Global Hypertranscription in the Mouse Embryonic Germline

Abstract

Summary Primordial germ cells (PGCs) are vital for inheritance and evolution. Their transcriptional program has been extensively studied and is assumed to be well-known. We report here a remarkable global upregulation of the transcriptome of mouse PGCs compared to somatic cells. Using cell-number normalized genome-wide analyses, we uncover significant transcriptional amplification in PGCs, including mRNAs, rRNA and transposable elements. Hypertranscription preserves tissue-specific gene expression patterns, correlates with cell size, and can still be detected in E15.5 male germ cells, when proliferation has ceased. PGC hypertranscription occurs at the level of nascent transcription, is accompanied by increased translation rates, and is driven by Myc factors n-Myc and l-Myc (but not c-Myc) and by P-TEFb. This study provides a paradigm for transcriptional analyses during development and reveals a major global hyperactivity of the germline transcriptome.

A slow transcription rate causes embryonic lethality and perturbs kinetic coupling of neuronal genes

“…We observed that a slow RNAPII mutant caused embryonic lethality even in heterozygosity (Fig 2). There is evidence that the transcriptional output is crucial in specific developmental stages associated with stem cell expansion, as evidenced by their hypertranscription states (Koh et al, 2015;Percharde et al, 2017). It is possible that a slow elongation rate cannot sustain the high levels of mRNA production required at early stages of development.…”

EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells

“…Ezhip's pattern of expression is distinct from that of Ezh2, which is expressed tissue-wide, with the strongest expression observed in spleen. Analysis of public gene expression datasets from fetal gonads 36 indicates Ezhip is preferentially expressed in E13.5 primordial germ cells (PGCs) compared to somatic cells, correlating with germ cell markers such as Piwil2 or Prdm14 (Supplementary Figure 1G). Interestingly, Ezhip belongs to a set of genes referred to as "germlinereprogramming-responsive" that become active following PGC DNA demethylation 37 , as they are associated with strong CpG island promoters.…”

What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation

“…First, global changes in transcriptional output are not captured by standard RNA‐seq methods. For example, we recently used cell‐number normalized RNA‐seq to document that the mouse embryonic germline is in a state of global hypertranscription, including at TEs . Second, a high proportion of LINE1 RNA is chromatin associated, and this fraction tends to be resistant to standard extraction of total cellular RNA .…”

“…[79] TEs such as LINE1 and various ERVs become globally demethylated and expressed during the major waves of epigenetic erasure that take place during preimplantation and germline development (Figure 1). [80][81][82][83][84][85] Similarly, a relaxation of H3K9me2-based repression of TEs occurs in PGCs, contributing to their derepression. [86][87][88] As described above, many TE families act as important cis-elements for gene regulation.…”

“…For example, we recently used cell-number normalized RNA-seq to document that the mouse embryonic germline is in a state of global hypertranscription, including at TEs. [85] Second, a high proportion of LINE1 RNA is chromatin associated, and this fraction tends to be resistant to standard extraction of total cellular RNA. [91] Using approaches such as RNA FISH or enrichment for chromatin-bound RNA may provide a more faithful picture of LINE1 RNA abundance.…”