jie

jie is a spatial genome aligner. This package parses true chromatin imaging signal from noise by aligning signals to a reference DNA polymer model.

The codename is a tribute to the Chinese homophones:

• 接 (jiē) : to connect, DNA appearing as dots under imaging, as if to trace out a constellation
• 结 (jié) : a knot, a nod to the mysterious and often entangled structures of DNA
• 解 (jiĕ) : to solve, to untie, our bid to uncover these structures amid noise and uncertainty
• 姐 (jiĕ) : sister, our ability to resolve tightly paired replicated chromatids

Installation

Step 1 - Clone this repository:

git clone https://github.com/b2jia/jie.git
cd jie

Step 2 - Create a new conda environment and install dependencies:

conda env create --name jie --file=environment.yml
conda activate jie

Step 3 - Install jie:

pip install -e .

To test, run:

cd test
python -W ignore test_jie.py

Usage

jie is an exposition of chromatin tracing using polymer physics. The main function of this package is to illustrate the utility and power of spatial genome alignment.

jie is NOT an all-purpose spatial genome aligner. Chromatin imaging is a nascent field and data collection is still being standardized. This aligner may not be compatible with different imaging protocols and data formats, among other variables.

We provide a vignette under jie/jupyter/, with emphasis on inspectability. This walks through the intuition of our spatial genome alignment and polymer fiber karyotyping routines:

00-spatial-genome-alignment-walk-thru.ipynb

We also provide a series of Jupyter notebooks (jie/jupyter/), with emphasis on reproducibility. This reproduces figures from our accompanying manuscript:

01-seqFISH-plus-mouse-ESC-spatial-genome-alignment.ipynb
02-seqFISH-plus-mouse-ESC-polymer-fiber-karyotyping.ipynb
03-seqFISH-plus-mouse-brain-spatial-genome-alignment.ipynb
04-seqFISH-plus-mouse-brain-polymer-fiber-karyotyping.ipynb
05-bench-mark-spatial-genome-agignment-against-chromatin-tracing-algorithm.ipynb  

A command-line tool forthcoming.

Motivation

Multiplexed DNA-FISH is a powerful imaging technology that enables us to peer directly at the spatial location of genes inside the nucleus. Each gene appears as tiny dot under imaging.

Pivotally, figuring out which dots are physically linked would trace out the structure of chromosomes. Unfortunately, imaging is noisy, and single-cell biology is extremely variable. The two confound each other, making chromatin tracing prohibitively difficult!

For instance, in a diploid cell line with two copies of a gene we expect to see two spots. But what happens when we see:

• Extra signals:

  • Is it noise?

    • Off-target labeling: The FISH probes might inadvertently label an off-target gene

  • Or is it biological variation?

    • Aneuploidy: A cell (ie. cancerous cell) may have more than one copy of a gene
    • Cell cycle: When a cell gets ready to divide, it duplicates its genes

• Missing signals:

  • Is it noise?

    • Poor probe labeling: The FISH probes never labeled the intended target gene

  • Or is it biological variation?

    • Copy Number Variation: A cell may have a gene deletion

If true signal and noise are indistinguishable, how do we know we are selecting true signals during chromatin tracing? It is not obvious which spots should be connected as part of a chromatin fiber. This dilemma was first aptly characterized by Ross et al. (https://journals.aps.org/pre/abstract/10.1103/PhysRevE.86.011918), which is nothing short of prescient...!

jie is, conceptually, a spatial genome aligner that disambiguates spot selection by checking each imaged signal against a reference polymer physics model of chromatin. It relies on the key insight that the spatial separation between two genes should be congruent with its genomic separation.

It makes no assumptions about the expected copy number of a gene, and when it traces chromatin it does so instead by evaluating the physical likelihood of the chromatin fiber. In doing so, we can uncover copy number variations and even sister chromatids from multiplexed DNA-FISH imaging data.

Citation

• Jia, B.B. et al. A spatial genome aligner for resolving chromatin architectures from multiplexed DNA-FISH. Nature Biotechnology (2022) doi:10.1038/s41587-022-01568-9

Contact

Author

Bojing (Blair) Jia

Email

b2jia at eng dot ucsd dot edu

Position

MD-PhD Student, Ren Lab

For other work related to single-cell biology, 3D genome, and chromatin imaging, please visit Prof. Bing Ren's website: http://renlab.sdsc.edu/