The relationship between genome structure and function

AM Oudelaar, DR Higgs - Nature Reviews Genetics, 2021 - nature.com
Precise patterns of gene expression in metazoans are controlled by three classes of
regulatory elements: promoters, enhancers and boundary elements. During differentiation …

Enhancer redundancy in development and disease

EZ Kvon, R Waymack, M Gad, Z Wunderlich - Nature Reviews Genetics, 2021 - nature.com
Shadow enhancers are seemingly redundant transcriptional cis-regulatory elements that
regulate the same gene and drive overlapping expression patterns. Recent studies have …

Pig genome functional annotation enhances the biological interpretation of complex traits and human disease

Z Pan, Y Yao, H Yin, Z Cai, Y Wang, L Bai… - Nature …, 2021 - nature.com
The functional annotation of livestock genomes is crucial for understanding the molecular
mechanisms that underpin complex traits of economic importance, adaptive evolution and …

Amphioxus functional genomics and the origins of vertebrate gene regulation

F Marlétaz, PN Firbas, I Maeso, JJ Tena, O Bogdanovic… - Nature, 2018 - nature.com
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly
distinctive genomes that have been sculpted by two whole-genome duplications. Here we …

Universal DNA methylation age across mammalian tissues

AT Lu, Z Fei, A Haghani, TR Robeck, JA Zoller, CZ Li… - Nature aging, 2023 - nature.com
Aging, often considered a result of random cellular damage, can be accurately estimated
using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we …

Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

H Suresh, M Crow, N Jorstad, R Hodge… - Nature Ecology & …, 2023 - nature.com
Enhanced cognitive function in humans is hypothesized to result from cortical expansion
and increased cellular diversity. However, the mechanisms that drive these phenotypic …

Association of OPRM1 functional coding variant with opioid use disorder: a genome-wide association study

H Zhou, CT Rentsch, Z Cheng, RL Kember… - JAMA …, 2020 - jamanetwork.com
Importance With the current opioid crisis, it is important to improve understanding of the
biological mechanisms of opioid use disorder (OUD). Objectives To detect genetic risk …

A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

L Jin, Q Tang, S Hu, Z Chen, X Zhou, B Zeng… - Nature …, 2021 - nature.com
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of
tissue specialization processes underlying economically valuable traits and accelerate their …

GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model

X Yang, G Liu, G Feng, D Bu, P Wang, J Jiang, S Chen… - Cell Research, 2024 - nature.com
Deciphering universal gene regulatory mechanisms in diverse organisms holds great
potential for advancing our knowledge of fundamental life processes and facilitating clinical …

Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes

V Sundaram, J Wysocka - Philosophical Transactions of …, 2020 - royalsocietypublishing.org
Eukaryotic gene regulation is mediated by cis-regulatory elements, which are embedded
within the vast non-coding genomic space and recognized by the transcription factors in a …