branch
Division of Cancer Biology
National Cancer Institute (NCI) mietzj@mail.nih.gov

Members:

Terry Bishop, Ph.D.
Program Director, Division of Extramural Research and Training
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) BishopT@EXTRA.NIDDK.NIH.GOV

Anthony Carter, Ph.D.
Program Director, Division of Genetics and Developmental Biology
National Institute of General Medical Sciences (NIGMS)  CarterAn@nigms.nih.gov

Lisa H. Chadwick, Ph.D.
Program Administrator, Division of Extramural Research Training
National Institute of Environmental Health Sciences (NIEHS) chadwickl@niehs.nih.gov

Richard Conroy, Ph.D.
Program Director, Division of Applied Science & Technology
National Institute of Biomedical Imaging and Bioengineering (NIBIB) Richard.Conroy@nih.gov

Sean Hanlon, Ph.D.
Program Manager, Office of Physical Sciences – Oncology
National Cancer Institute (NCI) hanlonse@mail.nih.gov

Patricia (Trish) Labosky, Ph.D.
Program Leader, Office of Strategic Coordination
Office of the Director, National Institutes of Health (NIH) patricia.labosky@nih.gov

Mike Pazin, Ph.D.
Program Director, Functional Genomics
National Human Genome Research Institute (NHGRI) pazinm@mail.nih.gov

Lisa Postow, Ph.D.
Program Director, Airway Biology & Disease Branch
National Heart, Lung, and Blood Institute (NHLBI) lisa.postow@nih.gov

Matt Reilly, Ph.D.
Program Director, Genetics & Proteomics
National Institute on Alcohol Abuse and Alcoholism (NIAAA) reillymt@mail.nih.gov

Robert Riddle, Ph.D.
Program Director, Neurogenetics Cluster
National Institute on Neurological Disorders and Stroke (NINDS) riddler@ninds.nih.gov

John Satterlee, Ph.D.
Program Director, Genetics and Molecular Neurobiology Research Branch
National Institute on Drug Abuse (NIDA) satterleej@nida.nih.gov

Geetha Senthil, Ph.D.
Program Officer, Translational Genomics
National Institute of Mental Health (NIMH) senthilgs@mail.nih.gov

Jose M. Velazquez, Ph.D.
Director, Cell Biology Program
National Institute on Aging (NIA) jvelazqu@mail.nih.gov

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4. What kind of research and technologies fall under this initiative?

The research and technologies are varied for each initiative. Please see Section I under Research Objectives for each of the 4DN FOAs.

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5. What role does the NIH have in this cooperative agreement?

The role of NIH staff in this cooperative agreement is spelled out in Section VI of each FOA and will be defined further in the terms and conditions of award. In brief, the NIH 4DN Program working group members will have substantial scientific and programmatic involvement during the project period of this award through technical assistance, advice, and coordination.  However, the role of NIH 4DN Program working group members will be to facilitate and not to direct the activities.
 
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6. Will these FOAs be reissued?

At present we have no plans to re-issue these FOAs.

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7. How many meetings will project PIs/co-PIs be required to attend each year?

Project PIs/co-PIs should budget for travel to annual meetings during the course of the award.

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8. Will site visits be conducted?

It is possible that site visits will be conducted on a periodic basis as part of monitoring the progress of awarded grants.

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9. Do I have to submit a detailed budget for the competing and noncompeting awards or can I use the modular format?

Applicants are asked to submit a detailed budget and justification. Please see Section V.1 for each FOA.

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10. Can work be performed outside the US?

Yes, as primary applicant institution or as a subcontract to the US-based institution. Justification for inclusion of work to be performed outside the US must be provided in the grant application and if selected for funding, foreign clearance will be required prior to release of a Notice of Award (NoA).

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11. Can additional PIs be added during the course of the Project Period?

Yes. Addition of new key personnel is subject to approval by NIH and should not result in any increase in the approved budget.

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12. Can changes be made to the Research Plan during the Project period as new information is obtained?

Since the awards are cooperative agreements, the NIH 4DN Program working group through the Project Officer of the award will work with the investigators if minor changes to the research approach are needed during the course of the project. However, the research plan must remain true to what was peer-reviewed.

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13. What are the plans for data and resource sharing for this program?

Awardees will be encouraged to publish and publicly release and disseminate results, data, and other products of the study, concordant with the study protocol and governance and the approved plan for making data and materials available to the scientific community and NIH. Awardees will work collectively with the NIH to develop and implement an appropriate rapid data release policy that will be applicable to all awardees in the consortium. Once the 4DN awards have been made, a 4DN Network Steering Committee (4DN-SC) that is responsible for joint governance of 4DN Network activities will be constituted (see Section VI of all 4DN FOAs). The 4DN-SC will be tasked, among other things, with establishing agreements that address the following issues: (1) procedures for data sharing among consortium members, data sharing with the scientific community outside of the 4DN Network, and data sharing with industry partners; (2) procedures for safeguarding confidential information, including without limitation, any data generated by the consortium as well as information and/or data received from external collaborators; (3) procedures for addressing ownership of intellectual property resulting from aggregate multi-party data; (4) procedures for sharing tools and reagents under an overarching MTA amongst consortium members that operationalizes material transfer in an efficient and expeditious manner; (5) publication policy for the entire 4DN Network, determining timing, authorship, and content of co-publications, in order to facilitate collaborations and co-publications by consortium members while protecting each 4DN Network investigator’s primary ownership and authorship of their data and discoveries.

All 4DN investigators must facilitate the public release and dissemination of results, data, reagents, technologies, and other products generated through their 4DN awards in a timely manner via the 4DN Network Virtual Resource Repository (4DN-VRR) that will be built and managed by the 4DN Network Organizational Hub (4DN-OH) to collect, curate and disseminate information regarding data, critical tools, and reagents being developed by the 4DN Network. The 4DN-VRR will be accessible through the 4DN Network Portal. 4DN investigators are expected to share data and resources generated through this award in accordance with the approved plan for making quality-assured data and materials available to the scientific community and the NIH as written in the final version of the grant application, and consistent with sharing policies and recommendations developed and approved by the 4DN-SC and NIH sharing policies.

 

This page last reviewed on August 19, 2016