[PDF][PDF] Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks

SN Wright, BS Leger, SB Rosenthal, SN Liu, T Jia… - Cell reports, 2023 - cell.com
A vexing observation in genome-wide association studies (GWASs) is that parallel analyses
in different species may not identify orthologous genes. Here, we demonstrate that cross …

DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome

T Zhang, L Li, H Sun, G Wang - Bioinformatics, 2023 - academic.oup.com
Motivation Enhancers are vital cis-regulatory elements that regulate gene expression.
Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer …

Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation

KL Kim, GJ Rahme, VY Goel, CA El Farran, AS Hansen… - Molecular Cell, 2024 - cell.com
Enhancer-gene communication is dependent on topologically associating domains (TADs)
and boundaries enforced by the CCCTC-binding factor (CTCF) insulator, but the underlying …

Boundary stacking interactions enable cross-TAD enhancer–promoter communication during limb development

TC Hung, DM Kingsley, AN Boettiger - Nature Genetics, 2024 - nature.com
Although promoters and their enhancers are frequently contained within a topologically
associating domain (TAD), some developmentally important genes have their promoter and …

[HTML][HTML] A broad m6A modification landscape in inflammatory bowel disease

K Nie, J Yi, Y Yang, M Deng, Y Yang… - Frontiers in cell and …, 2022 - frontiersin.org
Background and aims: N6-methyladenosine (m6A) is the most common post-transcriptional
modification on eukaryotic mRNA, affecting mRNA's fate. The role of m6A regulation in …

[HTML][HTML] Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation

RM Boileau, KX Chen, R Blelloch - Genome Biology, 2023 - Springer
Background Enhancers are essential in defining cell fates through the control of cell-type-
specific gene expression. Enhancer activation is a multi-step process involving chromatin …

OpenXGR: a web-server update for genomic summary data interpretation

C Bao, S Wang, L Jiang, Z Fang, K Zou… - Nucleic Acids …, 2023 - academic.oup.com
How to effectively convert genomic summary data into downstream knowledge discovery
represents a major challenge in human genomics research. To address this challenge, we …

[HTML][HTML] Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease

T C. Silva, JI Young, L Zhang, L Gomez… - Nature …, 2022 - nature.com
To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic
and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA …

Technologies, strategies, and cautions when deconvoluting genome‐wide association signals: FTO in focus

MC Pahl, SFA Grant, RL Leibel… - Obesity …, 2023 - Wiley Online Library
Genome‐wide association studies have revealed a plethora of genetic variants that
correlate with polygenic conditions. However, causal molecular mechanisms have proven …

[HTML][HTML] An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs

EB Fauman, C Hyde - BMC bioinformatics, 2022 - Springer
Background A genome-wide association study (GWAS) correlates variation in the genotype
with variation in the phenotype across a cohort, but the causal gene mediating that impact is …