Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.

During cell division, transcription factors (TFs) are removed from chromatin twice, during DNA synthesis and during condensation of chromosomes. How TFs can efficiently find their sites following these stages has been unclear. Here, we have analyzed the binding pattern of expressed TFs in human colorectal cancer cells. We find that binding of TFs is highly clustered and that the clusters are enriched in binding motifs for several major TF classes. Strikingly, almost all clusters are formed around cohesin, and loss of cohesin decreases both DNA accessibility and binding of TFs to clusters. We show that cohesin remains bound in S phase, holding the nascent sister chromatids together at the TF cluster sites. Furthermore, cohesin remains bound to the cluster sites when TFs are evicted in early M phase. These results suggest that cohesin-binding functions as a cellular memory that promotes re-establishment of TF clusters after DNA replication and chromatin condensation.

Transcriptionally active enhancers in human cancer cells.

The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here, we use transient transcriptome sequencing (TT-seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven types of cancer. These enhancers were associated with cell type-specific gene expression, enriched for genetic variants that predispose to cancer, and included functionally verified enhancers. Enhancer-promoter (E-P) pairing by correlation of transcription activity revealed ~ 40,000 putative E-P pairs, which were depleted for housekeeping genes and enriched for transcription factors, cancer-associated genes, and 3D conformational proximity. The cell type specificity and transcription activity of target genes increased with the number of paired putative enhancers. Our results represent a rich resource for future studies of gene regulation by enhancers and their role in driving cancerous cell growth.

DNA-dependent formation of transcription factor pairs alters their binding specificity.

Gene expression is regulated by transcription factors (TFs), proteins that recognize short DNA sequence motifs. Such sequences are very common in the human genome, and an important determinant of the specificity of gene expression is the cooperative binding of multiple TFs to closely located motifs. However, interactions between DNA-bound TFs have not been systematically characterized. To identify TF pairs that bind cooperatively to DNA, and to characterize their spacing and orientation preferences, we have performed consecutive affinity-purification systematic evolution of ligands by exponential enrichment (CAP-SELEX) analysis of 9,400 TF-TF-DNA interactions. This analysis revealed 315 TF-TF interactions recognizing 618 heterodimeric motifs, most of which have not been previously described. The observed cooperativity occurred promiscuously between TFs from diverse structural families. Structural analysis of the TF pairs, including a novel crystal structure of MEIS1 and DLX3 bound to their identified recognition site, revealed that the interactions between the TFs were predominantly mediated by DNA. Most TF pair sites identified involved a large overlap between individual TF recognition motifs, and resulted in recognition of composite sites that were markedly different from the individual TF's motifs. Together, our results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.

PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments.

MOTIVATION: Transcription factor (TF) binding can be studied accurately in vivo with ChIP-exo and ChIP-Nexus experiments. Only fraction of TF binding mechanisms are yet fully understood and accurate knowledge of binding locations and patterns of TFs is key to understanding binding that is not explained by simple positional weight matrix models. ChIP-exo/Nexus experiments can also offer insight on the effect of single nucleotide polymorphism (SNP) at TF binding sites on expression of the target genes. This is an important mechanism of action for disease-causing SNPs at non-coding genomic regions. RESULTS: We describe a peak caller PeakXus that is specifically designed to leverage the increased resolution of ChIP-exo/Nexus and developed with the aim of making as few assumptions of the data as possible to allow discoveries of novel binding patterns. We apply PeakXus to ChIP-Nexus and ChIP-exo experiments performed both in Homo sapiens and in Drosophila melanogaster cell lines. We show that PeakXus consistently finds more peaks overlapping with a TF-specific recognition sequence than published methods. As an application example we demonstrate how PeakXus can be coupled with unique molecular identifiers (UMIs) to measure the effect of a SNP overlapping with a TF binding site on the in vivo binding of the TF. AVAILABILITY AND IMPLEMENTATION: Source code of PeakXus is available at https://github.com/hartonen/PeakXus CONTACT: tuomo.hartonen@helsinki.fi or jussi.taipale@ki.se.

Photoluminescence enhancement study in a Bi-doped Cs2AgInCl6 double perovskite by pressure and temperature-dependent self-trapped exciton emission.

Here, we report a halide precursor acid precipitation method to synthesize Cs2AgIn1-xBixCl6 (x = 0, 0.02, 0.04, 0.08, 0.16, 0.32, 0.64, and 1) microcrystals. Cs2AgInCl6 and Bi derivative double perovskites show broadband white light emission via self-trapped excitons (STEs) and have achieved the highest internal quantum efficiency of up to 52.4% at x = 0.08. Synchrotron X-ray diffraction confirmed the linear increase of lattice parameters and cell volume with Bi3+ substitution at In3+ sites. Absorbance, photocurrent excitation, and photoluminescence excitation spectra are used to observe possible transitions from the valence to the conduction band or free exciton (FE) states as well as transitions within local Bi3+ states. The broadband photoluminescence is quenched via a single nonradiative process with an activation energy ΔE = 1490 cm-1 for Cs2AgIn0.92Bi0.08Cl6. Under normal conditions, we observed STE emission, but applying external pressure alters the electronic structure such that at elevated pressure, the only emission via the FE state is observed. We anticipate that structure, temperature and pressure-dependent photoluminescence studies will help the future use of a single-source lead-free double perovskite for white light-emitting diode applications.

Enhancement of self-trapped excitons and near-infrared emission in Bi3+/Er3+ co-doped Cs2Ag0.4Na0.6InCl6 double perovskite.

Erbium (Er) complexes are used as optical gain materials for signal generation in the telecom C-band at 1540 nm, but they need a sensitizer to enhance absorption. Na+ substitution for Ag+ and Bi3+ doping at the In3+ site is a possible strategy to enhance the broadband emission of Cs2AgInCl6, which could be used as a sensitizer for energy transfer to rare-earth elements. Herein, self-trapped exciton (STE) energy transfer to Er3+ at 1540 nm in double perovskite is reported. An acid precipitation method was used to synthesize Cs2AgInCl6 and its derivatives with Er3+, Bi3+, and Na+. Bare Cs2AgInCl6:Er emission signals were found to be weak at 1540 nm, but Bi3+ doping increased them by 12 times, and Bi3+ and Na+ doping increased signal intensity by up to 25 times. Electron paramagnetic resonance spectroscopy characterized a decrease in axial symmetry over the Er3+ ions after the substitutions of Na+ and Bi3+ in Cs2AgInCl6 at low temperatures (<7 K) for the first time. Moreover, an increase in pressure compressed the structure, which tuned the STE transition for free exciton emission, and a further increase in pressure distorted the cubic phase above 70 kbar.

Sequence determinants of human gene regulatory elements.

DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger sequence space than the human genome using massively parallel reporter assays (MPRAs). Machine learning models revealed that transcription factors (TFs) generally act in an additive manner with weak grammar and that most enhancers increase expression from a promoter by a mechanism that does not appear to involve specific TF-TF interactions. The enhancers themselves can be classified into three types: classical, closed chromatin and chromatin dependent. We also show that few TFs are strongly active in a cell, with most activities being similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening and enhancing, promoting and determining transcription start site (TSS) activity, consistent with the view that the TF binding motif is the key atomic unit of gene expression.

Recent Developments in Lead-Free Double Perovskites: Structure, Doping, and Applications.

Lead-free perovskite structures have been recently attracting considerable attention because of their eco-friendly nature and properties, such as their lead-based structure. In this work, we reviewed the lead-free double perovskite (LFDP) structure because of its unique electronic dimensions, chemical stability, and substitutional chemistry compared with other lead-free structures. We highlighted the recent progress on crystal structure prediction, synthesis methods, metal dopants, and ligand passivation on LFDPs. LFDPs are useful for several applications, such as solar cells, light-emitting diodes, degradation of photocatalytic dyes, sensors, and X-ray detectors. This report provides a summary of recent progress as a reference for further research on lead-free perovskite structures.

Improvement in quantum yield by suppression of trions in room temperature synthesized CsPbBr3 perovskite quantum dots for backlight displays.

Surface defects and synthesis methods play important roles in the photoluminescence quantum yield (PLQY), stability, and the device performance of lead halide perovskite quantum dots (PQDs). In this study, we report a quadruple-ligand (tri-n-octylphosphine, didodecyldimethylammonium bromide, tetraoctylammonium bromide, and oleic acid) assisted room-temperature method for synthesizing CsPbBr3 QDs (RT-CsPbBr3) with an absolute PLQY of 83%. X-ray photoelectron spectroscopy confirms the high completeness of the Pb-Br octahedron through the absence of lead ions and presence of more bromide ions on the surface of RT-CsPbBr3 QDs. The exciton dynamics of RT-CsPbBr3 QDs is studied by using femtosecond transient absorption, time-resolved PL, and single-dot spectroscopy, which provide strong evidence of the suppression of trion formation compared with the hot injection-synthesized CsPbBr3 (HI-CsPbBr3) QDs. The white light-emitting diode (LED) fabricated with RT-CsPbBr3 PQDs and a K2SiF6:Mn4+ phosphor for backlight applications achieved a wide color gamut of 124% of the National Television System Committee (NTSC) standard.

Cubic CeO2 implanted reduced graphene oxide-based highly sensitive biosensor for non-invasive oral cancer biomarker detection.

Herein, we report a cerium oxide nanocubes (ncCeO2)-reduced graphene oxide (RGO)-based nanocomposite for the detection of oral cancer biomarker, cytokeratin fragment-21-1 (Cyfra-21-1), using the electrochemical technique. Nanocomposite of ncCeO2-RGO was prepared by the in situ reduction of graphene oxide (GO), in the presence of ncCeO2, using hydrazine hydrate. Raman spectra confirmed the presence of ncCeO2 in the matrix of RGO. The chemical composition of the ncCeO2-RGO nanocomposite was determined by X-ray photoelectron spectroscopy (XPS). X-ray diffraction (XRD) studies have indicated the presence of crystalline ncCeO2 and the amorphous nature of RGO. Thin films of ncCeO2-RGO composites were spin coated onto the indium tin oxide (ITO) coated glass surface and used for the co-immobilization of specific antibody of Cyfra-21-1 by N-ethyl-N-(3-dimethyl aminopropyl)carbodiimide hydrochloride and N-hydroxysuccinimide (EDC-NHS) coupling chemistry. Electrochemical response studies were monitored by using the differential pulse voltammetry (DPV) technique in the range of 0.625 pg mL-1 to 15 ng mL-1. The best linear response was observed in the range of 0.625 pg mL-1 to 0.01 ng mL-1, with a low detection limit of 0.625 pg mL-1. The sensitivity was found to be 14.5 µA ng-1 mL cm-2 with R2 0.98, which was an improvement compared to the results from previously reported work. This BSA/anti-Cyfra-21-1/ncCeO2-RGO/ITO immunosensor shows selectivity towards Cyfra-21-1 in the presence of glucose, sodium chloride (NaCl), mucin 16 (MUC-16) and interleukin 8 (IL-8).

Contribution of allelic imbalance to colorectal cancer.

Point mutations in cancer have been extensively studied but chromosomal gains and losses have been more challenging to interpret due to their unspecific nature. Here we examine high-resolution allelic imbalance (AI) landscape in 1699 colorectal cancers, 256 of which have been whole-genome sequenced (WGSed). The imbalances pinpoint 38 genes as plausible AI targets based on previous knowledge. Unbiased CRISPR-Cas9 knockout and activation screens identified in total 79 genes within AI peaks regulating cell growth. Genetic and functional data implicate loss of TP53 as a sufficient driver of AI. The WGS highlights an influence of copy number aberrations on the rate of detected somatic point mutations. Importantly, the data reveal several associations between AI target genes, suggesting a role for a network of lineage-determining transcription factors in colorectal tumorigenesis. Overall, the results unravel the contribution of AI in colorectal cancer and provide a plausible explanation why so few genes are commonly affected by point mutations in cancers.

Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth.

The gene desert upstream of the MYC oncogene on chromosome 8q24 contains susceptibility loci for several major forms of human cancer. The region shows high conservation between human and mouse and contains multiple MYC enhancers that are activated in tumor cells. However, the role of this region in normal development has not been addressed. Here we show that a 538 kb deletion of the entire MYC upstream super-enhancer region in mice results in 50% to 80% decrease in Myc expression in multiple tissues. The mice are viable and show no overt phenotype. However, they are resistant to tumorigenesis, and most normal cells isolated from them grow slowly in culture. These results reveal that only cells whose MYC activity is increased by serum or oncogenic driver mutations depend on the 8q24 super-enhancer region, and indicate that targeting the activity of this element is a promising strategy of cancer chemoprevention and therapy.

Impact of cytosine methylation on DNA binding specificities of human transcription factors.

The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

Structural insights into the DNA-binding specificity of E2F family transcription factors.

The mammalian cell cycle is controlled by the E2F family of transcription factors. Typical E2Fs bind to DNA as heterodimers with the related dimerization partner (DP) proteins, whereas the atypical E2Fs, E2F7 and E2F8 contain two DNA-binding domains (DBDs) and act as repressors. To understand the mechanism of repression, we have resolved the structure of E2F8 in complex with DNA at atomic resolution. We find that the first and second DBDs of E2F8 resemble the DBDs of typical E2F and DP proteins, respectively. Using molecular dynamics simulations, biochemical affinity measurements and chromatin immunoprecipitation, we further show that both atypical and typical E2Fs bind to similar DNA sequences in vitro and in vivo. Our results represent the first crystal structure of an E2F protein with two DBDs, and reveal the mechanism by which atypical E2Fs can repress canonical E2F target genes and exert their negative influence on cell cycle progression.

CTCF/cohesin-binding sites are frequently mutated in cancer.

Cohesin is present in almost all active enhancer regions, where it is associated with transcription factors. Cohesin frequently colocalizes with CTCF (CCCTC-binding factor), affecting genomic stability, expression and epigenetic homeostasis. Cohesin subunits are mutated in cancer, but CTCF/cohesin-binding sites (CBSs) in DNA have not been examined for mutations. Here we report frequent mutations at CBSs in cancers displaying a mutational signature where mutations in A•T base pairs predominate. Integration of whole-genome sequencing data from 213 colorectal cancer (CRC) samples and chromatin immunoprecipitation sequencing (ChIP-exo) data identified frequent point mutations at CBSs. In contrast, CRCs showing an ultramutator phenotype caused by defects in the exonuclease domain of DNA polymerase ɛ (POLE) displayed significantly fewer mutations at and adjacent to CBSs. Analysis of public data showed that multiple cancer types accumulate CBS mutations. CBSs are a major mutational hotspot in the noncoding cancer genome.

A novel selectable marker based on Aspergillus niger arginase expression.

Selectable markers are valuable tools in transforming asexual fungi like Aspergillus niger. An arginase (agaA) expression vector and a suitable arginase-disrupted host would define a novel nutritional marker/selection for transformation. The development of such a marker was successfully achieved in two steps. The single genomic copy of A. niger arginase gene was disrupted by homologous integration of the bar marker. The agaA disruptant was subsequently complemented by transforming it with agaA expression vectors. Both citA and trpC promoters were able to drive the expression of arginase cDNA. Such agaA+ transformants displayed arginase expression pattern distinct from that of the parent strain. The results are also consistent with a single catabolic route for arginine in this fungus. A simple yet novel arginine-based selection for filamentous fungal transformation is thus described.

Utility of Aspergillus niger citrate synthase promoter for heterologous expression.

Citrate synthase is a central player in the acidogenic metabolism of Aspergillus niger. The 5' upstream sequence (0.9kb DNA) of citrate synthase gene (citA) from A. niger NCIM 565 was analyzed and its promoter function demonstrated through the heterologous expression of two proteins. The cloned citrate synthase promoter (PcitA) sequence was able to express bar coding sequence thereby conferring phosphinothricin resistance. This sequence was further analyzed by systematic deletions to define an effective but compact functional promoter. The PcitA driven egfp expression showed that PcitA was active in all differentiation cell-stages of A. niger. EGFP expression was highest on non-repressible carbon sources like acetate and glycerol. Mycelial EGFP levels increased during acidogenic growth suggesting that PcitA is functional throughout this cultivation. A. niger PcitA is the first Krebs cycle gene promoter used to express heterologous proteins in filamentous fungi.