Deciphering the 3D genome organization across species from Hi-C data DOI Creative Commons

Aleksei Shkolikov,

Aleksandra A. Galitsyna, Mikhail S. Gelfand

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

Abstract Three-dimensional (3D) genome organization plays a critical role in gene expression regulation and function. Recent advances Hi-C Micro-C data across various species provide insights into the mechanisms governing 3D formation, such as loop extrusion. While visual patterns like topologically associating domains (TADs) loops are conserved species, underlying biological may differ. Both species-specific architectural factors DNA sequences influence chromatin folding, complicating comparative studies on evolution of genome. This work leverages existing machine learning to explore folding predict structures from sequences. Here, we present Chimaera (convolutional neural network for maps prediction using autoencoder representation), that not only predicts sequence, but also enables search, quantification, interpretation associations between patterns. Firstly, demonstrate or contact sequences, enabling extraction key mechanisms. By exploring latent representations generated by Chimaera, offer tool building an unsupervised atlas features insulation, loops, stripes, fountains/jets. We capabilities detecting quantifying signatures insulation fountains data, applying it well-characterized processes cell cycle embryogenesis. Additionally, perform targeted search sequence elements associated with specific structures, advancing our understanding organization. extending multiple confirm CTCF generating vertebrates BEAF-32 Drosophila , identify motifs previously reported mouse . In Dictyostelium demonstrates importance arrangement strand formation confirming hypothesis about impact convergent positioning this amoeba. A pronounced diverse effect genes is evident when predicting interactions other organisms. Finally, train model one then apply cross-predict how genomes organisms might fold within cellular environment original species. thereby test whether transferable reveal evolutionary similarities chromatin-based cluster tree ranging plants mammals. Key takeaways genomic interaction Chimaera’s unique architecture integrates encoder, allowing recurring their offers unified metric 3D-genome features, exploration validation complex hypotheses regarding principles including sequence-specific at protein binding sites genes. tasks biology demonstrating its ability consequences rearrangements, mutations, insertions.

Language: Английский

Mechanistic insights into ferroptosis and apoptosis pathways: Synergistic effects of multi-organ toxicity and transgenerational effects induced by co-exposure of epoxiconazole and aflatoxin B1 in zebrafish DOI Creative Commons

Ruike Wang,

Qi Zhang, Gang Chen

et al.

Journal of Advanced Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

1
Adaptive Significance of Non-coding RNAs: Insights from Cancer Biology DOI Creative Commons
John F. McDonald

Molecular Biology and Evolution, Journal Year: 2025, Volume and Issue: 42(1)

Published: Jan. 1, 2025

Abstract The molecular basis of adaptive evolution and cancer progression are both complex processes that share many striking similarities. potential significance environmentally-induced epigenetic changes is currently an area great interest in evolutionary biology. In the field biology intense effort has been focused on contribution stress-induced non-coding RNAs (ncRNAs) activation associated with elevated mutation rates acquisition environmentally traits. Examples this process presented combined more recent findings demonstrating ncRNAs transferable from somatic to germline cells leading cross-generational inheritance acquired fact have implicated transient response various plants animals environmental stress consistent Based these collective observations, a general model as well specific testable hypotheses proposed how ncRNA-mediated responses may facilitate transition long-term biological adaptation evolution.

Language: Английский

Citations

0
Cytosine Methylation is a marker of Viral Gene Transfer across the eukaryotes DOI Creative Commons
Luke A. Sarre, Gabriela P. Peralta, Pedro Romero Charria

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

Abstract Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable element silencing and host gene regulation. To further explore these claims, in this study, we reevaluate the evolutionary origins of methyltransferases characterise cytosine on underexplored lineages, including amoebozoan Acanthamoeba castellanii , glaucophyte Cyanophora paradoxa heterolobosean Naegleria gruberi . Our analysis methyltransferase evolution reveals a rich eukaryotic repertoire, several lineages likely subsequently acquiring enzymes through lateral transfer (LGT). In three species examined, is enriched young elements silenced genes, suggesting an repressive function, without transcription-linked body plants animals. Notably, closest homologues many silenced, methylated genes diverse eukaryotes belong viruses, giant viruses. Given widespread occurrence pattern groups, propose that was mechanism originally acquired from bacterial donors which used mitigate expression viral elements, function may persist creating permissive atmosphere for LGT lineages. These findings highlight importance epigenetic information annotate genomes, as it helps delimit potentially adaptive LGTs parasitic elements.

Language: Английский

Citations

0
Deciphering the 3D genome organization across species from Hi-C data DOI Creative Commons

Aleksei Shkolikov,

Aleksandra A. Galitsyna, Mikhail S. Gelfand

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

Abstract Three-dimensional (3D) genome organization plays a critical role in gene expression regulation and function. Recent advances Hi-C Micro-C data across various species provide insights into the mechanisms governing 3D formation, such as loop extrusion. While visual patterns like topologically associating domains (TADs) loops are conserved species, underlying biological may differ. Both species-specific architectural factors DNA sequences influence chromatin folding, complicating comparative studies on evolution of genome. This work leverages existing machine learning to explore folding predict structures from sequences. Here, we present Chimaera (convolutional neural network for maps prediction using autoencoder representation), that not only predicts sequence, but also enables search, quantification, interpretation associations between patterns. Firstly, demonstrate or contact sequences, enabling extraction key mechanisms. By exploring latent representations generated by Chimaera, offer tool building an unsupervised atlas features insulation, loops, stripes, fountains/jets. We capabilities detecting quantifying signatures insulation fountains data, applying it well-characterized processes cell cycle embryogenesis. Additionally, perform targeted search sequence elements associated with specific structures, advancing our understanding organization. extending multiple confirm CTCF generating vertebrates BEAF-32 Drosophila , identify motifs previously reported mouse . In Dictyostelium demonstrates importance arrangement strand formation confirming hypothesis about impact convergent positioning this amoeba. A pronounced diverse effect genes is evident when predicting interactions other organisms. Finally, train model one then apply cross-predict how genomes organisms might fold within cellular environment original species. thereby test whether transferable reveal evolutionary similarities chromatin-based cluster tree ranging plants mammals. Key takeaways genomic interaction Chimaera’s unique architecture integrates encoder, allowing recurring their offers unified metric 3D-genome features, exploration validation complex hypotheses regarding principles including sequence-specific at protein binding sites genes. tasks biology demonstrating its ability consequences rearrangements, mutations, insertions.

Language: Английский

Citations

0