The GC content as a main factor shaping the amino acid usage during bacterial evolution process

MZ Du, C Zhang, H Wang, S Liu, W Wei… - Frontiers in …, 2018 - frontiersin.org
Understanding how proteins evolve is important, and the order of amino acids being
recruited into the genetic codons was found to be an important factor shaping the amino acid …

CompoDynamics: a comprehensive database for characterizing sequence composition dynamics

S Jiang, Q Du, C Feng, L Ma, Z Zhang - Nucleic acids research, 2022 - academic.oup.com
Sequence compositions of nucleic acids and proteins have significant impact on gene
expression, RNA stability, translation efficiency, RNA/protein structure and molecular …

Physicochemical foundations of life that direct evolution: chance and natural selection are not evolutionary driving forces

D Auboeuf - Life, 2020 - mdpi.com
The current framework of evolutionary theory postulates that evolution relies on random
mutations generating a diversity of phenotypes on which natural selection acts. This …

Systematic analysis of mouse genome reveals distinct evolutionary and functional properties among circadian and ultradian genes

S Castellana, T Mazza, D Capocefalo, N Genov… - Frontiers in …, 2018 - frontiersin.org
In living organisms, biological clocks regulate 24 h (circadian) molecular, physiological, and
behavioral rhythms to maintain homeostasis and synchrony with predictable environmental …

Splicing complexity as a pivotal feature of alternative exons in mammalian species

F Zhao, Y Yan, Y Wang, Y Liu, R Yang - BMC genomics, 2023 - Springer
Background As a significant process of post-transcriptional gene expression regulation in
eukaryotic cells, alternative splicing (AS) of exons greatly contributes to the complexity of the …

3′ untranslated regions of tumor suppressor genes evolved specific features to favor cancer resistance

D Huang, X Wang, Z Huang, Y Liu, X Liu, T Gin… - Oncogene, 2022 - nature.com
Cancer-related genes have evolved specific genetic and genomic features to favor tumor
suppression. Previously we reported that tumor suppressor genes (TSGs) acquired high …

Codon selection reduces GC content bias in nucleic acids encoding for intrinsically disordered proteins

CJ Oldfield, Z Peng, VN Uversky, L Kurgan - Cellular and Molecular Life …, 2020 - Springer
Protein-coding nucleic acids exhibit composition and codon biases between sequences
coding for intrinsically disordered regions (IDRs) and those coding for structured regions …

Protein intrinsic disorder negatively associates with gene age in different eukaryotic lineages

S Banerjee, S Chakraborty - Molecular BioSystems, 2017 - pubs.rsc.org
The emergence of new protein-coding genes in a specific lineage or species provides raw
materials for evolutionary adaptations. Until recently, the biology of new genes emerging …

Single-hit inactivation drove tumor suppressor genes out of the X chromosome during evolution

X Wang, W Hu, X Li, D Huang, Q Li, H Chan, J Zeng… - Cancer Research, 2022 - AACR
Cancer-related genes are under intense evolutionary pressure. In this study, we conjecture
that X-linked tumor suppressor genes (TSG) are not protected by the Knudson's two-hit …

Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance

D Huang, X Wang, Y Liu, Z Huang, X Hu… - Briefings in …, 2021 - academic.oup.com
Tumor suppressor genes (TSGs) exhibit distinct evolutionary features. We speculated that
TSG promoters could have evolved specific features that facilitate their tumor-suppressing …