A growing number of OMICS- and imaging-based methods have been developed to characterize the chromatin architecture in mammalian cells. Individually, each method provides a snapshot of the chromatin organization but falls short in depicting the full picture. To gain a better understanding of the chromatin structure, a collaborative research project is conceived by members of the Nuclear Organization and Function Interdisciplinary Consortium (NOFIC). The overarching goal of this project is to study the chromatin organization of a panel of common genetic loci in a heterogeneous set of common cell lines using a diverse array of OMICS- and imaging-based technologies. Systematic comparisons of the different assays will be carried out to reveal the strengths and weaknesses of each method, to generate appropriate data standards, and to learn how different chromatin architectural features such as loops and TADs present themselves when examined using different methodologies. Results from this collaborative project are expected to greatly improve our understanding of the nuclear organization and its dynamics in mammalian cells, and provide important guidelines for expanding such studies to additional cell types and biological contexts.

• Agendas and minutes from phone calls

• Signup for presentations

• Data generation plan (Google sheets)

• Data analysis sandbox, with links to analysis products
• 2019 Dec:Joint Analysis Marker Paper Outline
• 2019 May: Joint Analysis paper plan tracking table
• 2019 January: Joint Analysis paper plan
• 2018 July: Draft analysis design for the integrative analysis.
• 2017 September: Joint Analysis discussion points during annual meeting
• 2017 August: Discussion on biological questions for 4DN joint analysis
• 2017 April:Joint Analysis Project Design(initated by NOFIC)
• Joint Analysis Data @ the 4DN Data Portal
• More info on Available Derived Results
• (Outdated) Groups, assays, cell line information
• (Outdated) Selected genetic loci

• Microscope Calibration Project

Job Dekker, Job.Dekker@umassmed.edu

Feng Yue, yuefeng.psu@gmail.com

From March 1, 2018, the meetings of JAWG and DAWG merge together to the weekly 4DN JAWG/DAWG Meeting. From Oct 3, 2019, the JAWG/DAWG meeting becomes a biweekly meeting.

The 4DN JAWG/DAWG Meeting is once every two weeks, onThursday at 1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time)

You can use email address meeting-4dn-dj@4dnucleome.org to send emails to all the JAWG/DAWG meeting members.

Joint Analysis presentations:

1. Everyone is welcome to give a presentation at the meetings, and in particular, we are interested in work relevant to the JA effort, for example, algorithms or effort related to data modeling or integration. Please sign up in the linked Google sheet.
2. Scheduled report of data generation and analysis group: Google sheet

WebEx Meeting Information

Biweekly Call - 4DN JAWG/DAWG Meeting

Once every two weeks, on Thursday（from Oct 3, 2019)

1:00-2:00 pm ET (Eastern Time), 10:00-11:00 am PT (Pacific Time)

Click here to Join WebEx meeting

Meeting number: 805 283 801

Meeting password: uJe93m63

Host key: 347076

Join by phone

+1-415-655-0002 US Toll

Access code: 805 283 801

WEBEX EMERGENCY CONTACT INFORMATION:
KATE RIVERA
858-822-1626 (OFFICE)

Meeting Chairs

• Job Dekker, Job.Dekker@umassmed.edu
• Feng Yue, yuefeng.psu@gmail.com
• William Noble, wnoble@uw.edu
• Peter Kharchenko, peter_kharchenko@hms.harvard.edu

We encourage to share your slides. All the slides are only shared within the 4DN network. They are stored in 4DN Google Drive. You need to use your 4DN associated google account to view the slides.

If you want to share your slides, please sent them to Zhangming (Frank) email: yanzm@ucsd.edu

• Older JA presentation archives (2018 - 2019)

• November 12, 2020
  • Meeting Agenda:
    • Presentation by Dr. Caterina Strambio De Castillia: Micro-Meta App, an interactive tool for the collection of microscopy metadata based on the 4DN-OME tiered system of guidelines
    • Presentation by Drs. Kaustav Sengupta and Dariusz Plewczynski: Phase condensation by percolation model with the single chromatin loop resolution
• October 29, 2020
  • Meeting Agenda:
    • Presentation by Dr. Andrew D Stephens: HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics.
    • Presentation by Dr. Jennifer E. Phillips-Cremins: Dissecting the genome’s structure function-relationship during replication
• October 15, 2020
  • Meeting Agenda:
    • Presentation by Dr. Kai Sandvold Beckwith (Ellenberg Lab): A method to resolve the nanoscale fold of chromosomal DNA below five kilobase resolution in single human cells under near-native conditions
• October 1, 2020
  • Meeting Agenda:
    • Presentation by Dr. Andrew Belmont: Integrative genome-wide analysis of nuclear compartmentalization in human cells
    • Presentation by Dr. David Grunwald: Meta-max: an easy-to-use calibration tool to maximize the value of fluorescence microscopy data
• September 17, 2020
  • Meeting Agenda:
    • Presentation by Dr. Minji Kim (Ruan Lab): Cohesin-mediated chromatin folding dynamics and transcriptional interactions
    • Presentation by Xingzhao Wen (Zhong Lab): Genome-wide RNA-chromatin interaction reveals RNA localization specificity along the nucleus radial axis
• September 3, 2020
  • Meeting Agenda:
    • Presentation by Dr. Daofeng Li (Wang Lab): Update on the WashU Epigenome Browser — Supporting 4DN and Beyond
• August 20, 2020
  • Meeting Agenda:
    • Presentation by Dr. Burak Alver: 4DN Data Portal and JAWG Data
    • Presentation by Dr. Derek Janssens: High-Throughput Chromatin Profiling Identifies Pathological Chromatin Signatures in Pediatric Acute Leukemia
• August 6, 2020
  • Meeting Agenda:
    • Presentation by Dr. Frank Alber: Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling
    • Presentation by Dr. Betul Akgol Oksuz: Comprehensive evaluation of 3C parameters identifies optimal methods for compartment or loop detection
• July 23, 2020
  • Meeting Agenda:
    • Presentation by Dr. Jie Liu: Connecting high-resolution 3D chromatin organization with epigenomics
    • Presentation by Dr. Caterina Strambio De Castillia: Minimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
• July 9, 2020
  • Meeting Agenda:
    • Presentation by Ruochi Zhang (Ma Lab): Exploiting single cell Hi-C data using Higashi
    • Presentation by Dr. Warren Winick-Ng (Pombo Lab): Cell-type specialization in the brain is encoded by specific long-range chromatin topologies
    • Presentation by Riccardo Calandrelli (Zhong Lab): Dynamic Changes in RNA-Chromatin Interactome Promote Endothelial Dysfunction
• June 25, 2020
  • Meeting Agenda:
    • Presentation by Dr. Jian Ma: Nucleome Browser: A multimodal, interactive data exploration platform for the 4D Nucleome (15+5 mins)
    • Presentation by Dr. Naoki Kubo (Ren Lab): Active role of CTCF in enhancer-promoter contacts and gene expression (15+5 mins)
    • Presentation by Dr. Hui Huang (Ren Lab): CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains (15+5 mins)
  • Recordings: https://drive.google.com/file/d/1OV0yWfU_T1aaPvSi49Ei6gKFdAhxu8Fj/view
• May 14, 2020
  • Meeting Agenda:
    • Presentation by Jian Ma: Integrative analysis of nuclear compartmentalization in human cell
    • Presentation by Alber Lab: Analysis of structure function correlations and subnuclear compartmentalization from genome structure modeling
• April 16, 2020
  • Meeting Agenda:
    • Presentation by Luca Fiorillo and Francesco Musella (Nicodemi’s Lab): Comparison of the Hi-C, GAM and SPRITE methods by use of polymer models of chromatin
• April 2, 2020
  • Meeting Agenda:
    • Planning the set of 4DN papers, the marker paper, and the Mol Cell review.
• February 20, 2020
  • Meeting Agenda:
    • Presentation by Luca Fiorillo and Francesco Musella (Nicodemi Lab): Comparison of the Hi-C, GAM and SPRITE by use of polymer models of chromatin
    • Presentation by Xingzhao Wen (Zhong Lab): Joint analysis of global RNA-DNA interaction data (iMARGI) and other 4DN omics data
• February 6, 2020
  • Meeting Agenda:
    • Presentation by Pombo Lab: Selection of H1 hESC genomic features and genomic window classification for joint analysis 3D-1D integration
• January 9, 2020
  • Meeting Agenda:
    • Updates by every group on current ongoing analyses
    • Discussion of coordination of paper submission

• Older Meeting Archives (2017 - 2019)

• Working Protocol
  • Draft version
• Questionnaire of locus engineering efforts in 4DN
  • Questionnaire Form
  • Result Table
• Data generation plan
  • Table
• Discussion on biological questions for 4DN joint analysis (July 2017)
  • Google Doc
• Joint Analysis Discussion during Annual Meeting (Sept 2017)
  • Google Doc
• Defining durable goods (Sept 2017)
  • Google Doc

Please use joint-4dn-analysis@4dnucleome.org to send an email to the JAWG mailing group.

As currently JAWG and DAWG are working together, so we have another JAWG/DAWG joint mailing group, which includes all the JAWG and DAWG people: meeting-4dn-dj@4dnucleome.org