Article
Multidisciplinary Sciences
Taeheon Lee, Sangseon Lee, Minji Kang, Sun Kim
Summary: This study introduces DeepHier, a deep learning model that learns representations of GPCR family hierarchy from protein sequences with a unified single model. A novel loss term based on metric learning is used to incorporate hierarchical relations between proteins, successfully capturing the hierarchical relationships between sequences.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Ryan Loker, Jordyn E. Sanner, Richard S. Mann
Summary: Hox proteins modulate segment identity by changing chromatin accessibility and binding of transcription factors like Scalloped in a spatially-regulated manner, with their transcriptional activity dependent on the availability of cofactors.
Article
Biochemical Research Methods
Martin Hoelzer, Manja Marz
Summary: PoSeiDon is an easy-to-use pipeline that helps researchers find recombination events and sites under positive selection in protein-coding sequences. The tool builds an alignment, estimates a best-fitting substitution model, performs recombination analysis, and detects positively selected sites according to different models, with results summarized in a user-friendly HTML page.
Article
Multidisciplinary Sciences
Tereza Clarence, Nicolas S. M. Robert, Fatih Sarigol, Xiao Fu, Paul A. Bates, Oleg Simakov
Summary: Animal genomes are organized into conserved chromosomes that form distinct evolutionary units. By using chromosomal modeling, researchers have inferred the three-dimensional topology of animal genomes. They have identified evolutionarily conserved three-dimensional networks and novel interactors associated with known gene linkages. This evidence suggests that the spatial organization of animal genomes, termed spatiosynteny, plays a role in understanding the conservation of chromosomes.
Article
Plant Sciences
Hongtao Song, Qi Wang, Zhonghua Zhang, Kui Lin, Erli Pang
Summary: This study presents a computational approach to predict putative cis-regulatory elements in the Cucurbitaceae genomes. The researchers identified a large number of cis-regulatory elements using whole-genome alignment and validated their predictions using various datasets. The results provide valuable resources for functionally annotating conserved non-coding sequences and studying their regulatory roles in Cucurbitaceae genomes.
HORTICULTURE RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Elise Parey, Diego Fernandez-Aroca, Stephanie Frost, Ainhoa Uribarren, Thomas J. Park, Markus Zottl, Ewan St John Smith, Camille Berthelot, Diego Villar
Summary: Changes in gene regulation play a crucial role in the phenotypic differences between species. In this study, researchers investigate the regulatory evolution in the heart and liver of African mole-rats and other rodent species using epigenomic profiling. The study reveals the association between specific regulatory changes and phenotypic adaptations, such as metabolic pathways, in mole-rats. Additionally, the study proposes a phylogenetic modeling framework that improves upon the existing methods and has broad implications for comparative functional genomics.
Article
Biochemistry & Molecular Biology
Conor J. Kelly, Carol G. Chitko-McKown, Edward B. Chuong
Summary: This study reveals the role of lineage-specific transposable elements (TEs) in shaping the evolution of immune responses in cattle and their potential contribution to immune gene regulatory differences across modern breeds and individuals.
Article
Cell Biology
Juliana Gusson Roscito, Katrin Sameith, Bogdan Mikhailovich Kirilenko, Nikolai Hecker, Sylke Winkler, Andreas Dahl, Miguel Trefaut Rodrigues, Michael Hiller
Summary: A comparative genomic analysis of limbless reptiles reveals that shared divergence occurs more often at the level of signaling pathways and patterning mechanisms, rather than in individual limb regulatory elements. Different mechanisms, such as different regulatory elements associated with the same limb genes and/or patterning mechanisms, may contribute to limb loss in reptiles.
Article
Multidisciplinary Sciences
Eeshit Dhaval Vaishnav, Carl G. de Boer, Jennifer Molinet, Moran Yassour, Lin Fan, Xian Adiconis, Dawn A. Thompson, Joshua Z. Levin, Francisco A. Cubillos, Aviv Regev
Summary: This study builds sequence-to-expression models using deep neural networks to analyze the expression levels of promoter DNA sequences in Saccharomyces cerevisiae, and reveals principles of regulatory evolution. The findings show that regulatory evolution is rapid and subject to diminishing returns epistasis, conflicting expression objectives in different environments constrain expression adaptation, and stabilizing selection on gene expression leads to the moderation of regulatory complexity.
Article
Genetics & Heredity
Jumpei Ito, Yasunari Seita, Shohei Kojima, Nicholas F. Parrish, Kotaro Sasaki, Kei Sato
Summary: This study reveals that hominoid-specific insertions of endogenous retroviruses, known as LTR5_Hs, contribute to the fine-tuning of the gene regulatory network shared between primordial germ cells (PGCs) and naive pluripotent cells. These insertions are preferentially bound by transcription factors and epigenetically activated, leading to coordinated alteration of gene expression in these cells. This suggests that these retroviral insertions have played a role in rewiring the gene regulatory network during hominoid evolution.
Article
Plant Sciences
Weichao Ren, Zhehui Jiang, Meiqi Zhang, Lingyang Kong, Houliang Zhang, Yunwei Liu, Qifeng Fu, Wei Ma
Summary: This study sequenced the chloroplast genome of the rare alpine tree species Salix floderusii for the first time and identified important genes, highly variable regions, and phylogenetic relationships. The findings provide a foundation for further research on genetic improvement of Salix floderusii.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Yuyun Zhang, Zijuan Li, Yu'e Zhang, Kande Lin, Yuan Peng, Luhuan Ye, Yili Zhuang, Meiyue Wang, Yilin Xie, Jingyu Guo, Wan Teng, Yiping Tong, Wenli Zhang, Yongbiao Xue, Zhaobo Lang, Yijing Zhang
Summary: The majority of transcription factor binding sites in the wheat genome are embedded in transposable elements, contributing to adaptive evolution. Some non-transposable element derived binding sites share high sequence similarity with transposable element embedded sites, potentially originating from Triticeae-specific transposable elements. Transposable element-derived binding sites are linked to wheat-specific gene responses, indicating they play a crucial role in driving regulatory innovations.
Article
Cell Biology
Stefano Secchia, Mattia Forneris, Tobias Heinen, Oliver Stegle, Eileen E. M. Furlong
Summary: This study combines single-cell regulatory genomics with loss-of-function mutants to systematically evaluate the functional input of transcription factors (TFs) and uncover cellular and molecular phenotypes. By performing experiments at different time points during Drosophila embryo development, the researchers reconstruct the developmental trajectories and identify the TFs and enhancers involved in major muscle types. They also develop a single-nucleus genotyping strategy to assess mutant phenotypes and discover new ones while revealing regulatory input and mode of action.
DEVELOPMENTAL CELL
(2022)
Article
Multidisciplinary Sciences
Xing Guo, Dongming Fang, Sunil Kumar Sahu, Shuai Yang, Xuanmin Guang, Ryan Folk, Stephen A. Smith, Andre S. Chanderbali, Sisi Chen, Min Liu, Ting Yang, Shouzhou Zhang, Xin Liu, Xun Xu, Pamela S. Soltis, Douglas E. Soltis, Huan Liu
Summary: Chloranthales are the last major mesangiosperm lineage without a nuclear genome assembly, but a high-quality genome assembly of Chloranthus spicatus has now been achieved, providing insights into the evolutionary relationships and genome evolution of mesangiosperms. This study sheds light on the unique characteristics of Chloranthales and magnoliids compared to other angiosperms, and contributes to a better understanding of angiosperm diversification and phylogeny.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Mohannad Dardiry, Gabi W. Eberhard, Hanh J. Witte, Christian Roedelsperger, James Lightfoot, Ralf Sommer
Summary: This study reveals the genetic mechanism underlying the phenotypic plasticity in the predatory nematode Pristionchus pacificus. It identifies a core developmental gene and a QTL that control the expression of cannibalistic morph, which is composed of several cis-regulatory elements. The comparisons of other predatory nematodes further support the rapid evolution of these cis-regulatory elements, demonstrating their important roles in plastic trait expression and control of nematode cannibalism.