DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

Yamamoto, Junichi; Hagiwara, Yuri; Chiba, Kunitoshi; Isobe, Tomoyasu; Narita, Takashi; Handa, Hiroshi; Yamaguchi, Yuki

doi:10.1038/ncomms5263

Cited by 91 publications

(115 citation statements)

References 52 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…ChIP assays were performed as previously described (46). Chromatins were solubilized by micrococcal nuclease digestion, and immunoprecipitation was performed with Dynabeads protein G (Dynal).…”

Section: Methodsmentioning

confidence: 99%

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

Cao

Yamamoto

Isobe

et al. 2015

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

bRestores TBP function 1 (Rtf1) is generally considered to be a subunit of the Paf1 complex (PAF1C), a multifunctional protein complex involved in histone modification and transcriptional or posttranscriptional regulation. Rtf1, however, is not stably associated with the PAF1C in most species except Saccharomyces cerevisiae, and its biochemical functions are not well understood. Here, we show that human Rtf1 is a transcription elongation factor that may function independently of the PAF1C. Rtf1 requires "Rtf1 coactivator" activity, which is most likely unrelated to the PAF1C or DSIF, for transcriptional activation in vitro. A mutational study revealed that the Plus3 domain of human Rtf1 is critical for its coactivator-dependent function. Transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation studies in HeLa cells showed that Rtf1 and the PAF1C play distinct roles in regulating the expression of a subset of genes. Moreover, contrary to the finding in S. cerevisiae, the PAF1C was apparently recruited to the genes examined in an Rtf1-independent manner. The present study establishes a role for human Rtf1 as a transcription elongation factor and highlights the similarities and differences between the S. cerevisiae and human Rtf1 proteins. Restores TBP (TATA box-binding protein) function 1 (Rtf1) was identified as a suppressor of a TBP mutant in Saccharomyces cerevisiae (1). Subsequent genetic and biochemical studies in yeast have shown that Rtf1 functions as a component of the polymerase-associated factor 1 (Paf1) complex (PAF1C) containing Paf1, Ctr9, Leo1, and Cdc73 (2-5). The PAF1C is a multifunctional protein complex whose primary role is to facilitate histone modifications, such as H2B monoubiquitination at K123 and H3 methylation at K4 and K79 (6-12). The PAF1C also plays important roles in transcription elongation through chromatin, as well as on naked DNA (13-16). Furthermore, the PAF1C is involved in transcription termination and 3= processing of polyadenylated and nonpolyadenylated .Paf1, Ctr9, Leo1, Cdc73, and Rtf1 are highly conserved in eukaryotes; however, the subunit compositions of the PAF1C vary among species. Purification of the PAF1C from human HeLa cells yielded a five-subunit complex lacking Rtf1 but containing Ski8 as an additional subunit (22,26,27). Similarly, coimmunoprecipitation studies in zebrafish, Drosophila, and Schizosaccharomyces pombe showed that PAF1C homologs in these species lack a stably associated Rtf1 subunit (28-30). At the functional level, however, Rtf1 and other PAF1C subunits have a number of similarities. For example, knockout or knockdown of Rtf1 and other PAF1C subunits results in similar defects in histone modifications in all the species examined (27,28,31). At the organismal level, inhibition of Rtf1 and other PAF1C subunits causes similar defects in epidermal morphogenesis in Caenorhabditis elegans and in somitogenesis and cardiomyocyte development in zebrafish (29,32,33). Rtf1 and Paf1 colocalize with each other and with RNA polymerase II (RNAPII) in...

show abstract

Section: Methodsmentioning

confidence: 99%

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

Cao

Yamamoto

Isobe

et al. 2015

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Other than processing the 3 ′ end of snRNAs, Integrator is also implicated in Pol II pause release and transcription elongation (Gardini et al 2014;Yamamoto et al 2014). To distinguish whether the reduced miRNA levels in the absence of Int11 are due to a processing or a transcriptional defect, we carried out RNase protection assays (RPAs) by annealing 32 P-body-labeled RNA probes complementary to pri-miR-HSUR4 with total RNA from transfected 293T cells and digesting with single-strand-specific RNases (Fig.…”

Section: Resultsmentioning

confidence: 99%

The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends

et al. 2015

View full text Add to dashboard Cite

Herpesvirus saimiri (HVS) is an oncogenic γ-herpesvirus that produces microRNAs (miRNAs) by cotranscription of precursor miRNA (pre-miRNA) hairpins immediately downstream from viral small nuclear RNAs (snRNA). The host cell Integrator complex, which recognizes the snRNA 3 ′ end processing signal (3 ′ box), generates the 5 ′ ends of HVS pre-miRNA hairpins. Here, we identify a novel 3 ′ box-like sequence (miRNA 3 ′ box) downstream from HVS premiRNAs that is essential for miRNA biogenesis. In vivo knockdown and rescue experiments confirmed that the 3 ′ end processing of HVS pre-miRNAs also depends on Integrator activity. Interaction between Integrator and HVS primary miRNA (pri-miRNA) substrates that contain only the miRNA 3 ′ box was confirmed by coimmunoprecipitation and an in situ proximity ligation assay (PLA) that we developed to localize specific transient RNA-protein interactions inside cells. Surprisingly, in contrast to snRNA 3 ′ end processing, HVS pre-miRNA 3 ′ end processing by Integrator can be uncoupled from transcription, enabling new approaches to study Integrator enzymology.

show abstract

“…12 Recent studies indicate that the integrator complex is required in many steps of the transcription cycle: 39-end processing and termination of nonpolyadenylated snRNA and replicative histone genes, pause release at immediate early genes, and biogenesis of transcripts required from distal regulatory elements (enhancers). [13][14][15][16][17] The association of SSB1/2 with the INTS3 complex indicates the potential for SSBs to influence transcription and RNA processing. 15 Furthermore, the target sites of INTS3-SSB complexes are favorable to the formation of DNA:RNA hybrids (R-loops), structures in which nascent RNA transcripts fall back on the template DNA, leaving the nontemplate ssDNA exposed.…”

mentioning

confidence: 99%

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress

Shi

vụ

Boucher

et al. 2017

Blood

View full text Add to dashboard Cite

show abstract

DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes

Cited by 91 publications

References 52 publications

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex

The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress

Contact Info

Product

Resources

About