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

By A. Jolma, Yimeng Yin, K. Nitta, Kashyap Dave, A. Popov, Minna Taipale, M. Enge, Teemu Kivioja, E. Morgunova, Jussi Taipale. 2015

529 citations recorded by the source corpus.

Subfields: Molecular Biology

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Citations in the corpus

Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “Initial PWM models were generated using these seeds using the multinomial method (21), and the seed was subsequently refined by expert analysis [see (26, 64)].”
Transcriptional Addiction in Cancer (2017, unknown): “The master TFs bind cooperatively to enhancer DNA elements and recruit coactivators and the transcription apparatus (Banerji et al., 1981; Benoist and Chambon, 1981; Bulger and Groudine, 2011; Gruss et al., 1981; Jolma et al., 2015; Lelli et al., 2012; Levine et al., 2014; Malik and Roeder, 2010; On”
Gene regulatory network inference in the era of single-cell multi-omics (2023, background): “• Binding assays (ChIP-seq, CUT&Tag, CAP-SELEX) • Chromosome conformation capture techniques • Expression quantitative trait loci • Perturbation assays Fig.”
The Human Transcription Factors. (2018, unknown): “…we have drawn heavily upon motif collections such as TRANSFAC (Matys et al., 2006), JASPAR (Mathelier et al., 2016), HT-SELEX (Jolma et al., 2013; Jolma et al., 2015; Yin et al., 2017), UniPROBE (Hume et al., 2015), and CisBP (Weirauch et al., 2014), along with previous catalogs of human TFs…”
Mapping genome-wide transcription-factor binding sites using DAP-seq (2017, methodology): “In vitro TFBS identification methods such as Protein Binding Microarrays (PBM) and High Throughput Systematic Evolution of Ligands by Exponential Enrichment (HT-SELEX) have achieved the highest throughput for deducing TF binding specificities in vitro 9–11 , but these methods use short synthetic oli”
Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, methodology): “In fact, SELEX analysis using consecutive affinity purification to interrogate pairwise TF-binding specificities (CAP-SELEX [Jolma et al., 2015]) has demonstrated that hancer Architecture and underlying motif requirements. flexibility of motif organization, and selective constraint across…”
Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins (2022, unknown): “With HT-SELEX, we sequenced and then analyzed the bound populations of molecules selected from a randomized oligo pool after all three selection cycles (Nitta et al. 2015).”