Topic
Chromatin binding
About: Chromatin binding is a research topic. Over the lifetime, 1157 publications have been published within this topic receiving 58338 citations.
Papers published on a yearly basis
Papers
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Abstract: We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available.
17,849 citations
TL;DR: The unbiased sequence interrogation of the genuine chromatin binding sites suggests that direct ER binding requires the presence of Forkhead factor binding in close proximity, demonstrating the necessity of FoxA1 in mediating an estrogen response in breast cancer cells.
1,456 citations
TL;DR: It is suggested that hyperdynamic binding of structural chromatin proteins is a functionally important hallmark of pluripotent ES cells that contributes to the maintenance of plasticity in undifferentiated ES cells and to establishing higher-order chromatin structure.
1,074 citations
TL;DR: Three striking aspects of the initial chromatin binding events include an unexpected role for c-Myc in facilitating OSK chromatin engagement, the primacy of O, S, and K as pioneer factors at enhancers of genes that promote reprogramming, and megabase-scale chromatin domains spanned by H3K9me3 that prevent initial OSKM binding and impede the efficiency of reprograming.
913 citations
Kyriaki Michailidou1, Jonathan Beesley2, Sara Lindström3, Sander Canisius +280 more•Institutions (76)
TL;DR: 15 new loci associated with breast cancer at P < 5 × 10−8 are identified, and one association appears to be driven by an amino acid substitution encoded in EXO1, which is found in women of European ancestry.
Abstract: Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1.
641 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2022 | 2 |
| 2021 | 114 |
| 2020 | 90 |
| 2019 | 120 |
| 2018 | 80 |
| 2017 | 62 |