The prokaryotic CRISPR (clustered regularly interspaced palindromic repeats)-associated protein, Cas9, has been widely adopted as a tool for editing, imaging, and regulating eukaryotic genomes. However, our understanding of how to select single-guide RNAs (sgRNAs) that mediate efficient Cas9 activity is incomplete, as we lack insight into how chromatin impacts Cas9 targeting. To address this gap, we analyzed large-scale genetic screens performed in human cell lines using either nuclease-active or nuclease-dead Cas9 (dCas9). We observed that highly active sgRNAs for Cas9 and dCas9 were found almost exclusively in regions of low nucleosome occupancy. In vitro experiments demonstrated that nucleosomes in fact directly impede Cas9 binding and cleavage, while chromatin remodeling can restore Cas9 access. Our results reveal a critical role of eukaryotic chromatin in dictating the targeting specificity of this transplanted bacterial enzyme, and provide rules for selecting Cas9 target sites distinct from and complementary to those based on sequence properties.DOI: http://dx.doi.org/10.7554/eLife.12677.001

The RNA-guided CRISPR-associated protein Cas9 is used for genome editing, transcriptional modulation, and live-cell imaging. Cas9-guide RNA complexes recognize and cleave double-stranded DNA sequences on the basis of 20-nucleotide RNA-DNA complementarity, but the mechanism of target searching in mammalian cells is unknown. Here, we use single-particle tracking to visualize diffusion and chromatin binding of Cas9 in living cells. We show that three-dimensional diffusion dominates Cas9 searching in vivo, and off-target binding events are, on average, short-lived (<1 second). Searching is dependent on the local chromatin environment, with less sampling and slower movement within heterochromatin. These results reveal how the bacterial Cas9 protein interrogates mammalian genomes and navigates eukaryotic chromatin structure.

Mediator is a large, modular protein complex remotely conserved from yeast to man that conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. In Saccharomyces cerevisiae, Mediator is thought to be composed of 24 subunits organized in four sub-complexes, termed the head, middle, tail and Cdk8 (Srb8-11) modules. In this work, we have used screening and pair-wise two-hybrid approaches to investigate protein-protein contacts between budding yeast Mediator subunits. The derived interaction map includes the delineation of numerous interaction domains between Mediator subunits, frequently corresponding to segments that have been conserved in evolution, as well as novel connections between the Cdk8 (Srb8-11) and head modules, the head and middle modules, and the middle and tail modules. The two-hybrid analysis, together with co-immunoprecipitation studies and gel filtration experiments revealed that Med31 (Soh1) is associated with the yeast Mediator that therefore comprises 25 subunits. Finally, analysis of the protein interaction network within the Drosophila Mediator middle module indicated that the structural organization of the Mediator complex is conserved from yeast to metazoans. The resulting interaction map provides a framework for delineating Mediator structure-function and investigating how Mediator function is regulated.

The advent of new technologies for the imaging of living cells has made it possible to determine the properties of transcription, the kinetics of polymerase movement, the association of transcription factors, and the progression of the polymerase on the gene. We report here the current state of the field and the progress necessary to achieve a more complete understanding of the various steps in transcription. Our Consortium is dedicated to developing and implementing the technology to further this understanding.

In human cells, PinX1 protein has recently been shown to regulate telomere length by repressing the telomerase. In this work, we show that the putative yeast homolog of PinX1, encoded by the YGR280c open reading frame (ORF), is a new component of the ribosomal RNA processing machinery. The protein has a KK(E/D) C-terminal domain typical of nucleolar proteins and bears a putative RNA interacting domain widespread in eukaryotes called the G-patch. The protein was hence renamed Gno1p (G-patch nucleolar protein). GNO1 deletion results in a large growth defect due to the inhibition of the pre-ribosomal RNA processing first cleavage steps at sites A 0 , A 1 , and A 2 . Furthermore, Gno1p is involved in the final 3 -end trimming of U18 and U24 small nucleolar RNAs. A mutational analysis showed that the G-patch of Gno1p is essential for both functions, whereas the KK(E/D) repeats are only required for U18 small nucleolar RNA maturation. We found that PinX1 complemented the gno1-⌬ mutation, suggesting that it has a dual function in telomere length regulation and ribosomal RNA maturation in agreement with its telomeric and nucleolar localization in human cells. Conversely, we found that Gno1p does not exhibit the in vivo telomerase inhibitor activity of PinX1.Since Fontana discovered the nucleolus in 1790 (1), generations of scientists have studied this nucleolar structure by light microscopy. The nucleolus was described as a large and dense globular blotch in the nucleus of eukaryotic cells. Its primary function in ribosome biosynthesis was only found in the 1960s, but the precise role of proteins and RNAs known to participate in this process is still not well understood, and many other components remain to be discovered.Ribosome biosynthesis is a complex process requiring more than a hundred different gene products. It begins with the transcription of ribosomal RNA (rRNA) by the RNA polymerases (Pol) 1 I and III (reviewed in Ref. 2). In yeast, the 35 S pre-rRNA is transcribed by Pol I in the nucleolus and then processed into the mature rRNAs 25 S, 18 S, and 5.8 S (reviewed in Ref. 3). The 5 S rRNA is independently transcribed by Pol III. The 18 S rRNA associates with ribosomal proteins to form the small 40 S subunit of the ribosome. The 25 S, 5.8 S, and 5 S rRNAs form the large 60 S ribosomal subunit with a distinct set of proteins. A complete ribosome contains ϳ80 ribosomal proteins, but the recent elucidation of the crystallographic structure of the ribosome implies that the rRNA is the catalytic core of the translational machinery (4 -6).The various rRNA precursors and cleavage sites necessary to form the mature rRNAs from the 35 S pre-rRNA are well known (reviewed in Ref. 7). Most of our knowledge on rRNA processing comes from studies in Saccharomyces cerevisiae because of the power of genetic manipulations in this organism. The 35 S pre-rRNA undergoes excision of external transcribed spacers (ETS) and internal transcribed spacers (ITS) and numerous exonucleolytic digestions of 5Ј-and 3Ј-extremities. Additionally, m...

The transcription initiation and elongation steps of protein-coding genes usually rely on unrelated protein complexes. However, the TFIIS elongation factor is implicated in both processes. We found that, in the absence of the Med31 Mediator subunit, yeast cells required the TFIIS polymerase II (Pol II)-binding domain but not its RNA cleavage stimulatory activity that is associated with its elongation function. We also found that the TFIIS Pol II-interacting domain was needed for the full recruitment of Pol II to several promoters in the absence of Med31. This work demonstrated that, in addition to its thoroughly characterized role in transcription elongation, TFIIS is implicated through its Pol II-binding domain in the formation or stabilization of the transcription initiation complex in vivo.RNA polymerase II ͉ Saccharomyces cerevisiae ͉ transcription regulation ͉ Med31 ͉ Mediator subunit T he transcription of protein-coding eukaryotic genes by RNA polymerase II (Pol II) requires three successive steps: initiation, elongation, and termination. Transcription initiation of class II genes involves the binding of activators to regulatory sequences; the recruitment of RNA Pol II to the core promoter via interactions with activators, coactivators, and general transcription factors; and the initiation reaction per se with DNA strand opening and abortive initiation (1). A major coactivator target of transcriptional activators is the Mediator (2, 3). One of its activities is the recruitment and/or stabilization of Pol II at core promoters (4). After transcription initiation, Pol II enters elongation, during which it can be arrested because of the presence of specific DNA sequences that promote pausing, or because of obstacles such as DNA damage or bound proteins. To avoid or escape arrest, Pol II requires different elongation factors, including TFIIS (5). Evidence suggests that TFIIS could be implicated in both initiation and elongation.In vitro, TFIIS can reactivate arrested elongation complexes by stimulating endonucleolytic cleavage by Pol II of the nascent RNA (5). TFIIS is composed of three domains that fold independently, as demonstrated by NMR analysis of its structure (6, 7). Cleavage-stimulating activity minimally requires the Cterminal two-thirds of the protein, that is, its domain II and III separated by a 15-aa linker (7,8). Domain II forms a three-helix bundle followed by three short helices, with a basic patch on the third helix (␣-3) that is essential for TFIIS binding to Pol II (7). Crystallographic analysis of a TFIIS-Pol II complex confirmed that this basic patch lies at the TFIIS-Pol II interface (7,8). TFIIS binding to Pol II is required for domain III to reach the Pol II active site. Domain III forms a zinc ribbon that contains a conserved RSADE motif, responsible for the stimulation of RNA cleavage (7,8).TFIIS is also implicated in transcription initiation. First, the deletion of the DST1 gene, encoding TFIIS in yeast, is colethal with the deletion of the gene encoding the Med31 subunit of the Medi...

To bridge the gap between in vivo and in vitro molecular mechanisms, we dissected the transcriptional control of the endogenous histone gene cluster (His-C) by single-cell imaging. A combination of quantitative immunofluorescence, RNA FISH, and FRAP measurements revealed atypical promoter recognition complexes and differential transcription kinetics directing histone H1 versus core histone gene expression. While H1 is transcribed throughout S phase, core histones are only transcribed in a short pulse during early S phase. Surprisingly, no TFIIB or TFIID was detectable or functionally required at the initiation complexes of these promoters. Instead, a highly stable, preloaded TBP/TFIIA "pioneer" complex primes the rapid initiation of His-C transcription during early S phase. These results provide mechanistic insights for the role of gene-specific core promoter factors and implications for cell cycle-regulated gene expression.

The prokaryotic CRISPR (clustered regularly interspaced palindromic repeats)-associated protein, Cas9, has been widely adopted as a tool for editing, imaging, and regulating eukaryotic genomes. However, our understanding of how to select single-guide RNAs (sgRNAs) that mediate efficient Cas9 activity is incomplete, as we lack insight into how chromatin impacts Cas9 targeting. To address this gap, we analyzed large-scale genetic screens performed in human cell lines using either nuclease-active or nuclease-dead Cas9 (dCas9). We observed that highly active sgRNAs for Cas9 and dCas9 were found almost exclusively in regions of low nucleosome occupancy. In vitro experiments demonstrated that nucleosomes in fact directly impede Cas9 binding and cleavage, while chromatin remodeling can restore Cas9 access. Our results reveal a critical role of eukaryotic chromatin in dictating the targeting specificity of this transplanted bacterial enzyme, and provide rules for selecting Cas9 target sites distinct from and complementary to those based on sequence properties.