Molecular quantitative trait loci
Understanding functional effects of genetic variants is one of the key challenges in human
genetics, as much of disease-associated variation is located in non-coding regions with …
genetics, as much of disease-associated variation is located in non-coding regions with …
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
Comprehensive enhancer discovery is challenging because most enhancers, especially
those contributing to complex diseases, have weak effects on gene expression. Our gene …
those contributing to complex diseases, have weak effects on gene expression. Our gene …
Current challenges in understanding the role of enhancers in disease
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 …
work in a cell-type-specific manner. In addition, they are suggested to be major contributors …
[HTML][HTML] Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes
NJ Rinzema, K Sofiadis, SJD Tjalsma… - Nature Structural & …, 2022 - nature.com
Developmental gene expression is often controlled by distal regulatory DNA elements called
enhancers. Distant enhancer action is restricted to structural chromosomal domains that are …
enhancers. Distant enhancer action is restricted to structural chromosomal domains that are …
[PDF][PDF] 3D chromatin maps of the human pancreas reveal lineage-specific regulatory architecture of T2D risk
Summary Three-dimensional (3D) chromatin organization maps help dissect cell-type-
specific gene regulatory programs. Furthermore, 3D chromatin maps contribute to …
specific gene regulatory programs. Furthermore, 3D chromatin maps contribute to …
Genome-wide analysis of somatic noncoding mutation patterns in cancer
We established a genome-wide compendium of somatic mutation events in 3949 whole
cancer genomes representing 19 tumor types. Protein-coding events captured well …
cancer genomes representing 19 tumor types. Protein-coding events captured well …
Genetics of the human microglia regulome refines Alzheimer's disease risk loci
Microglia are brain myeloid cells that play a critical role in neuroimmunity and the etiology of
Alzheimer's disease (AD), yet our understanding of how the genetic regulatory landscape …
Alzheimer's disease (AD), yet our understanding of how the genetic regulatory landscape …
[HTML][HTML] WhichTF is functionally important in your open chromatin data?
Y Tanigawa, ES Dyer, G Bejerano - PLOS Computational Biology, 2022 - journals.plos.org
We present WhichTF, a computational method to identify functionally important transcription
factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an …
factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an …
Interpreting non-coding disease-associated human variants using single-cell epigenomics
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence
variants in the human genome to common traits and diseases. However, translating this …
variants in the human genome to common traits and diseases. However, translating this …
Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery
Most signals in genome-wide association studies (GWAS) of complex traits point to
noncoding genetic variants with putative gene regulatory effects. However, currently …
noncoding genetic variants with putative gene regulatory effects. However, currently …