ZC3H4 restricts non-coding transcription in human cells

Abstract

The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene termination factors, we identified ZC3H4. However, its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is metazoan-specific - interesting when considering its impact on enhancer RNAs that are absent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as a factor that plays an important role in restricting non-coding transcription in multi-cellular organisms.

Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9

“…Although many antisense transcripts contain multiple AAUAAA sequences, most still terminate RBBP6-independently (Supplementary Figures 1B and C). Similarly, we recently showed that the PAS-dependent 5'3' exonucleolytic torpedo terminator, XRN2, does not affect antisense transcriptional termination 9 . Therefore, although some antisense transcripts are polyadenylated, most antisense transcription can terminate using PAS-independent mechanisms.…”

“…Reciprocally, promoter-proximal transcription from lowly expressed protein-coding transcription is INTS11-sensitive, which could reflect low CDK9 activity at those loci. We and others recently described the Restrictor complex as restraining antisense transcription 9,44,45 . Unlike Integrator, which associates with NELF-bound RNAPII 36 , Restrictor is proximal to the distinct PAF-bound RNAPII 9 .…”

“…We and others recently described the Restrictor complex as restraining antisense transcription 9,44,45 . Unlike Integrator, which associates with NELF-bound RNAPII 36 , Restrictor is proximal to the distinct PAF-bound RNAPII 9 . Thus, various complexes may target different forms of RNAPII before and after CDK9 activity.…”

“…In addition to CDK9, multiple studies demonstrate a role for U1 snRNA in promoting elongation through protein-coding genes 5,6,8,46 . U1 promotes RNAPII elongation and shields transcription from early PAS-dependent termination and the Restrictor complex 5,9 . The U1mediated suppression of premature PAS-dependent termination inspired the original model of promoter directionality.…”

“…U1 snRNA promotes RNAPII elongation through protein-coding genes by binding to RNA and preventing early termination [5][6][7] . RNA-bound U1 prevents early termination by inhibiting PASs and antagonising other attenuation mechanisms, which include the PP1 regulator, PNUTS, and the Restrictor complex 8,9 . In contrast, U1 binding sites are rarer in short antisense transcripts, which are often rich in PAS sequences that are proposed to promote transcriptional termination 10 .…”