Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects

ME Rogalska, C Vivori, J Valcárcel - Nature Reviews Genetics, 2023 - nature.com
The removal of introns from mRNA precursors and its regulation by alternative splicing are
key for eukaryotic gene expression and cellular function, as evidenced by the numerous …

The causes of evolvability and their evolution

JL Payne, A Wagner - Nature Reviews Genetics, 2019 - nature.com
Evolvability is the ability of a biological system to produce phenotypic variation that is both
heritable and adaptive. It has long been the subject of anecdotal observations and …

Mutation effects predicted from sequence co-variation

TA Hopf, JB Ingraham, FJ Poelwijk, CPI Schärfe… - Nature …, 2017 - nature.com
Many high-throughput experimental technologies have been developed to assess the
effects of large numbers of mutations (variation) on phenotypes. However, designing …

Deep generative models of genetic variation capture the effects of mutations

AJ Riesselman, JB Ingraham, DS Marks - Nature methods, 2018 - nature.com
The functions of proteins and RNAs are defined by the collective interactions of many
residues, and yet most statistical models of biological sequences consider sites nearly …

Variant interpretation: functional assays to the rescue

LM Starita, N Ahituv, MJ Dunham, JO Kitzman… - The American Journal of …, 2017 - cell.com
Classical genetic approaches for interpreting variants, such as case-control or co-
segregation studies, require finding many individuals with each variant. Because the …

The causes and consequences of genetic interactions (epistasis)

J Domingo, P Baeza-Centurion… - Annual review of …, 2019 - annualreviews.org
The same mutation can have different effects in different individuals. One important reason
for this is that the outcome of a mutation can depend on the genetic context in which it …

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

R Tuladhar, Y Yeu, J Tyler Piazza, Z Tan… - Nature …, 2019 - nature.com
The introduction of insertion-deletions (INDELs) by non-homologous end-joining (NHEJ)
pathway underlies the mechanistic basis of CRISPR-Cas9-directed genome editing …

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

D Esposito, J Weile, J Shendure, LM Starita… - Genome biology, 2019 - Springer
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …

Scalable functional assays for the interpretation of human genetic variation

D Tabet, V Parikh, P Mali, FP Roth… - Annual Review of …, 2022 - annualreviews.org
Scalable sequence–function studies have enabled the systematic analysis and cataloging of
hundreds of thousands of coding and noncoding genetic variants in the human genome …

Inferring protein 3D structure from deep mutation scans

NJ Rollins, KP Brock, FJ Poelwijk, MA Stiffler… - Nature …, 2019 - nature.com
We describe an experimental method of three-dimensional (3D) structure determination that
exploits the increasing ease of high-throughput mutational scans. Inspired by the success of …