PUBLICATION
A new and improved algorithm for the quantification of chromatin condensation from microscopic data shows decreased chromatin condensation in regenerating axolotl limb cells
- Authors
- Sosnik, J., Vieira, W.A., Webster, K.A., Siegfried, K.R., McCusker, C.D.
- ID
- ZDB-PUB-171013-6
- Date
- 2017
- Source
- PLoS One 12: e0185292 (Journal)
- Registered Authors
- Siegfried, Kellee, Sosnik, Julian, Webster, Kaitlyn
- Keywords
- none
- MeSH Terms
-
- Algorithms*
- Ambystoma mexicanum
- Animals
- Cell Differentiation
- Cell Nucleus/metabolism*
- Cells, Cultured
- Chromatin/chemistry*
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Embryonic Development/physiology
- Extremities/embryology*
- Induced Pluripotent Stem Cells/cytology
- Induced Pluripotent Stem Cells/metabolism*
- Zebrafish/genetics*
- Zebrafish/growth & development
- Zebrafish/metabolism
- PubMed
- 29023511 Full text @ PLoS One
Citation
Sosnik, J., Vieira, W.A., Webster, K.A., Siegfried, K.R., McCusker, C.D. (2017) A new and improved algorithm for the quantification of chromatin condensation from microscopic data shows decreased chromatin condensation in regenerating axolotl limb cells. PLoS One. 12:e0185292.
Abstract
The nuclear landscape plays an important role in the regulation of tissue and positional specific genes in embryonic and developing cells. Changes in this landscape can be dynamic, and are associated with the differentiation of cells during embryogenesis, and the de-differentiation of cells during induced pluripotent stem cell (iPSC) formation and in many cancers. However, tools to quantitatively characterize these changes are limited, especially in the in vivo context, where numerous tissue types are present and cells are arranged in multiple layers. Previous tools have been optimized for the monolayer nature of cultured cells. Therefore, we present a new algorithm to quantify the condensation of chromatin in two in vivo systems. We first developed this algorithm to quantify changes in chromatin compaction and validated it in differentiating spermatids in zebrafish testes. Our algorithm successfully detected the typical increase in chromatin compaction as these cells differentiate. We then employed the algorithm to quantify the changes that occur in amphibian limb cells as they participate in a regenerative response. We observed that the chromatin in the limb cells de-compacts as they contribute to the regenerating organ. We present this new tool as an open sourced software that can be readily accessed and optimized to quantify chromatin compaction in complex multi-layered samples.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping