Determinants of enhancer and promoter activities of regulatory elements

R Andersson, A Sandelin - Nature Reviews Genetics, 2020 - nature.com
The proper activities of enhancers and gene promoters are essential for coordinated
transcription within a cell. Although diverse methodologies have been developed to identify …

A brief history of human disease genetics

M Claussnitzer, JH Cho, R Collins, NJ Cox… - Nature, 2020 - nature.com
A primary goal of human genetics is to identify DNA sequence variants that influence
biomedical traits, particularly those related to the onset and progression of human disease …

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 …

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

Y Luo, BC Hitz, I Gabdank, JA Hilton… - Nucleic acids …, 2020 - academic.oup.com
Abstract The Encyclopedia of DNA Elements (ENCODE) is an ongoing collaborative
research project aimed at identifying all the functional elements in the human and mouse …

Genomic frontiers in congenital heart disease

SU Morton, D Quiat, JG Seidman… - Nature Reviews …, 2022 - nature.com
The application of next-generation sequencing to study congenital heart disease (CHD) is
increasingly providing new insights into the causes and mechanisms of this prevalent birth …

Molecular and evolutionary processes generating variation in gene expression

MS Hill, P Vande Zande, PJ Wittkopp - Nature Reviews Genetics, 2021 - nature.com
Heritable variation in gene expression is common within and between species. This
variation arises from mutations that alter the form or function of molecular gene regulatory …

A single-cell massively parallel reporter assay detects cell-type-specific gene regulation

S Zhao, CKY Hong, CA Myers, DM Granas, MA White… - Nature …, 2023 - nature.com
Massively parallel reporter gene assays are key tools in regulatory genomics but cannot be
used to identify cell-type-specific regulatory elements without performing assays serially …

Towards a comprehensive catalogue of validated and target-linked human enhancers

M Gasperini, JM Tome, J Shendure - Nature Reviews Genetics, 2020 - nature.com
The human gene catalogue is essentially complete, but we lack an equivalently vetted
inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers …

Compatibility rules of human enhancer and promoter sequences

DT Bergman, TR Jones, V Liu, J Ray, E Jagoda, L Siraj… - Nature, 2022 - nature.com
Gene regulation in the human genome is controlled by distal enhancers that activate specific
nearby promoters. A proposed model for this specificity is that promoters have sequence …

EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species

T Gao, J Qian - Nucleic acids research, 2020 - academic.oup.com
Enhancers are distal cis-regulatory elements that activate the transcription of their target
genes. They regulate a wide range of important biological functions and processes …