Resolving Chromosome-Centric Human Proteome with Translating mRNA Analysis: A Strategic Demonstration

Chromosome-centric human proteome
project (C-HPP) aims at differentiating
chromosome-based and tissue-specific protein compositions in terms
of protein expression, quantification, and modification. We previously
found that the analysis of translating mRNA (mRNA attached to ribosome-nascent
chain complex, RNC-mRNA) can explain over 94% of mRNA-protein abundance.
Therefore, we propose here to use full-length RNC-mRNA information
to illustrate protein expression both qualitatively and quantitatively.
We performed RNA-seq on RNC-mRNA (RNC-seq) and detected 12 758
and 14 113 translating genes in human normal bronchial epithelial
(HBE) cells and human colorectal adenocarcinoma Caco-2 cells, respectively.
We found that most of these genes were mapped with >80% of coding
sequence coverage. In Caco-2 cells, we provided translating evidence
on 4180 significant single-nucleotide variations. While using RNC-mRNA
data as a standard for proteomic data integration, both translating
and protein evidence of 7876 genes can be acquired from four interlaboratory
data sets with different MS platforms. In addition, we detected 1397
noncoding mRNAs that were attached to ribosomes, suggesting a potential
source of new protein explorations. By comparing the two cell lines,
a total of 677 differentially translated genes were found to be nonevenly
distributed across chromosomes. In addition, 2105 genes in Caco-2
and 750 genes in HBE cells are expressed in a cell-specific manner.
These genes are significantly and specifically clustered on multiple
chromosomes, such as chromosome 19. We conclude that HPP/C-HPP investigations
can be considerably improved by integrating RNC-mRNA analysis with
MS, bioinformatics, and antibody-based verifications.