[HTML][HTML] Revealing gene function and transcription relationship by reconstructing gene-level chromatin interaction
Chromatin is hierarchically organized in human interphase nuclei. Dynamic chromatin
interactions are thought to influence gene transcription and cell fate determination. A …
interactions are thought to influence gene transcription and cell fate determination. A …
De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture
M Di Pierro, RR Cheng… - Proceedings of the …, 2017 - National Acad Sciences
Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell
type. Here, we show that this chromatin architecture can be predicted de novo using …
type. Here, we show that this chromatin architecture can be predicted de novo using …
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding
Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables
diverse transcriptional programs to arise from a single genetic blueprint, whereas its …
diverse transcriptional programs to arise from a single genetic blueprint, whereas its …
Methods for mapping 3D chromosome architecture
R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …
understanding the role of chromatin topology in gene regulation. Several methods are …
A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions
Chromosome conformation capture methods are being increasingly used to study three-
dimensional genome architecture in multiple cell types and species. An important challenge …
dimensional genome architecture in multiple cell types and species. An important challenge …
Compartmentalization with nuclear landmarks yields random, yet precise, genome organization
The 3D organization of eukaryotic genomes plays an important role in genome function.
While significant progress has been made in deciphering the folding mechanisms of …
While significant progress has been made in deciphering the folding mechanisms of …
Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling
Background The sequence of a genome is insufficient to understand all genomic processes
carried out in the cell nucleus. To achieve this, the knowledge of its threedimensional …
carried out in the cell nucleus. To achieve this, the knowledge of its threedimensional …
Single‐cell imaging of genome organization and dynamics
Probing the architecture, mechanism, and dynamics of genome folding is fundamental to our
understanding of genome function in homeostasis and disease. Most chromosome …
understanding of genome function in homeostasis and disease. Most chromosome …
Unraveling the 3D genome: genomics tools for multiscale exploration
VI Risca, WJ Greenleaf - Trends in Genetics, 2015 - cell.com
A decade of rapid method development has begun to yield exciting insights into the 3D
architecture of the metazoan genome and the roles it may play in regulating transcription …
architecture of the metazoan genome and the roles it may play in regulating transcription …