Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

Abstract

BackgroundThe 3′ untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3′ ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3′UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation.ResultsWe show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3′UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases.ConclusionsThese results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment

“…Alternatively, if 22G RNA expression causes mRNA silencing, a negative correlation between the levels of mRNA and 22G RNA is expected. Data on gonadal mRNA expression in both C. elegans sexes was available from a previous study [54]. We first grouped genes in 20 bins according to their 22G RNA expression level.…”

“…Mean normalized mRNA [54] and 22G RNA reads detected in hermaphrodite and male gonads (data in 20 bins according to 22G RNA level; number of genes per bin: 4 – 1101 in hermaphrodites, 5 – 1343 in males; mean: solid line, outliers: open circles). mRNA expression is globally decreased for the top 5% of genes (shaded area) with high levels of 22G RNA.…”

Persistent chromatin states, pervasive transcription, and sharedcis-regulatory sequences have shaped theC. elegansgenome

“…An estimated 70% of RNA transcripts are thought to be processed by SL trans-splicing and might be of polycistronic origin, however the genomic regulatory context in terms of C. elegans development remains unclear. We decided to map continuous stretches of Pol II transcription (transcription units) genomewide in order to examine how transcriptional and post-transcriptional RNA regulatory patterns may have influenced embryonic gene expression patterns (Merritt et al 2008;Elewa et al 2015;Lima et al 2017;West et al 2018).…”

The C. elegans 3’-UTRome V2: an updated genomic resource to study 3’-UTR biology

“…A second 3’-UTRome was later published using a different mapping pipeline (Jan et al 2011), confirming most of the previous data such as isoform numbers, PAS usage, etc. Other datasets were made available later, mostly focusing on tissue-specific 3’-UTRs and alternative polyadenylation (Haenni et al 2012; Blazie et al 2015; Blazie et al 2017; Chen et al 2017; Diag et al 2018; West et al 2018).…”