Sentence examples for binding to peak sequences from inspiring English sources
Twist1 binding to peak sequences associated with Wnt pathway genes was confirmed by ChIP-qPCR in E12.5 ECCs and E10.5 limb buds.
In limb buds, Twist1 binding to peak sequences associated with wingless-related MMTV integration site 5B (Wnt5b), lymphoid enhancer binding factor 1 (Lef1), nemo like kinase (Nlk), casein kinase 1, epsilon (Csnk1e), disabled 2 interacting protein (Dab2ip), mutated in colorectal cancers (Mcc), and frizzled homolog 3 (Fzd3) were confirmed.
Genomic sequences for each of the binding peak sequences (~50 bp to 750 bp in length) were obtained using Genomatix Software Suite v2.7.
The binding peak sequences included in each of the three regions obtained (ERα only, ERβ only or ERα+ERβ) were then re-analyzed for the presence of ERE or hERE elements.
As these proportions depend on the particular chromatin states existing in the cell types, we also compared the relative abundances of TE-derived DNA in the regions of accessible chromatin of HEK293 and K562 cells with the relative abundances of TE-derived DNA in the binding peak sequences (see Table 1 and Materials and Methods).
The bedtools Getfasta function was used to extract peak sequences.
We also observe enrichment of specific SNPs in GABPα+CREB1 peaks, a pattern similar to what is observed on the ETS-CRE arrays, providing evidence that preferential GABPα binding to these sequences occurs only when CREB1 is colocalized in vivo.
Some of these changes may be related to the inclusion of Exd and Hth binding motifs in the peak sequences; notably the dark green k-mer containing the core Exd motif TGAT [ 13] is more enriched.
To characterize CaRF binding to the chCaRE sequences, we first tested the ability of CaRF to bind the specific chCaRE motif (5'-AAAGCGAGGC-3') found in a CaRF ChIP peak from the promoter of the Camk2n1 gene (camCaRE, Figure 5d).
