Biology subjects

Sternberg, P.

Publications and source records attributed to Sternberg, P..

3 recordsLinked to original sources

bioRxiv2018

Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis

Piwi-interacting RNAs (piRNAs) control transposable elements widely across metazoans but have rapidly evolving biogenesis pathways. In Caenorhabditis elegans, almost all piRNA loci are found within two 3Mb clusters on Chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce a [~]28 nt precursor transcript. Here, we use comparative epigenomics across nematodes to gain insight into piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA biogenesis. We describe two alternative modes of piRNA organisation in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, whilst in other species, typified by Pristionchus pacificus, piRNAs are distributed genome-wide within introns of actively transcribed genes. In both groups, piRNA production depends on downstream sequence signals associated with RNA polymerase II pausing, which synergise with the chromatin environment to control piRNA precursor transcription.

genomics↗

bioRxiv2017

A study of allelic series using transcriptomic phenotypes in a metazoan

Although transcriptomes have recently been used to perform epistasis analyses, they are not yet used to study intragenic function/structure relationships. We developed a theoretical framework to study allelic series using transcriptomic phenotypes. As a proof-of-concept, we apply our methods to an allelic series of dpy-22, a highly pleiotropic Caenorhabditis elegans gene orthologous to the human gene MED12, which is a subunit of the Mediator complex. Our methods identify functional regions within dpy-22 that modulate Mediator activity upon various genetic modules.

genetics↗

bioRxiv2016

Transcriptomic Description of an Endogenous Female State in C. elegans

Understanding genome and gene function in a whole organism requires us to fully understand the life cycle and the physiology of the organism in question. Although it is traditionally though of as a hermaphrodite, C. elegans XX animals become (endogenous) females after 3 days of egg-laying. The molecular physiology of this state has not been studied as intensely as other parts of the life cycle, in spite of documented changes in behavior and metabolism that occur at this stage. To study the female state of C. elegans, we designed an experiment to measure the transcriptome of 1st day adult females, endogenous, 6th day adult females, as well as mutant feminized worms that never go through a hermaphrodite stage at these time points. Using this experimental design, we were able to measure the effects of biological aging from the transition into the female state. We find that spermless young adult animals partially phenocopy 6 day old wild-type animals that have depleted their sperm after egg-laying, and that spermless animals also exhibit fewer transcriptomic changes associated with aging throughout these 6 days. Our results indicate that sperm loss is responsible for some of the naturally occuring transcriptomic changes that occur during the life cycle of these animals. These changes involve a variety of factors, and they are enriched in transcription factors canonically associated with neuronal development and differentiation. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.

genetics↗