Martín, Guiomar Márquez, Yamile Mantica, Federica Duque, Paula Irimia, Manuel
Published in
Genome Biology
BackgroundAlternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehen...
Wang, Yuchuan Zhang, Yang Zhang, Ruochi van Schaik, Tom Zhang, Liguo Sasaki, Takayo Peric-Hupkes, Daniel Chen, Yu Gilbert, David M. van Steensel, Bas
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Published in
Genome Biology
We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for modulating genome function. As a proof-of-principle, we use SPIN to integrate nuclear compartment mapping (TSA-seq and DamID) and chromatin inte...
Chia, Minghao Li, Cai Marques, Sueli Pelechano, Vicente Luscombe, Nicholas M. van Werven, Folkert J.
Published in
Genome Biology
BackgroundThe start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniqu...
Wu, Xujia Xiao, Songhua Zhang, Maolei Yang, Lixuan Zhong, Jian Li, Bo Li, Fanying Xia, Xin Li, Xixi Zhou, Huangkai
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Published in
Genome Biology
BackgroundAberrant activation of the Hedgehog pathway drives tumorigenesis of many cancers, including glioblastoma. However, the sensitization mechanism of the G protein-coupled-like receptor smoothened (SMO), a key component of Hedgehog signaling, remains largely unknown.ResultsIn this study, we describe a novel protein SMO-193a.a. that is essenti...
Lyon, Matthew S. Andrews, Shea J. Elsworth, Ben Gaunt, Tom R. Hemani, Gibran Marcora, Edoardo
Published in
Genome Biology
GWAS summary statistics are fundamental for a variety of research applications yet no common storage format has been widely adopted. Existing tabular formats ambiguously or incompletely store information about genetic variants and associations, lack essential metadata and are typically not indexed yielding poor query performance and increasing the ...
Zhang, Kaixuan He, Ming Fan, Yu Zhao, Hui Gao, Bin Yang, Keli Li, Faliang Tang, Yu Gao, Qiang Lin, Tao
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Published in
Genome Biology
BackgroundTartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited.ResultsHere, we report a comprehensive data...
Ross, Caroline Jane Rom, Aviv Spinrad, Amit Gelbard-Solodkin, Dikla Degani, Neta Ulitsky, Igor
Published in
Genome Biology
BackgroundAnimal genomes contain thousands of long noncoding RNA (lncRNA) genes, a growing subset of which are thought to be functionally important. This functionality is often mediated by short sequence elements scattered throughout the RNA sequence that correspond to binding sites for small RNAs and RNA binding proteins. Throughout vertebrate evo...
Luhmann, Nina Holley, Guillaume Achtman, Mark
Published in
Genome Biology
BlastFrost is a highly efficient method for querying 100,000s of genome assemblies, building on Bifrost, a dynamic data structure for compacted and colored de Bruijn graphs. BlastFrost queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes o...
Moelling, Karin
Published in
Genome Biology
Jia, Jizeng Xie, Yilin Cheng, Jingfei Kong, Chuizheng Wang, Meiyue Gao, Lifeng Zhao, Fei Guo, Jingyu Wang, Kai Li, Guangwei
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Published in
Genome Biology
BackgroundPolyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown.ResultsWe probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely cult...
