Non-coding driver mutations in human cancer

K Elliott, E Larsson - Nature Reviews Cancer, 2021 - nature.com
Tumour formation involves random mutagenic events and positive evolutionary selection
acting on a subset of such events, referred to as driver mutations. A decade of careful …

Incomplete penetrance and variable expressivity: from clinical studies to population cohorts

R Kingdom, CF Wright - Frontiers in Genetics, 2022 - frontiersin.org
The same genetic variant found in different individuals can cause a range of diverse
phenotypes, from no discernible clinical phenotype to severe disease, even among related …

The evolution, evolvability and engineering of gene regulatory DNA

ED Vaishnav, CG de Boer, J Molinet, M Yassour, L Fan… - Nature, 2022 - nature.com
Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal
phenotype and fitness,–. Constructing complete fitness landscapes, in which DNA …

Controlling gene expression with deep generative design of regulatory DNA

J Zrimec, X Fu, AS Muhammad, C Skrekas… - Nature …, 2022 - nature.com
Abstract Design of de novo synthetic regulatory DNA is a promising avenue to control gene
expression in biotechnology and medicine. Using mutagenesis typically requires screening …

Evolution by gene loss

R Albalat, C Cañestro - Nature Reviews Genetics, 2016 - nature.com
The recent increase in genomic data is revealing an unexpected perspective of gene loss as
a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This …

MicroRNA and transcription factor: key players in plant regulatory network

AFA Samad, M Sajad, N Nazaruddin, IA Fauzi… - Frontiers in plant …, 2017 - frontiersin.org
Recent achievements in plant microRNA (miRNA), a large class of small and non-coding
RNAs, are very exciting. A wide array of techniques involving forward genetic, molecular …

Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing

J Attig, F Agostini, C Gooding, AM Chakrabarti, A Singh… - Cell, 2018 - cell.com
Long mammalian introns make it challenging for the RNA processing machinery to identify
exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection …

Evolution of binding preferences among whole-genome duplicated transcription factors

T Gera, F Jonas, R More, N Barkai - Elife, 2022 - elifesciences.org
Throughout evolution, new transcription factors (TFs) emerge by gene duplication,
promoting growth and rewiring of transcriptional networks. How TF duplicates diverge was …

Massively parallel reporter assays and variant scoring identified functional variants and target genes for melanoma loci and highlighted cell-type specificity

E Long, J Yin, KM Funderburk, M Xu, J Feng… - The American Journal of …, 2022 - cell.com
The most recent genome-wide association study (GWAS) of cutaneous melanoma identified
54 risk-associated loci, but functional variants and their target genes for most have not been …

Chromatin dependencies in cancer and inflammation

I Marazzi, BD Greenbaum, DHP Low… - Nature reviews Molecular …, 2018 - nature.com
Multiple cell-signalling pathways converge on chromatin to induce gene expression
programmes. The inducible transcriptional programmes that are established as a result of …