ZCCHC8 is required for the degradation of pervasive transcripts originating from multiple genomic regulatory features
Collins, J. W.; Martin, D.; Genomics and Computational Biology Core, ; Wang, S.; Yamada, K. M.
Show abstract
The vast majority of mammalian genomes are transcribed as non-coding RNA in what is referred to as "pervasive transcription." Recent studies have uncovered various families of non-coding RNA transcribed upstream of transcription start sites. In particular, highly unstable promoter upstream transcripts known as PROMPTs have been shown to be targeted for exosomal degradation by the nuclear exosome targeting complex (NEXT) consisting of the RNA helicase MTR4, the zinc-knuckle scaffold ZCCHC8, and the RNA binding protein RBM7. Here, we report that in addition to its known RNA substrates, ZCCHC8 is required for the targeted degradation of pervasive transcripts produced at CTCF binding sites, open chromatin regions, promoters, promoter flanking regions, and transcription factor binding sites. Additionally, we report that a significant number of RIKEN cDNAs and predicted genes display the hallmarks of PROMPTs and are also substrates for ZCCHC8 and/or NEXT complex regulation suggesting these are unlikely to be functional genes. Our results suggest that ZCCHC8 and/or the NEXT complex may play a larger role in the global regulation of pervasive transcription than previously reported.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Genomic context sensitivity of insulator function 95%
- Cell type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem-cell like cells 95%
- Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain 95%
Similar papers in this journal
Similar papers in this journal
- Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation 95%
- The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure. 95%
- SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state 95%
Similar papers in this journal
- Intellectual disability-associated factor Zbtb11 cooperates with NRF-2/GABP to control mitochondrial function 95%
- Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires Bicc1-Ccr4 RNA degradation complex 95%
- A high-content RNAi screen reveals multiple roles for long noncoding RNAs in cell division 95%
Similar papers in this journal
- Bidirectional cooperation between Ubtf1 and SL1 determines RNA Polymerase I promoter recognition in cell and is negatively affected in the UBTF-E210K neuroregression syndrome. 95%
- PNLDC1 catalysis and postnatal germline function are required for piRNA trimming, LINE1 silencing, and spermatogenesis in mice 95%
- Independent recruitment of PRC1 and PRC2 by human XIST 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.