scholarly journals Deciphering essential cistromes using genome-wide CRISPR screens

2019 ◽  
Vol 116 (50) ◽  
pp. 25186-25195 ◽  
Author(s):  
Teng Fei ◽  
Wei Li ◽  
Jingyu Peng ◽  
Tengfei Xiao ◽  
Chen-Hao Chen ◽  
...  
Keyword(s):  
Predictive Models ◽  
Binding Sites ◽  
Regulatory Elements ◽  
High Accuracy ◽  
Essential Genes ◽  
Ctcf Binding ◽  
Prostate Cancer Cells ◽  
Regression Methods ◽  
Genome Wide ◽  
Breast And Prostate Cancer

Although millions of transcription factor binding sites, or cistromes, have been identified across the human genome, defining which of these sites is functional in a given condition remains challenging. Using CRISPR/Cas9 knockout screens and gene essentiality or fitness as the readout, we systematically investigated the essentiality of over 10,000 FOXA1 and CTCF binding sites in breast and prostate cancer cells. We found that essential FOXA1 binding sites act as enhancers to orchestrate the expression of nearby essential genes through the binding of lineage-specific transcription factors. In contrast, CRISPR screens of the CTCF cistrome revealed 2 classes of essential binding sites. The first class of essential CTCF binding sites act like FOXA1 sites as enhancers to regulate the expression of nearby essential genes, while a second class of essential CTCF binding sites was identified at topologically associated domain (TAD) boundaries and display distinct characteristics. Using regression methods trained on our screening data and public epigenetic profiles, we developed a model to predict essential cis-elements with high accuracy. The model for FOXA1 essentiality correctly predicts noncoding variants associated with cancer risk and progression. Taken together, CRISPR screens of cis-regulatory elements can define the essential cistrome of a given factor and can inform the development of predictive models of cistrome function.

Androgen receptor: acting in the three-dimensional chromatin landscape of prostate cancer cells

2011 ◽  
Vol 5 (1) ◽  
Author(s):  
Harri Makkonen ◽  
Jorma J. Palvimo
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Cancer Cells ◽  
Binding Sites ◽  
Target Genes ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Loop Formation ◽  
Prostate Cancer Cells

AbstractAndrogen receptor (AR) acts as a hormone-controlled transcription factor that conveys the messages of both natural and synthetic androgens to the level of genes and gene programs. Defective AR signaling leads to a wide array of androgen insensitivity disorders, and deregulated AR function, in particular overexpression of AR, is involved in the growth and progression of prostate cancer. Classic models of AR action view AR-binding sites as upstream regulatory elements in gene promoters or their proximity. However, recent wider genomic screens indicate that AR target genes are commonly activated through very distal chromatin-binding sites. This highlights the importance of long-range chromatin regulation of transcription by the AR, shifting the focus from the linear gene models to three-dimensional models of AR target genes and gene programs. The capability of AR to regulate promoters from long distances in the chromatin is particularly important when evaluating the role of AR in the regulation of genes in malignant prostate cells that frequently show striking genomic aberrations, especially gene fusions. Therefore, in addition to the mechanisms of DNA loop formation between the enhancer bound ARs and the transcription apparatus at the target core promoter, the mechanisms insulating distally bound ARs from promiscuously making contacts and activating other than their normal target gene promoters are critical for proper physiological regulation and thus currently under intense investigation. This review discusses the current knowledge about the AR action in the context of gene aberrations and the three-dimensional chromatin landscape of prostate cancer cells.

Tree-Based Modeling Techniques

2019 ◽  
pp. 1-18
Author(s):  
Dileep Kumar G.
Keyword(s):  
Predictive Models ◽  
Data Science ◽  
Linear Models ◽  
High Accuracy ◽  
Gradient Boosting ◽  
Regression Methods ◽  
Data Analyst ◽  
Linear Relationships ◽  
Learning Techniques ◽  
Modeling Techniques

Tree-based learning techniques are considered to be one of the best and most used supervised learning methods. Tree-based methods empower predictive models with high accuracy, stability, and ease of interpretation. Unlike linear models, they map non-linear relationships pretty well. These methods are adaptable at solving any kind of problem at hand (classification or regression). Methods like decision trees, random forest, gradient boosting are being widely used in all kinds of machine learning and data science problems. Hence, for every data analyst, it is important to learn these algorithms and use them for modeling. This chapter guide the learner to learn tree-based modeling techniques from scratch.

scholarly journals Genome-wide analysis of androgen receptor binding sites in prostate cancer cells

2015 ◽  
Vol 9 (6) ◽  
pp. 2319-2324 ◽  
Author(s):  
YUE CHENG ◽  
PAN YU ◽  
XIUZHI DUAN ◽  
CHUNHUA LIU ◽  
SIQI XU ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Cancer Cells ◽  
Receptor Binding ◽  
Binding Sites ◽  
Prostate Cancer Cells ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals The Integrity of piRNA Clusters is Abolished by Insulators in the Drosophila Germline

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 209 ◽  
Author(s):  
Elizaveta Radion ◽  
Olesya Sokolova ◽  
Sergei Ryazansky ◽  
Pavel Komarov ◽  
Yuri Abramov ◽  
...  
Keyword(s):  
Binding Sites ◽  
Regulatory Elements ◽  
Evolutionary Constraints ◽  
Heterochromatin Protein 1 ◽  
Heterochromatin Protein ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Pirna Cluster ◽  
A Genome ◽  
Cluster Activity

Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the retrotransposon gypsy. To understand how insulators contribute to piRNA cluster activity, we studied the effects of transgenes containing gypsy insulators on local organization of endogenous piRNA clusters. We show that transgene insertions interfere with piRNA precursor transcription, small RNA production and the formation of piRNA cluster-specific chromatin, a hallmark of which is Rhino, the germline homolog of the heterochromatin protein 1 (HP1). The mutations of Su(Hw) restored the integrity of piRNA clusters in transgenic strains. Surprisingly, Su(Hw) depletion enhanced the production of piRNAs by the domesticated telomeric retrotransposon TART, indicating that Su(Hw)-dependent elements protect TART transcripts from piRNA processing machinery in telomeres. A genome-wide analysis revealed that Su(Hw)-binding sites are depleted in endogenous germline piRNA clusters, suggesting that their functional integrity is under strict evolutionary constraints.

scholarly journals The native cistrome and sequence motif families of the maize ear

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009689
Author(s):  
Savannah D. Savadel ◽  
Thomas Hartwig ◽  
Zachary M. Turpin ◽  
Daniel L. Vera ◽  
Pei-Yau Lung ◽  
...  
Keyword(s):  
High Resolution ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Regulatory Elements ◽  
Chromatin Interaction ◽  
Sequence Motif ◽  
Binding Prediction ◽  
Interaction Sites ◽  
Genome Wide ◽  
Dna Regulatory Elements

Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas.

scholarly journals RedChIP identifies noncoding RNAs associated with genomic sites occupied by Polycomb and CTCF proteins

2021 ◽  
Vol 119 (1) ◽  
pp. e2116222119
Author(s):  
Alexey A. Gavrilov ◽  
Rinat I. Sultanov ◽  
Mikhail D. Magnitov ◽  
Aleksandra A. Galitsyna ◽  
Erdem B. Dashinimaev ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Wide Spectrum ◽  
Noncoding Rnas ◽  
Ctcf Binding ◽  
Polycomb Repressive Complex 2 ◽  
Proximity Ligation ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Architectural Protein

Nuclear noncoding RNAs (ncRNAs) are key regulators of gene expression and chromatin organization. The progress in studying nuclear ncRNAs depends on the ability to identify the genome-wide spectrum of contacts of ncRNAs with chromatin. To address this question, a panel of RNA–DNA proximity ligation techniques has been developed. However, neither of these techniques examines proteins involved in RNA–chromatin interactions. Here, we introduce RedChIP, a technique combining RNA–DNA proximity ligation and chromatin immunoprecipitation for identifying RNA–chromatin interactions mediated by a particular protein. Using antibodies against architectural protein CTCF and the EZH2 subunit of the Polycomb repressive complex 2, we identify a spectrum of cis- and trans-acting ncRNAs enriched at Polycomb- and CTCF-binding sites in human cells, which may be involved in Polycomb-mediated gene repression and CTCF-dependent chromatin looping. By providing a protein-centric view of RNA–DNA interactions, RedChIP represents an important tool for studies of nuclear ncRNAs.

scholarly journals TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide

2018 ◽  
Author(s):  
Kyster K. Nanan ◽  
David M. Sturgill ◽  
Maria F. Prigge ◽  
Morgan Thenoz ◽  
Allissa A. Dillman ◽  
...  
Keyword(s):  
Binding Sites ◽  
Genomic Dna ◽  
Multiple Roles ◽  
Ctcf Binding ◽  
Cellular Model ◽  
Potential Mechanism ◽  
Dynamic Regulation ◽  
Genome Wide

SummaryThe mechanisms supporting dynamic regulation of CTCF binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC) as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ∼13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.

scholarly journals Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation

2015 ◽  
Vol 112 (27) ◽  
pp. E3535-E3544 ◽  
Author(s):  
Kelan Chen ◽  
Jiang Hu ◽  
Darcy L. Moore ◽  
Ruijie Liu ◽  
Sarah A. Kessans ◽  
...  
Keyword(s):  
Epigenetic Regulation ◽  
Transcriptional Control ◽  
Regulatory Elements ◽  
Ctcf Binding ◽  
Dna And Rna ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Binding Factor ◽  
Structural Maintenance Of Chromosomes ◽  
Hinge Domain

Structural maintenance of chromosomes flexible hinge domain containing 1 (Smchd1) is an epigenetic repressor with described roles in X inactivation and genomic imprinting, but Smchd1 is also critically involved in the pathogenesis of facioscapulohumeral dystrophy. The underlying molecular mechanism by which Smchd1 functions in these instances remains unknown. Our genome-wide transcriptional and epigenetic analyses show that Smchd1 binds cis-regulatory elements, many of which coincide with CCCTC-binding factor (Ctcf) binding sites, for example, the clustered protocadherin (Pcdh) genes, where we show Smchd1 and Ctcf act in opposing ways. We provide biochemical and biophysical evidence that Smchd1–chromatin interactions are established through the homodimeric hinge domain of Smchd1 and, intriguingly, that the hinge domain also has the capacity to bind DNA and RNA. Our results suggest Smchd1 imparts epigenetic regulation via physical association with chromatin, which may antagonize Ctcf-facilitated chromatin interactions, resulting in coordinated transcriptional control.

scholarly journals Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF

2016 ◽  
Author(s):  
Ivana Jerković ◽  
Daniel M. Ibrahim ◽  
Guillaume Andrey ◽  
Stefan Haas ◽  
Peter Hansen ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Binding Sites ◽  
Hox Genes ◽  
Ctcf Binding ◽  
Proximity Ligation Assay ◽  
Homeotic Genes ◽  
Sequence Specificity ◽  
Individual Genome ◽  
Genome Wide ◽  
Group 1

AbstractHomeotic genes code for key transcription factors (HOX-TFs) that pattern the animal body plan. During embryonic development, Hox genes are expressed in overlapping patterns and function in a partially redundant manner. In vitro biochemical screens probing the HOX-TF sequence specificity revealed largely overlapping sequence preferences, indicating that co-factors might modulate the biological function of HOX-TFs. However, due to their overlapping expression pattern, high protein homology, and insufficiently specific antibodies, little is known about their genome-wide binding preferences. In order to overcome this problem, we virally expressed tagged versions of limb-expressed posterior Hox genes (Hoxa9-13, and Hoxd9-13) in primary mesenchymal limb progenitor cells (micromass). We determined the effect of each HOX-TF on cellular differentiation (chondrogenesis) and gene expression and found that groups of HOX-TFs induce distinct regulatory programs. We used ChIP-seq to determine their individual genome-wide binding profiles and identified between 12,540 and 27,466 binding sites for each of the nine HOX-TFs. Principal Component Analysis (PCA) of binding profiles revealed that the HOX-TFs are clustered in two subgroups (Group 1: HOXA/D9, HOXA/D10, HOXD12, and HOXA13 and Group 2: HOXA/D11 and HOXD13), which are characterized by differences in their sequence specificity and by the presence of cofactor motifs. Specifically, we identified CTCF binding sites in Group 1, indicating that this subgroup of HOX-proteins cooperates with CTcf. We confirmed this interaction by an independent biological assay (proximity ligation assay) and showed that CTCF is a novel HOX cofactor that specifically associates with Group 1 HOX-TFs, pointing towards a possible interplay between HOX-TFs and chromatin architecture.

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