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New results suggest that the spatial organization of chromatin in embryonic stem cells may be important for maintenance of the pluripotent state, whereas the nuclear architecture of differentiated cells facilitates formation of transcriptionally active zones with shared transcription and splicing machinery.
As to the shared transcription factors between At and Dt subgenomes, these exhibit subfunctionalization, in that two copies partition the ancestral function [47].
The ompB promoters in Rmona601 and Rmontanensis700 drove expression of aberrant DsRed2, GFPuv and CAT mRNAs regardless of the orientations of the expression cassettes or the presence of independent or single shared transcription terminators.
Indeed, transcription has been detected in these regions, and the recruitment of genomic regions on different chromosomes to a shared transcription factory could lead to the interchromosomal associations observed in 4Cv.
Cooperativity of miRNAs is evaluated by their shared transcription factors and functional coherence of target genes.
Another is shared transcription factor recognition sites in the regulatory regions of those genes [ 10].
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Consequently microRNAs are assumed to share transcription regulatory sites and to be co-expressed with coding mRNA transcripts.
We next sought to assess evolutionary constraints on promoter sequence by examining the tendency of orthologous promoters to share transcription factor binding motifs.
In the near future, the ease of plugin development will makes it possible to look for TS enriched in genes sharing transcription factor and miRNA specific motifs in their non-coding regions.
Therefore, they would share transcription factor binding sites (TFBS) for these TFs.
Genes that are divergently expressed (i.e. share a promoter) usually share transcription factors, and show similar regulation.
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