Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (~40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families, and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology, and also identifies putative regulatory roles for unstudied TFs

Probing scrambling using statistical correlations between randomized measurements

We propose and analyze a protocol to study quantum information scrambling using statistical correlations between measurements, which are performed after evolving a quantum system from randomized initial states. We prove that the resulting correlations precisely capture the so-called out-of-time-ordered correlators and can be used to probe chaos in strongly-interacting, many-body systems. Our protocol requires neither reversing time evolution nor auxiliary degrees of freedom, and can be realized in state-of-the-art quantum simulation experiments.Comment: This version v2 (8 pages, 7 figures) includes important new results compared to our original submission. (1) We present a protocol and corresponding mathematical proof to access OTOCs with local operations, and which can be realized in quantum simulation experiments with available technology. (2) We illustrate the realization of the protocols with different examples for Hubbard and spin model

A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters

The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic determination of yeast transcription factor DNA-binding specificities. We obtained binding specificities for 112 DNA-binding proteins representing 19 distinct structural classes, one-third of which have not been previously reported. Several newly discovered binding sequences have striking genomic distributions relative to transcription start sites, supporting their biological relevance and suggesting a role in promoter architecture. Among these are Rsc3 binding sequences, containing the core CGCG, which are found preferentially ~100 bp upstream of transcription start sites. Mutation of RSC3 results in a dramatic increase in nucleosome occupancy in hundreds of proximal promoters containing a Rsc3 binding element, but has little impact on promoters lacking Rsc3 binding sequences, indicating that Rsc3 plays a broad role in targeting nucleosome exclusion at yeast promoters

Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors

Using DNA microarrays, we compared global transcript stability profiles following chemical inhibition of transcription to rpb1-1 (a temperature-sensitive allele of yeast RNA polymerase II). Among the five inhibitors tested, the effects of thiolutin and 1,10-phenanthroline were most similar to rpb1-1. A comparison to various microarray data already in the literature revealed similarity between mRNA stability profiles and the transcriptional response to stresses such as heat shock, consistent with the fact that the general stress response includes a transient shutoff of general mRNA transcription. Genes encoding factors involved in rRNA synthesis and ribosome assembly, which are often observed to be coordinately down-regulated in yeast microarray data, were among the least stable transcripts. We examined the effects of deletions of genes encoding deadenylase components Ccr4p and Pan2p and putative RNA-binding proteins Pub1p and Puf4p on the genome-wide pattern of mRNA stability after inhibition of transcription by chemicals and/or heat stress. This examination showed that Ccr4p, the major yeast mRNA deadenylase, contributes to the degradation of transcripts encoding both ribosomal proteins and rRNA synthesis and ribosome assembly factors and mediates a large part of the transcriptional response to heat stress. Pan2p and Puf4p also contributed to the degradation rate of these mRNAs following transcriptional shutoff, while Pub1p preferentially stabilized transcripts encoding ribosomal proteins. Our results indicate that the abundance of ribosome biogenesis factors is controlled at the level o

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding

Abstract Background The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. Results Here, we show that the C2H2-ZF expansion in metazoans is facilitated by contribution of non-base-contacting residues to DNA binding energy, allowing base-contacting specificity residues to mutate without catastrophic loss of DNA binding. In contrast, C2H2-ZF DNA binding in fungi, plants, and other lineages is constrained by reliance on base-contacting residues for DNA-binding functionality. Reconstructions indicate that virtually every DNA triplet was recognized by at least one C2H2-ZF domain in the common progenitor of placental mammals, but that extant C2H2-ZF domains typically bind different sequences from these ancestral domains, with changes facilitated by non-base-contacting residues. Conclusions Our results suggest that the evolution of C2H2-ZFs in metazoans was expedited by the interaction of non-base-contacting residues with the DNA backbone. We term this phenomenon “kaleidoscopic evolution,” to reflect the diversity of both binding motifs and binding motif transitions and the facilitation of their diversification

A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription

<div><p>Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription, yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified. We profiled a compendium of 50 yeast strains carrying conditional alleles or complete deletions of genes involved in transcriptional regulation, histone biology, and chromatin remodeling, as well as compounds that target transcription and histone deacetylases, to assess their respective roles in nucleosome positioning and transcription. We find that nucleosome patterning in genes is affected by many factors, including the CAF-1 complex, Spt10, and Spt21, in addition to previously reported remodeler ATPases and histone chaperones. Disruption of these factors or reductions in histone levels led genic nucleosomes to assume positions more consistent with their intrinsic sequence preferences, with pronounced and specific shifts of the +1 nucleosome relative to the transcription start site. These shifts of +1 nucleosomes appear to have functional consequences, as several affected genes in Ino80 mutants exhibited altered expression responses. Our parallel expression profiling compendium revealed extensive transcription changes in intergenic and antisense regions, most of which occur in regions with altered nucleosome occupancy and positioning. We show that the nucleosome-excluding transcription factors Reb1, Abf1, Tbf1, and Rsc3 suppress cryptic transcripts at their target promoters, while a combined analysis of nucleosome and expression profiles identified 36 novel transcripts that are normally repressed by Tup1/Cyc8. Our data confirm and extend the roles of chromatin remodelers and chaperones as major determinants of genic nucleosome positioning, and these data provide a valuable resource for future studies.</p></div

Nucleosomes disrupted in remodeler ATPase mutants are in more intrinsically preferred positions.

<p>A) WT (top row) and Chd1, Ino80 and Isw1 deletion mutant (middle row) occupancy profiles at genic nucleosome positions are shown in comparison to occupancy profiles (<i>in vitro</i> occupancy) based on intrinsic sequence preferences obtained from Kaplan et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003479#pgen.1003479-Kaplan2" target="_blank">[27]</a> (bottom row). Each panel corresponds to a genic nucleosome position, numbered relative to the TSS, and plots the <i>in vivo</i> or predicted occupancy for genes with a positive (red), negative (green), or no shift (blue) in nucleosomes at that position. Solid lines reflect the mean occupancy in a smoothing window with a bandwidth of 25 bp, with the corresponding 95% confidence interval indicated by shaded areas of the same color. B) Overview of the effects of nucleosome shifts at each +1 to +4 position on neighboring nucleosomes in the same genic array. Each panel shows the average shift profile (solid lines) and 95% confidence interval (shaded area) for all nucleosomes in the same array for genes with a positive (red), negative (green) or no shifts (blue) at the indicated genic nucleosome position (black triangle).</p

Global nucleosome occupancy profiles.

<p>A) Schematic overview of compendium mutants and conditions. B) Average nucleosome occupancy relative to the curated transcription start sites of 5,043 <i>S. cerevisiae</i> genes, expressed as the log2 ratio of probe intensities of MNase-treated nucleosomal DNA samples over un-crosslinked DNA samples. 52 mutants and conditions with a canonical nucleosome distribution are shown in the top panel and differentially colored according to average NDR occupancy. Mutants with disrupted global nucleosome occupancy profiles are shown below.</p

Profiles of genic nucleosome shifts.

<p>Box plots of nucleosome shifts for 20 conditions that show a median deviation of at least 4 base pairs for at least one genic nucleosome position, organized in 7 functional groups: A) remodeler ATPases, B) histone depletion, C) CAF-1 complex subunits, D) Elongation factors and chaperones, E) histone gene regulators, F) transcription disruption and G) all other factors. Boxes correspond to the spread between the upper and lower quartile, with medians indicated by a solid horizontal line, and whiskers extend up to 1.5 times the inter-quartile range. Nucleosome positions are relative to the transcription start site. Positive and negative numbers correspond to shifts away or towards the TSS, respectively.</p

Disruption of nucleosome-excluding general transcription factors results in cryptic promoter transcripts.

<p>A) Correlation between changes in promoter nucleosome occupancy (left panels, yellow/blue) and transcription changes across the gene body and 1 kb intergenic flanking regions (right panels, red/green). In each panel, genes are ranked according to the average change in NDR nucleosome occupancy. NDRs were defined as the 200 bp region directly upstream of curated transcription start sites. B) Representative examples of promoter transcripts in each TF mutant (arrows). Positions of NDRs are highlighted in grey. C) Fraction of diverging and tandem genes among promoters that show significant changes in nucleosome occupancy and expression of cryptic transcripts. The number of promoter regions considered is indicated above each bar. D) Top: nucleosome occupancy relative to transcript starts for promoter transcripts in the <i>tbf1-ts</i>, <i>rap1-tet</i>, <i>abf1-ts</i> and <i>rsc3-ts</i> mutants. Bottom: changes in nucleosome occupancy compared to wild-type strains.</p