scholarly journals Underestimation of Heritability across the Molecular Layers of the Gene Expression Process

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2144
Author(s):  
Jihye Ryu ◽  
Chaeyoung Lee

We investigated the extent of the heritability underestimation for molecules from an infinitesimal model in mixed model analysis. To this end, we estimated the heritability of transcription, ribosome occupancy, and translation in lymphoblastoid cell lines from Yoruba individuals. Upon considering all genome-wide nucleotide variants, a considerable underestimation in heritability was observed for mRNA transcription (−0.52), ribosome occupancy (−0.48), and protein abundance (−0.47). We employed a mixed model with an optimal number of nucleotide variants, which maximized heritability, and identified two novel expression quantitative trait loci (eQTLs; p < 1.0 × 10−5): rs11016815 on chromosome 10 that influences the transcription of SCP2, a trans-eGene on chromosome 1—whose expression increases in response to MGMT downregulation-induced apoptosis, the cis-eGene of rs11016815—and rs1041872 on chromosome 11 that influences the ribosome occupancy of CCDC25 on chromosome 8 and whose cis-eGene encodes ZNF215, a transcription factor that potentially regulates the translation speed of CCDC25. Our results suggest that an optimal number of nucleotide variants should be used in a mixed model analysis to accurately estimate heritability and identify eQTLs. Moreover, a heterogeneous covariance structure based on gene identity and the molecular layers of the gene expression process should be constructed to better explain polygenic effects and reduce errors in identifying eQTLs.

2008 ◽  
Vol 39 (1) ◽  
pp. 89-90 ◽  
Author(s):  
J. Casellas ◽  
N. Ibáñez-Escriche ◽  
M. Martínez-Giner ◽  
L. Varona

2015 ◽  
Vol 47 (3) ◽  
pp. 284-290 ◽  
Author(s):  
Po-Ru Loh ◽  
George Tucker ◽  
Brendan K Bulik-Sullivan ◽  
Bjarni J Vilhjálmsson ◽  
Hilary K Finucane ◽  
...  

2021 ◽  
pp. 1-6
Author(s):  
Sebastiano Salvidio ◽  
Andrea Costa ◽  
Fabrizio Oneto

Abstract Animal personality is a relatively neglected field in amphibian research. In this study we assessed the influence of stomach flushing, a non-lethal technique used in amphibian dietary studies, on the boldness behaviour of the cave salamander Speleomantes strinatii. The time of emergence from a shelter located in an unfamiliar environment (a proxy for individual boldness) was measured in 26 cave salamanders before and after stomach flushing, while 14 non-flushed salamanders were tested as controls. Boldness was a repeatable behaviour for salamanders and larger individuals emerged from their shelter more rapidly than smaller ones. Linear mixed model analysis showed that flushing, sex and body condition had no effect on this behaviour. These findings are promising in the framework of the study of salamander personality. In particular, our results will be useful when exploring the relationship between individual trophic strategy and boldness, aggression or exploration behaviours in terrestrial salamanders.


2017 ◽  
Vol 10 (2) ◽  
Author(s):  
Paul D. Mihalyov ◽  
Virginia A. Nichols ◽  
Peter Bulli ◽  
Matthew N. Rouse ◽  
Michael O. Pumphrey

2019 ◽  
Vol 220 ◽  
pp. 8-16
Author(s):  
A. Saridaki ◽  
G. Antonakos ◽  
A.L. Hager-Theodorides ◽  
E. Zoidis ◽  
G. Tsiamis ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document