Massively parallel characterization of regulatory elements in the ...
Gene regulatory elements have a major effect on human brain development and neurodevelopmental disorders. We combined lentiMPRA and deep learning to annotate thousands of regulatory elements in the developing cortex and cerebral organoids.
Mapping the dynamic genetic regulatory architecture of
2023年11月30日 · Here we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues. To mitigate technical confounding, we...
Research progress in allele-specific expression and its regulatory ...
2013年4月23日 · Organisms possess characteristics to preferentially express a particular allele under regulatory factors, which is termed allele-specific expression (ASE). It is one of the important genetic factors that lead to phenotypic variation and can be used to identify the variance of gene regulation factors.
Unifying framework explaining how parental regulatory ... - Nature
2024年10月8日 · This study uses a thermodynamic model to show that many observed gene expression patterns in hybrids and allopolyploids can be explained by regulatory divergence between parents, revealing the ...
Allele Interaction – Single Locus Genetics Meets Regulatory Biology
The concepts homo- and heteroallelic allele interactions open for a systematic investigation of the relation between allele interaction sign motifs and gene regulatory mechanisms.
A vast resource of allelic expression data spanning human tissues
2020年9月11日 · Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning 54 human tissues for a total of 431 million measurements of AE at the SNP level and 153 million measurements at the haplotype level.
cis- and trans-regulatory contributions to a hierarchy of factors ...
2024年11月25日 · To disentangle the molecular mechanisms underlying the observed regulatory changes we created F 1 hybrids between female D. simulans and male D. sechellia, performed allele-specific RNA-seq with ...
Detection of allele-specific expression in spatial transcriptomics …
2024年7月8日 · A beta-binomial framework for modeling allele-specific expression in spatial transcriptomics. We generated Visium and Slide-seq data from four genetically identical female F1 hybrid (CAST x 129) mice (Additional file 1: Figs. S1, S2, Table S1, the “Methods” section). This hybrid strain is ideal for assessing allele-specific expression (ASE) as it contains a high rate of genetic differences ...
Trans-regulatory variant network contributes to missing …
2024年1月10日 · Allele-specific expression (ASE) analysis using purebred parental lines and their F1 hybrids to quantify the relative expression of two alleles in a diploid individual offers an alternative approach to detect cis- and trans-regulatory variants. Compared to eQTL studies, ASE-based studies focus on gene-level regulatory changes and thus are ...
Cis-Acting Regulatory Variation in the Human Genome | Science
2004年10月22日 · Regulatory polymorphisms are DNA elements that modify the expression level of a transcript or its isoforms. Current techniques can detect expression differences as low as 1.2-fold between samples or alleles; the phenotypic consequences (if any) of such small differences are likely to depend on the function of the gene in question.
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