Model Architecture
Figure 1: C.Origami Architecture (Left), input features: DNA sequence, CTCF ChIP-seq and ATAC-seq (Right))

Model Architecture

We developed Origami, a general model architecture based on CNN and transformers, to empower genomics studies. Origami incorporates both nucleotide-level DNA sequence and genomic signals (such as ATAC-seq signal) to make accurate, cell-type-specific predictions of genomic features. In this study, we demonstrate the model variant for predicting 3D chromatin architecture – C.Origami.

Cell type-specific Chromatin Architecture Prediction

Prediction Performance
Figure 2: High quality prediction

Given the DNA sequence, CTCF ChIP-seq and ATAC-seq signal, C.Origami makes de novo prediction of the Hi-C contact matrix within a 2Mb window. The prediction can be completed under 1 second with GPU.

In silico Genetic Perturbation and Screening

In silico genetic editing
Figure 3: An in silico genetic perturbation example in T cell

The high accuracy of prediction enables systematic in silico genetic studies of the 3D genome for cell type-specific factors – both cis-regulatory elements and trans-acting factors – that contribute to chromatin structures. Please refer to the full text for more applications and in silico experiments enabled by C.Origami.

Live Demo

Interactive live demo for IMR-90 and GM12878 prediction in real time. Reference genome fasta, cell type-specific CTCF ChIP-seq and ATAC-seq bigwigs are used as inputs.

Notes for the live demo:

  • The app is in alpha phase and might be unstable.
  • The next version will support custom sequence and bigwig/peaks inputs. Stay tuned!

Full Text

Cell type-specific prediction of 3D chromatin architecture Jimin Tan, Javier Rodriguez-Hernaez, Theodore Sakellaropoulos, Francesco Boccalatte, Iannis Aifantis, Jane Skok, David Fenyo, Bo Xia, Aristotelis Tsirigos; bioRxiv 2022.03.05.483136; doi: https://doi.org/10.1101/2022.03.05.483136

Code Availability

Code is currently beening documented and will be released shortly.