Current challenges in understanding the role of enhancers in disease

JB Zaugg, P Sahlén, R Andersson… - Nature structural & …, 2022 - nature.com
Enhancers play a central role in the spatiotemporal control of gene expression and tend to
work in a cell-type-specific manner. In addition, they are suggested to be major contributors …

Museum genomics

DC Card, B Shapiro, G Giribet, C Moritz… - Annual Review of …, 2021 - annualreviews.org
Natural history collections are invaluable repositories of biological information that provide
an unrivaled record of Earth's biodiversity. Museum genomics—genomics research using …

[HTML][HTML] A single-cell atlas of chromatin accessibility in the human genome

K Zhang, JD Hocker, M Miller, X Hou, J Chiou… - Cell, 2021 - cell.com
Current catalogs of regulatory sequences in the human genome are still incomplete and lack
cell type resolution. To profile the activity of gene regulatory elements in diverse cell types …

Short tandem repeats bind transcription factors to tune eukaryotic gene expression

CA Horton, AM Alexandari, MGB Hayes, E Marklund… - Science, 2023 - science.org
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter
gene expression, yet how they regulate transcription remains unknown. We found that STRs …

Multiple causal variants underlie genetic associations in humans

NS Abell, MK DeGorter, MJ Gloudemans, E Greenwald… - Science, 2022 - science.org
Associations between genetic variation and traits are often in noncoding regions with strong
linkage disequilibrium (LD), where a single causal variant is assumed to underlie the …

Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development

H Yu, M Chen, Y Hu, S Ou, X Yu, S Liang, N Li, M Yang… - Cell stem cell, 2022 - cell.com
Reprogramming of H3K9me3-dependent heterochromatin is required for early development.
How H3K9me3 is involved in early human development remains, however, largely unclear …

HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors

IE Vorontsov, IA Eliseeva, A Zinkevich… - Nucleic Acids …, 2024 - academic.oup.com
We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …

[图书][B] RNA, the epicenter of genetic information

J Mattick, P Amaral - 2023 - library.oapen.org
The origin story and emergence of molecular biology is muddled. The early triumphs in
bacterial genetics and the complexity of animal and plant genomes complicate an intricate …

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

BP de Almeida, F Reiter, M Pagani, A Stark - Nature genetics, 2022 - nature.com
Enhancer sequences control gene expression and comprise binding sites (motifs) for
different transcription factors (TFs). Despite extensive genetic and computational studies, the …

Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers

J He, W Wen, A Beeghly, Z Chen, C Cao… - Nature …, 2022 - nature.com
Transcriptome-wide association studies (TWAS) have successfully discovered many
putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene …