Here, using a massively parallel reporter assay (MPRA) of 209,440 sequences, we examine all possible pair and triplet combinations, permutations and orientations of eighteen liver-associated transcription factor binding sites (TFBS). We find that TFBS orientation and order have a major effect on ...
It was recently described that loss of the cell cycle regulator p21 was associated with a gain in EMT characteristics and an upregulation of the master EMT transcription factor ZEB1. In this study, in silico analysis was performed in combination with different in vitro and in vivo techniques to...
Computational methods scanning open chromatin profiles to find footprints have been shown to predict transcription factor binding sites (TFBS) with high accuracy in DNase-seq data [7,8]. Among others, computational footprinting has been used to detect the regulatory lexicon of several cell types [9...
FPKM values output by cufflinks, as described above, were used as inputs for the PCA. The analysis was done in R version 4.0.3. The R function “aov()” was used to perform a linear analysis of variance (ANOVA) at each gene, using each sample as a factor. The R function “qvalue...
Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, Kampa D, Piccolboni A, Sementchenko V, Cheng J, Williams AJ, et al: Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell. 2004, 116: 499...
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes BMC Bioinformatics, 6 (1) (2005), pp. 1-20 Google Scholar [29] Y. Wei, et al. iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multipl...
Disruption of transcription factor binding sites was done by mutagenesis using the QuikChange site-directed mutagenesis kit (Stratagene). Sense oligonucleotides were: 5′ Sp1, 5′-GTCCCAGAGTGATGTACTACGATCAGCCGCTCCCACATCC-3′;3′ Sp1, 5′-CTGATTTGGCTTTCCTTTACGACTTCCCACCCACCCAGG-3′; AP-1 (1...
(a) Transcription factor binding sites along the frdA and narG promoters. Black inverted arrows represent NarL high-affinity, 7-2-7 binding arrangements; white arrows represent NarL non-7-2-7 sites or NarL single heptameric sites; light gray inverted arrows represent FNR sites, a dark gray ...
Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically associated with the RNA polymerase (RNAP) σ70 holoenzy
For measuring expression levels, RNA was isolated from the human ES cells and differentiated cells using TRIzol (Invitrogen, 15596-026), further purified with RNeasy columns (QIAGEN, 74104) and DNase treated. RNA-seq library construction and data analysis was carried out as described previously9....