References of "Zhou, Yang 50031302"
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See detailAssessing Transcription Regulatory Elements To Evaluate the Expression Status of Missing Protein Genes on Chromosomes 11 and 19.
Kong, Nannan; Zhou, Yang UL; Xu, Shaohang et al

in Journal of proteome research (2015), 14(12), 4967-75

During an investigation of missing proteins with the RNA-seq data acquired from three liver cancer cell lines, the majority of the missing protein coding genes (MPGs) located at chromosome 11 (chr11) had ... [more ▼]

During an investigation of missing proteins with the RNA-seq data acquired from three liver cancer cell lines, the majority of the missing protein coding genes (MPGs) located at chromosome 11 (chr11) had no corresponding mRNAs, while a high percentage of the MPGs on chr19 were detected at the mRNA level. The phenomenon, which was also observed in more than 40 cell lines, led to an inquiry of causation of the different transcriptional statuses of the MPGs in the two chromosomes. We hypothesized that the special chromatin structure was a key element to regulate MPG transcription. Upon a systematical comparison of the effects of DNase I hypersensitive sites (DHSs), transcription factors (TFs), and histone modifications toward these genes or MPGs with/without mRNA evidence in chr11 and 19, we attributed the poor transcription of the MPGs to the weak capacity of these transcription regulatory elements, regardless of which chromosome the MPGs were located. We further analyzed the gene contents in chr11 and found a number of genes related to sensory functions in the presence of chr11. We postulate that a high number of sensory-related genes, which are located within special chromatin structure, could bring a low detection rate of MPGs in chr11. [less ▲]

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See detailInsights from ENCODE on Missing Proteins: Why beta-Defensin Expression Is Scarcely Detected.
Fan, Yang; Zhang, Yue; Xu, Shaohang et al

in Journal of proteome research (2015), 14(9), 3635-44

beta-Defensins (DEFBs) have a variety of functions. The majority of these proteins were not identified in a recent proteome survey. Neither protein detection nor the analysis of transcriptomic data based ... [more ▼]

beta-Defensins (DEFBs) have a variety of functions. The majority of these proteins were not identified in a recent proteome survey. Neither protein detection nor the analysis of transcriptomic data based on RNA-seq data for three liver cancer cell lines identified any expression products. Extensive investigation into DEFB transcripts in over 70 cell lines offered similar results. This fact naturally begs the question-Why are DEFB genes scarcely expressed? After examining DEFB gene annotation and the physicochemical properties of its protein products, we postulated that regulatory elements could play a key role in the resultant poor transcription of DEFB genes. Four regions containing DEFB genes and six adjacent regions on chromosomes 6, 8, and 20 were carefully investigated using The Encyclopedia of DNA Elements (ENCODE) information, such as that of DNase I hypersensitive sites (DHSs), transcription factors (TFs), and histone modifications. The results revealed that the intensities of these ENCODE features were globally weaker than those in the adjacent regions. Impressively, DEFB-related regions on chromosomes 6 and 8 containing several non-DEFB genes had lower ENCODE feature intensities, indicating that the absence of DEFB mRNAs might not depend on the gene family but may be reliant upon gene location and chromatin structure. [less ▲]

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