Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18?

The cutoff level applied in sequencing analysis varies according to the sequencing technology, sample type, and study purpose, which can largely affect the coverage and reliability of the data obtained. In this study, we aimed to determine the optimal combination of parameters for reliable RNA transcriptome data analysis. Toward this end, we compared the results obtained from different transcriptome analysis platforms (quantitative polymerase chain reaction, Illumina RNASeq, and Oxford Nanopore Technologies MinION) for the transcriptome encoded by human chromosome 18 (Chr 18) using the same sample types (HepG2 cells and liver tissue). A total of 275 protein-coding genes encoded by Chr 18 was taken as the gene set for evaluation. The combination of Illumina RNASeq and MinION nanopore technologies enabled the detection of at least one transcript for each protein-coding gene encoded by Chr 18. This combination also reduced the probability of false-positive detection of low-copy transcripts due to the simultaneous confirmation of the presence of a transcript by the two fundamentally different technologies: short reads essential for reliable detection (Illumina RNASeq) and long-read sequencing data (MinION). The combination of these technologies achieved complete coverage of all 275 protein-coding genes on Chr 18, identifying transcripts with non-zero expression levels. This approach can improve distinguishing the biological and technical reasons for the absence of mRNA detection for a given gene in transcriptomics.

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Systematic Analysis of Missing Proteins Provides Clues to Help Define All of the Protein-Coding Genes on Human Chromosome 1

Journal of Proteome Research ◽

10.1021/pr400900j ◽

2013 ◽

Vol 13 (1) ◽

pp. 114-125 ◽

Cited By ~ 20

Author(s):

Chengpu Zhang ◽

Ning Li ◽

Linhui Zhai ◽

Shaohang Xu ◽

Xiaohui Liu ◽

...

Keyword(s):

Human Chromosome ◽

Chromosome 1 ◽

Systematic Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Human Chromosome 1

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Abstract 055: Locating Genetic Determinants Of Translational Significance Using The Rat Genome

Hypertension ◽

10.1161/hyp.64.suppl_1.055 ◽

2014 ◽

Vol 64 (suppl_1) ◽

Author(s):

Ying Nie ◽

Sivarajan Kumaraswamy ◽

Xi Cheng ◽

Harshal Waghulde ◽

Blair Mel ◽

...

Keyword(s):

Blood Pressure ◽

Human Chromosome ◽

Chromosome 9 ◽

Genome Wide Association Studies ◽

Chromosome 2 ◽

Protein Coding ◽

Positional Candidate ◽

Genetic Elements ◽

Protein Coding Genes ◽

Rat Genome

Genome-wide association studies (GWAS) have detected associations of genetic elements on human chromosome 2 with hypertension but lack the ability to discern whether these associations are/are not causal factors for hypertension. Using rat genetic models of hypertension, we have identified that factors linked to the inheritance of hypertension map to rat chromosome 9, which is homologous to human chromosome 2. Here we report that by applying high resolution mapping approaches, we have prioritized two regions on rat chromosome 9, one spanning < 788kb and a second region spanning < 81.8kb, as genomic segments containing novel inherited genetic elements controlling blood pressure. The <788kb region contains 3 protein coding genes, Trmp8 , Spp2 and Arl4c , which are also associated with human hypertension. Of these, there was only one nonsynonymous polymorphism within the gene Spp2 between the Dahl S and S.SHR strains used to map this locus. The expression of Spp2 was significantly higher in the S.SHR rat compared with S. We therefore prioritize Spp2 as a positional candidate for the <788kb region. The <81.8kb region contains no known/predicted protein-coding genes. We hypothesized that polymorphisms within gene regulatory elements underlie the <81.8kb locus. By combining the locations of the relevant polymorphisms with promoters predicted by the Proscan promoter prediction software, 5 regions were prioritized for further analysis. Alleles from the normotensive R rat from 1 out of these 5 regions had a 5.14 fold higher luciferase activity compared with that of the hypertensive S rat alleles (p<0.05). This region maps from chr9:80880396 to chr9:80882643 (Rnor5.0) on the rat genome. The downstream target for this promoter activity is unknown. Interestingly, within 110,419bp downstream of this region, there is a predicted long non-coding RNA in the mouse (AK079660) and in humans ( DIRC4) . By RT-PCR using rat kidney, we detected a novel rat transcript that is potentially a rat homologue of the mouse and human predictions. Collectively, these data point to conserved syntenic regions in rats and humans that contain novel promoter sequence variants and variants within the conserved gene, Spp2 , as potential quantitative trait nucleotides for blood pressure regulation.

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DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors

10.1101/2020.03.08.982769 ◽

2020 ◽

Author(s):

Maria M. Mikedis ◽

Yuting Fan ◽

Peter K. Nicholls ◽

Tsutomu Endo ◽

Emily K. Jackson ◽

...

Keyword(s):

Rna Binding ◽

Rna Binding Proteins ◽

Protein Coding ◽

Protein Levels ◽

Protein Coding Genes ◽

Genetic Mouse Model ◽

Proliferation And Differentiation ◽

Gene Regulatory ◽

Spermatogonial Proliferation

AbstractFertility across metazoa requires the germline-specific DAZ family of RNA-binding proteins. Here we examine whether DAZL directly regulates progenitor spermatogonia using a conditional genetic mouse model and in vivo biochemical approaches combined with chemical synchronization of spermatogenesis. We find that the absence of Dazl impairs both expansion and differentiation of the spermatogonial progenitor population. In undifferentiated spermatogonia, DAZL binds the 3’ UTRs of ∼2,500 protein-coding genes. Some targets are known regulators of spermatogonial proliferation and differentiation while others are broadly expressed, dosage-sensitive factors that control transcription and RNA metabolism. DAZL binds 3’ UTR sites conserved across vertebrates at a UGUU(U/A) motif. By assessing ribosome occupancy in undifferentiated spermatogonia, we find that DAZL increases translation of its targets. In total, DAZL orchestrates a broad translational program that amplifies protein levels of key spermatogonial and gene regulatory factors to promote the expansion and differentiation of progenitor spermatogonia.

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DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors

eLife ◽

10.7554/elife.56523 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 4

Author(s):

Maria M Mikedis ◽

Yuting Fan ◽

Peter K Nicholls ◽

Tsutomu Endo ◽

Emily K Jackson ◽

...

Keyword(s):

Rna Binding ◽

Rna Binding Proteins ◽

Protein Coding ◽

Protein Levels ◽

Protein Coding Genes ◽

Genetic Mouse Model ◽

Proliferation And Differentiation ◽

Gene Regulatory ◽

Spermatogonial Proliferation

Fertility across metazoa requires the germline-specific DAZ family of RNA-binding proteins. Here we examine whether DAZL directly regulates progenitor spermatogonia using a conditional genetic mouse model and in vivo biochemical approaches combined with chemical synchronization of spermatogenesis. We find that the absence of Dazl impairs both expansion and differentiation of the spermatogonial progenitor population. In undifferentiated spermatogonia, DAZL binds the 3' UTRs of ~2,500 protein-coding genes. Some targets are known regulators of spermatogonial proliferation and differentiation while others are broadly expressed, dosage-sensitive factors that control transcription and RNA metabolism. DAZL binds 3' UTR sites conserved across vertebrates at a UGUU(U/A) motif. By assessing ribosome occupancy in undifferentiated spermatogonia, we find that DAZL increases translation of its targets. In total, DAZL orchestrates a broad translational program that amplifies protein levels of key spermatogonial and gene regulatory factors to promote the expansion and differentiation of progenitor spermatogonia.

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