We use these models to predict the binding energies of transcription factor binding sites to within 1 kBT of their measured values. We further explore how such a sequence-energy mapping relates to the mechanisms of trancriptional regulation in various promoter contexts. Specifically, we show that ...
4DNA序列分析
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of methyl-CpG-binding domain (MBD) proteins is unclear. Here we ...
The plus sign is for the symmetric case, i.e., the two sites couple repulsively, which hampers binding of both proteins, and the minus sign indicates the attractive antisymmetric case. Clearly, the opposite is the case for ComK. Rather than introducing bending, binding of ComK reduces ...
When fused to the GAL4 DNA-binding domain, either full- length QRAP2 or its N-terminus functioned effectively as a trans-activator in the yeast one-hybrid assay with its C-ter- minus completely inactive. Our data indicate that QRAP2 could be a new member of the AP2/EREBP transcription...
We retrieved 247 core-validated vertebrate transcript factor binding sites (TFBS) from theJASPAR 2024 database. Download thevertebrate dataset from here Download thebed files from hereas "jaspar_beds" Unpack and extract the relevant files from above. Place the contents intodata/TFBS/folder. ...
During transcription, one strand of DNA serves as a template for synthesizing RNA (this DNA is known as the “minus,”“antisense,”“noncoding,”“anticoding” or “transcribed” strand). Transcription begins by RNA polymerase binding to a promoter sequence in DNA. In prokaryotes, accessory...
The covalent joining ofpolynucleotidescatalyzed by theDNA ligaseis a necessary event inDNA repair, recombination, and most notablyDNA replicationwhich requires the joining of “Okazaki” fragments (the small, nascent ssDNA fragments generated from the copying of the minus strand). Initially searched fo...
BMO transcription factor binding prediction BMO (“Bee” MOdel of TF binding) builds on previous reports that the degree of chromatin accessibility around a motif15,16,17 and the presence of co-occurring motifs18 positively correlate with TF occupancy, corresponding to the analogy of TFs behaving ...
(Fig.3c, d). In addition, the distances between the IS and these pre-RC factors recapitulated independent biochemical methods measuring positioning of pre-RC factor binding sites30,31,32, such that the median distances between core IS (peak summit) and ORC1, ORC2 and MCM7 binding sites (...