Computational Methods for Analysis of the DNA-Binding Preferences of Cys2His2 Zinc-Finger Proteins
Küçük Resim Yok
Tarih
2018
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Humana Press Inc
Erişim Hakkı
info:eu-repo/semantics/closedAccess
Özet
Cys(2)His(2) zinc-finger proteins (C2H2-ZFPs) constitute the largest class of human transcription factors (TFs) and also the least characterized one. Determining the DNA sequence preferences of C2H2-ZFPs is an important first step toward elucidating their roles in transcriptional regulation. Among the most promising approaches for obtaining the sequence preferences of C2H2-ZFPs are those that combine machine--learning predictions with in vivo binding maps of these proteins. Here, we provide a protocol and guidelines for predicting the DNA-binding preferences of C2H2-ZFPs from their amino acid sequences using a machine learning-based recognition code. This protocol also describes the tools and steps to combine these predictions with ChIP-seq data to remove inaccuracies, identify the zinc-finger domains within each C2H2-ZFP that engage with DNA in vivo, and pinpoint the genomic binding sites of the C2H2-ZFPs.
Açıklama
Anahtar Kelimeler
Cys(2)His(2) zinc-finger proteins, Transcription factors, DNA motifs, ChIP-seq, Machine learning, Recognition code
Kaynak
Zinc Finger Proteins: Methods and Protocols
WoS Q Değeri
N/A
Scopus Q Değeri
Q3
Cilt
1867
