4dn-project.md

4D nucleome project

1. What is 4D Nucleome
   
2. Current dilemma in understanding 4D nucleome
   
3. Goals and Strategies
   
4. Structure of the 4DN Network
   
5. Data sharing and standards
   

What is 4D Nucleome

To determine how the genome operates, we need to understand not only the linear encoding of information along chromosomes, but also its three-dimensional organization and its dynamics across time, that is, the ‘4D nucleome’.

Current dilemma in understanding 4D nucleome

• Different experimental cell systems and approaches are used that together with the absence of shared benchmarks for assay performance have led to observations that cannot be directly compared.
• Iimited ability to integrate different data types (for example, chromatin interaction data and imaging-based distance measurements)。
• Lack of approaches that can measure and account for cell-to-cell variability in chromosome and nuclear organization.
• Lack of mechanistic insights into the relationships between chromosome conformation and nuclear processes, including transcription, DNA replication and chromosome segregation.

Goals and Strategies

Goals:

• Develop, benchmark, validate and standardize a wide array of technologies to analyse the 4D nucleome
• Integrate, analyse and model datasets obtained with these technologies to obtain a comprehensive view of the 4D nucleome
• Investigate the functional role of various structural features of chromosome organization in transcription, DNA replication and other nuclear processes.

###Strategies:

• A set of common cell lines will be studied to enable direct cross- validation of data that are obtained with different methods table.
• Standards for data formats and quality will be established so that data can be shared broadly.
• Computational and analytical tools will be developed to analyse individual datasets and to integrate, compare and cross-validate data obtained with different technologies.
• Develope multiple ways to measure how DNA and trans-acting factors influence on the 4D nucleosome.
• Develop a consistent terminology to describe nuclear features and biophysically derived principles guiding chromosome folding.
• Compare and integrate the wealth of information that is anticipated to be generated by the Network.
• Build a shared database and a public 4DN data browser includes all data, detailed protocols, engineered cell lines and reagents used across the Network.

Structure of the 4DN Network

Consortium	Institution Name	Objections
NOFIC (Nuclear Organization and Function Interdisciplinary Consortium)	UNIVERSITY OF SOUTHERN CALIFORNIA UNIV OF ILLINOIS URBANA-CHAMPAIGN UNIV OF MASSACHUSETTS MED SCH WORCESTER LUDWIG INSTITUTE FOR CANCER RESEARCH LTD JACKSON LABORATORY UNIV OF WASHINGTON	benchmark tools Find best approach Integrate approaches Draft model of 4DN
Imaging Tools	YALE UNIVERSITY CALIFORNIA INSTITUTE OF TECHNOLOGY PRINCETON UNIVERSITY EUROPEAN MOLECULAR BIOLOGY LABORATORY UNIV OF MASSACHUSETTS MED SCH WORCESTER UNIVERSITY OF CALIFORNIA AT DAVIS STANFORD UNIVERSITY SALK INSTITUTE FOR BIOLOGICAL STUDIES ALBERT EINSTEIN COLLEGE OF MEDICINE	High res method High-throughput dynamic imaging Live cell
DCIC (Network Data Coordination and Integration Center)	HARVARD MEDICAL SCHOOL WASHINGTON UNIVERSITY	collect, store, curate, display and analyze data develope efficient submission pipelines high-quality, well- annotated, public accessible user-friendly data portal
Network Organizational Hub	UNIVERSITY OF CALIFORNIA SAN DIEGO	web portal for 4DN integrated, bersatile data management retrieval, analysis and vis system train and update 4DN members and collaboraters
Nuclear Bodies and Compartments	PRINCETON UNIVERSITY SCRIPPS RESEARCH INSTITUTE PRINCETON UNIVERSITY FRED HUTCHINSON CANCER RES CENTER CALIFORNIA INSTITUTE OF TECHNOLOGY UNIV OF MASSACHUSETTS MED SCH WORCESTER COLUMBIA UNIVERSITY HEALTH SCIENCES	deciphering function of compartments nucleoplasmic phase transitions reversibly disrupt nuclear bodies
Nucleomics Tools	THE BABRAHAM INSTITUTE CALIFORNIA INSTITUTE OF TECHNOLOGY BAYLOR COLLEGE OF MEDICINE CORNELL UNIVERSITY UNIVERSITY OF PENNSYLVANIA	pipeline for single-cell hi-c map dynamic organization split pool barcoding distance-Hi-C super resolution vis

Data sharing and standards

• Need to develope common formats to represent three-dimensional interactions.
• Efficient data structure to store sparse matrix (interaction matrix is sparse)
• Standards to unify data and metadata from different manufacturers for imaging technologies.
• Define a set of appropriate metadata fields and minimum metadata requirements such that sufficient and useful details are available to other investigators outside the Network.
• Develope a set of measures for assessing data quality and determining appropriate thresholds.

#Reference [1] Dekker, Job, et al. "The 4D nucleome project." Nature 549.7671 (2017): 219.
[2] https://commonfund.nih.gov/4Dnucleome