To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive, it is common to use bioinformatics methods to group DNA segments into 3D regions with correlated contact patterns, such as Topologically associated domains and A/B compartments. Recently, another research direction emerged that treats the Hi-C data as a network of 3D contacts. In this representation, one can use community detection algorithms from complex network theory that group nodes into tightly connected mesoscale communities. However, because Hi-C networks are so densely connected, several node partitions may represent feasible solutions to the community detection problem but are indistinguishable unless including other data. Because this limitation is a fundamental property of the network, this problem persists regardless of the community-finding or data-clustering method. To help remedy this problem, we developed a method that charts the solution landscape of network partitions in Hi-C data from human cells. Our approach allows us to scan seamlessly through the scales of the network and determine regimes where we can expect reliable community structures. We find that some scales are more robust than others and that strong clusters may differ significantly. Our work highlights that finding a robust community structure hinges on thoughtful algorithm design or method cross-evaluation.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10415398 | PMC |
http://dx.doi.org/10.1038/s41598-023-39522-7 | DOI Listing |
Subcell Biochem
January 2025
Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences (ICB), Universidad Andres Bello, Santiago, Chile.
In animals, memory formation and recall are essential for their survival and for adaptations to a complex and often dynamically changing environment. During memory formation, experiences prompt the activation of a selected and sparse population of cells (engram cells) that undergo persistent physical and/or chemical changes allowing long-term memory formation, which can last for decades. Over the past few decades, important progress has been made on elucidating signaling mechanisms by which synaptic transmission leads to the induction of activity-dependent gene regulation programs during the different phases of learning (acquisition, consolidation, and recall).
View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
The spatial organization of the genome plays a critical role in regulating gene expression, cellular differentiation, and genome stability. This review provides an in-depth examination of the methodologies, computational tools, and frameworks developed to map the three-dimensional (3D) architecture of the genome, focusing on both ligation-based and ligation-free techniques. We also explore the limitations of these methods, including biases introduced by restriction enzyme digestion and ligation inefficiencies, and compare them to more recent ligation-free approaches such as Genome Architecture Mapping (GAM) and Split-Pool Recognition of Interactions by Tag Extension (SPRITE).
View Article and Find Full Text PDFSci Data
January 2025
Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
Coreius guichenoti, mainly distributed in upstream regions of the Yangtze River China, is currently on the brink of extinction and listed as national secondary protected animal. In this study, we aimed to obtain the chromosome-level genome of C. guichenoti using PacBio and Hi-C techniques.
View Article and Find Full Text PDFSci Data
January 2025
State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China.
The Yadong trout (Salmo trutta), a species endemic to the Yatung River in Tibet, China, was classified as a second-class protected species in the 20th century. Now, it is considered one of the most important fishery resources in China. In this study, we assembled a near-complete genome of the S.
View Article and Find Full Text PDFSci Data
January 2025
Shandong Key Laboratory of Disease Control in Mariculture, Key Laboratory of Benthic Fisheries Aquaculture and Enhancement, Marine Science Research Institute of Shandong Province (National Oceanographic Center, Qingdao), Qingdao, 266104, China.
Fat greenling (Hexagrammos otakii Jordan & Starks, 1895) is a valuable marine fish species, crucial for aquaculture in Northern China due to its high-quality meat and significant economic value. However, the aquaculture industry faces challenges such as trait degradation, early sexual maturity, and disease susceptibility, necessitating advanced genomic interventions for sustainable cultivation. This study presents the first chromosomal-level genome assembly of H.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!