The 3D-Evo space: evolution of gene expression and alternative splicing regulation

F Mantica, M Irimia - Annual Review of Genetics, 2022 - annualreviews.org
Animal species present relatively high levels of gene conservation, and yet they display a
great variety of cell type and tissue phenotypes. These diverse phenotypes are mainly …

[HTML][HTML] Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions

E Laine, MI Freiberger - Current Opinion in Structural Biology, 2025 - Elsevier
The mRNA splicing machinery has been estimated to generate 100,000 known protein-
coding transcripts for 20,000 human genes (Ensembl, Sept. 2024). However, this set is …

Specialization of the photoreceptor transcriptome by Srrm3-dependent microexons is required for outer segment maintenance and vision

L Ciampi, F Mantica, L López-Blanch… - Proceedings of the …, 2022 - National Acad Sciences
Retinal photoreceptors have a distinct transcriptomic profile compared to other neuronal
subtypes, likely reflecting their unique cellular morphology and function in the detection of …

RBPMS2 is a myocardial-enriched splicing regulator required for cardiac function

AA Akerberg, M Trembley, V Butty… - Circulation …, 2022 - Am Heart Assoc
Background: RBPs (RNA-binding proteins) perform indispensable functions in the post-
transcriptional regulation of gene expression. Numerous RBPs have been implicated in …

Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals

A Torres-Méndez, S Pop, S Bonnal, I Almudi… - Science …, 2022 - science.org
Alternative splicing increases neuronal transcriptomic complexity throughout animal
phylogeny. To delve into the mechanisms controlling the assembly and evolution of this …

Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons

H Li, Z Ding, ZY Fang, N Long, HY Ang… - Nucleic Acids …, 2024 - academic.oup.com
Alternative splicing (AS) generates multiple RNA isoforms and increases the complexities of
transcriptomes and proteomes. However, it remains unclear how RNA structures contribute …

Genome-Wide Identification, Characterization, and Expression Analysis of Tubby-like Protein (TLP) Gene Family Members in Woodland Strawberry (Fragaria vesca)

S Li, G Wang, L Chang, R Sun, R Wu, C Zhong… - International Journal of …, 2022 - mdpi.com
Tubby-like proteins (TLPs) play important roles in plant growth and development and in
responses to abiotic stress. However, TLPs in strawberry remain poorly studied. In this study …

Differential transcript usage across mammalian oocytes at the germinal vesicle and metaphase II stages

T Sananmuang, D Puthier, C Nguyen… - Theriogenology, 2024 - Elsevier
Ongoing progress in mRNA-Sequencing technologies has significantly contributed to the
refinement of assisted reproductive technologies. However, the prior investigations have …

Calceolariaceae809: A bait set for targeted sequencing of nuclear loci

N Medina, DC Tank, A Espíndola - Applications in Plant …, 2023 - Wiley Online Library
Abstract Premise The genus Calceolaria (Calceolariaceae) is emblematic of the Andes, is
hypothesized to have originated as a recent, rapid radiation, and has important taxonomic …

Computational Analysis of Alternative Splicing Using VAST-TOOLS and the VastDB Framework

A Gohr, F Mantica, A Hermoso-Pulido, J Tapial… - … Splicing: Methods and …, 2022 - Springer
Alternative splicing (AS) can vastly expand animal transcriptomes and proteomes. Two main
open questions in the field are how AS is regulated across cell/tissue types and disease …