Fourth, hypertranscribing cells endogenously accumulate promoter-proximal double strand breaks (DSBs), thus displaying a heightened dependency on DNA repair factors 12. Third, hypertranscribing cells upregulate protein synthesis/translational machinery, which is necessary for the continuous translation and steady-state maintenance of Chd1 and several other unstable euchromatic regulators 10. One notable factor is the ATP-dependent remodeler Chd1, which binds specifically to H3K4me3 and is required for the transcriptional output of proliferating epiblast cells 4. Second, hypertranscription is dependent on a decondensed and distinctly permissive chromatin landscape, maintained by the activity of euchromatic remodeling factors 10, 11. These changes occur at the level of both steady-state and nascent transcripts, and result in measurable increases in total cellular RNA content 4.
First, hypertranscribing cells display a transcriptome-wide increase in gene expression, including at housekeeping genes and ribosomal RNA (rRNA) 4, 9. However, the occurrence of hypertranscription in adult physiology remains largely unexploredĭespite the paucity of data in adult tissues, work in mouse embryos and mESCs has identified five recurring “hallmarks” of hypertranscription. Our group and others have reported evidence supporting the occurrence and functional relevance of hypertranscription in mouse embryogenesis and select human cancer cell types 3– 8. Hence, hypertranscription has been proposed to play major roles in developmental transitions, adult organ homeostasis, and tumorigenesis 2. This global shift powers biological phenomena requiring substantial increases in total biomass, such as rapid proliferation, secretion, and cell activation 1, 2. At the level of transcription, cells can meet these demands by entering a state of relative hypertranscription, which is characterized by a global upregulation of nascent transcriptional output 2. By applying this methodology across a diverse collection of cell states and contexts, we put forth hypertranscription as a general and dynamic cellular program that is pervasively employed during development, organ maintenance and regeneration.Ĭells dynamically regulate their biosynthetic capacities to fulfill the requirements of demanding cell state transitions 1. Our findings introduce an approach towards maximizing single-cell RNA-seq profiling. Our analyses reveal a common set of molecular pathways associated with hypertranscription across adult organs, including chromatin remodeling, DNA repair, ribosome biogenesis and translation. In addition to the association between hypertranscription and the stem/progenitor cell state, we dissect the relationship between transcriptional output and cell cycle, ploidy and secretory behavior. Hypertranscription marks cells with multilineage potential in adult organs, is redeployed in conditions of tissue injury, and can precede by 1-2 days bursts of proliferation during regeneration. We find that many different multipotent stem and progenitor cell populations are in a state of hypertranscription, including in the hematopoietic system, intestine and skin.
The results reveal a remarkable dynamic range in transcriptional output among adult cell types. Absolute scaling enables an estimation of total transcript abundances per cell, which we validate in embryonic stem cell (ESC) and germline data and apply to adult mouse organs at steady-state or during regeneration.
Here, we use molecule counting and spike-in normalization to develop absolute scaling of single-cell RNA sequencing data. This limitation is in large part due to the fact that modern sequencing approaches, including single-cell RNA sequencing (scRNA-seq), generally assume similar levels of transcriptional output per cell. Despite its potential widespread relevance, documented examples of hypertranscription remain few and limited predominantly to early development. Hypertranscription facilitates biosynthetically demanding cellular state transitions through global upregulation of the nascent transcriptome.