scholarly journals The Role of Nucleosome Positioning in the Evolution of Gene Regulation

PLoS Biology ◽  
2010 ◽  
Vol 8 (7) ◽  
pp. e1000414 ◽  
Author(s):  
Alexander M. Tsankov ◽  
Dawn Anne Thompson ◽  
Amanda Socha ◽  
Aviv Regev ◽  
Oliver J. Rando
Keyword(s):  
Gene Regulation ◽  
Nucleosome Positioning ◽  
Evolution Of Gene Regulation

scholarly journals Functional disease architectures reveal unique biological role of transposable elements

2018 ◽  
Author(s):  
Farhad Hormozdiari ◽  
Bryce van de Geijn ◽  
Joseph Nasser ◽  
Omer Weissbrod ◽  
Steven Gazal ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transposable Elements ◽  
Human Genome ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Biological Function ◽  
Functional Annotations ◽  
Evolution Of Gene Regulation ◽  
Analyze Data

AbstractTransposable elements (TE) comprise roughly half of the human genome. Though initially derided as “junk DNA”, they have been widely hypothesized to contribute to the evolution of gene regulation. However, the contribution of TE to the genetic architecture of diseases and complex traits remains unknown. Here, we analyze data from 41 independent diseases and complex traits (average N=320K) to draw three main conclusions. First, TE are uniquely informative for disease heritability. Despite overall depletion for heritability (54% of SNPs, 39±2% of heritability; enrichment of 0.72±0.03; 0.38-1.23 enrichment across four main TE classes), TE explain substantially more heritability than expected based on their depletion for known functional annotations (expected enrichment of 0.35±0.03; 2.11x ratio of true vs. expected enrichment). This implies that TE acquire function in ways that differ from known functional annotations. Second, older TE contribute more to disease heritability, consistent with acquiring biological function; SNPs inside the oldest 20% of TE explain 2.45x more heritability than SNPs inside the youngest 20% of TE. Third, Short Interspersed Nuclear Elements (SINE; one of the four main TE classes) are far more enriched for blood traits (2.05±0.30) than for other traits (0.96±0.09); this difference is far greater than expected based on the weaker depletion of SINEs for regulatory annotations in blood compared to other tissues. Our results elucidate the biological roles that TE play in the genetic architecture of diseases and complex traits.

To loop or not to loop: what is the role of TADs in enhancer function and gene regulation?

2021 ◽  
Vol 67 ◽  
pp. 119-129
Author(s):  
Gabriel R Cavalheiro ◽  
Tim Pollex ◽  
Eileen EM Furlong
Keyword(s):  
Gene Regulation ◽  
Enhancer Function

scholarly journals Epigenomic Analysis of RAD51 ChIP-seq Data Reveals cis-regulatory Elements Associated with Autophagy in Cancer Cell Lines

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2547
Author(s):  
Keunsoo Kang ◽  
Yoonjung Choi ◽  
Hyeonjin Moon ◽  
Chaelin You ◽  
Minjin Seo ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Homologous Recombination ◽  
Cell Lines ◽  
Regulatory Elements ◽  
Binding Motif ◽  
Genome Wide ◽  
E Box ◽  
Autophagy Pathway ◽  
Mcf 7

RAD51 is a recombinase that plays a pivotal role in homologous recombination. Although the role of RAD51 in homologous recombination has been extensively studied, it is unclear whether RAD51 can be involved in gene regulation as a co-factor. In this study, we found evidence that RAD51 may contribute to the regulation of genes involved in the autophagy pathway with E-box proteins such as USF1, USF2, and/or MITF in GM12878, HepG2, K562, and MCF-7 cell lines. The canonical USF binding motif (CACGTG) was significantly identified at RAD51-bound cis-regulatory elements in all four cell lines. In addition, genome-wide USF1, USF2, and/or MITF-binding regions significantly coincided with the RAD51-associated cis-regulatory elements in the same cell line. Interestingly, the promoters of genes associated with the autophagy pathway, such as ATG3 and ATG5, were significantly occupied by RAD51 and regulated by RAD51 in HepG2 and MCF-7 cell lines. Taken together, these results unveiled a novel role of RAD51 and provided evidence that RAD51-associated cis-regulatory elements could possibly be involved in regulating autophagy-related genes with E-box binding proteins.

scholarly journals Gene regulation contributes to explain the impact of early life socioeconomic disadvantage on adult inflammatory levels in two cohort studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristian Carmeli ◽  
Zoltán Kutalik ◽  
Pashupati P. Mishra ◽  
Eleonora Porcu ◽  
Cyrille Delpierre ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Gene Regulation ◽  
Cohort Studies ◽  
Early Life ◽  
Life Experiences ◽  
Socioeconomic Disadvantage ◽  
Mediating Role ◽  
The Impact ◽  
The Relationship

AbstractIndividuals experiencing socioeconomic disadvantage in childhood have a higher rate of inflammation-related diseases decades later. Little is known about the mechanisms linking early life experiences to the functioning of the immune system in adulthood. To address this, we explore the relationship across social-to-biological layers of early life social exposures on levels of adulthood inflammation and the mediating role of gene regulatory mechanisms, epigenetic and transcriptomic profiling from blood, in 2,329 individuals from two European cohort studies. Consistently across both studies, we find transcriptional activity explains a substantive proportion (78% and 26%) of the estimated effect of early life disadvantaged social exposures on levels of adulthood inflammation. Furthermore, we show that mechanisms other than cis DNA methylation may regulate those transcriptional fingerprints. These results further our understanding of social-to-biological transitions by pinpointing the role of gene regulation that cannot fully be explained by differential cis DNA methylation.

scholarly journals A Role of DNA-PK for the Metabolic Gene Regulation in Response to Insulin

Cell ◽  
2009 ◽  
Vol 136 (6) ◽  
pp. 1056-1072 ◽  
Author(s):  
Roger H.F. Wong ◽  
Inhwan Chang ◽  
Carolyn S.S. Hudak ◽  
Suzanne Hyun ◽  
Hiu-Yee Kwan ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Metabolic Gene
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