Article

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements

2023-06-05

Abstract excerpt

Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. Using SPICE, we successfully identified known composite elements, such as AP1-I...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: f479f11b-e0f6-50a2-9d30-a8d3899b03d3
DOI: 10.1101/2023.05.31.543110

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

A new pipeline SPICE identifies novel JUN-IKZF1 composite elementsDOI 10.1101/2023.05.31.543110Read

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activationSemantic proximity Read

PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs.Semantic proximity Read

CCSI: a database providing chromatin-chromatin spatial interaction information.Semantic proximity Read

Properties of STAT1 and IRF1 enhancers and the influence of SNPs.Semantic proximity Read

STAT3 Facilitates Super Enhancer Formation to Promote Fibroblast‐To‐Myofibroblast Differentiation by the Analysis of ATAC ‐Seq, RNA ‐Seq and ChIP ‐SeqSemantic proximity Read

Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria ParasiteSemantic proximity Read

Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA.Semantic proximity Read

A Systematic Study of Motif Pairs That May Facilitate Enhancer-Promoter InteractionsSemantic proximity Read

Asymmetric Conservation within Pairs of Co-occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-seq DataSemantic proximity Read

From motif to function: Inferring the functions of long zinc finger proteins through combinatorial selectionSemantic proximity Read

A common motif within the negative regulatory regions of multiple factors inhibits their transcriptional synergy.Semantic proximity Read

Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sitesSemantic proximity Read