Allele-specific gene expression can affect the results and interpretation of transcriptomic analyses in zebrafish mutants and has broader implications for work in other outbred organisms.

Allele-specific expression due to genetic differences, X-chromosome inactivation or genomic imprinting, varies dynamically throughout development, and may be explained by allele-specific differences in stability or the actions of tissue-specific enhancers.

Imprinted gene expression is set up during a critical window of early embryonic development, by the translation of parental imprints by oocyte-supplied Smchd1 into allele-specific gene silencing.

Embryonic gene expression is strongly influenced by maternal genetic variation and by embryonic variation that acts in cis but not in trans.

RNA sequencing of individuals within a wild baboon population reveals extensive power to detect functional regulatory variation, and suggests that the set of genes affected by such variation may be conserved across species.

Genes with parent-of-origin specific expression are not as numerous as previously reported and validated parentally-biased expressed genes tend to be peripheral to known imprinted domains indicating shared regional control.

Lymphocytes and monocytes maintain their cell surface HLA-B via different mechanisms, which in turn differently influence cell-surface expression, half-life and peptide receptivity of HLA-B allotypes.

Analyses of allelic- and socially-biased gene expression reveal that suppressed recombination causes most of the expression differences in the social supergene, with only few differences due to socially antagonistic selection.

Allele-specific expression, natural antisense transcripts, and developmental gene expression, but not RNA editing or developmental hourglass, act in concert to shape the transcriptome during the fruiting body formation of complex multicellular fungi.

The PRC2 Polycomb complex made in the mouse oocyte prevents transcriptional inactivation of the maternal X-chromosome in the early embryo.