The importance of poly(A) site choice

To ring out 2009, a brief mention of some studies that reinforce the conclusions mentioned in this essay.  The basic theme – it looks more and more as if poly(A) site choice can vary for many, many genes in humans, and that a general trend towards shorter 3’-untranslated regions(due to selection of poly(A) sites nearer the 5’ end of the mRNA) is seen in rapidly growing cells (such as stem cells and cancer cells). The consequences of this seem to be significant, as it seems as if shorter RNAs are more abundant, owing to an absence of RNA sequences that destabilize the mRNA.  In other words:  shorter 3′ UTRs = higher expression = more growth/less regulation.

The means by which such global trends in poly(A) site choice may be accomplished are not clear; this will undoubtedly be one of the areas of interest in the field of polyadenylation over the next few years.

Two more examples of this “genre”:

Singh P, Alley TL, Wright SM, Kadmar S, Schott W, Wilpan RY, Mills KD, Graber JH. 2009. Global changes in processing of mRNA 3′ untranslated regions characterize clinically distinct cancer subtypes.  Cancer Res. 69, 9422-9430.

The abstract:

Molecular cancer diagnostics are an important clinical advance in cancer management, but new methods are still needed. In this context, gene expression signatures obtained by microarray represent a useful molecular diagnostic. Here, we describe novel probe-level microarray analyses that reveal connections between mRNA processing and neoplasia in multiple tumor types, with diagnostic potential. We now show that characteristic differences in mRNA processing, primarily in the 3′-untranslated region, define molecular signatures that can distinguish similar tumor subtypes with different survival characteristics, with at least 74% accuracy. Using a mouse model of B-cell leukemia/lymphoma, we find that differences in transcript isoform abundance are likely due to both alternative polyadenylation (APA) and differential degradation. While truncation of the 3′-UTR is the most common observed pattern, genes with elongated transcripts were also observed, and distinct groups of affected genes are found in related but distinct tumor types. Genes with elongated transcripts are overrepresented in ontology categories related to cell-cell adhesion and morphology. Analysis of microarray data from human primary tumor samples revealed similar phenomena. Western blot analysis of selected proteins confirms that changes in the 3′-UTR can correlate with changes in protein expression. Our work suggests that alternative mRNA processing, particularly APA, can be a powerful molecular biomarker with prognostic potential. Finally, these findings provide insights into the molecular mechanisms of gene deregulation in tumorigenesis.

Ji Z, Tian B. 2009. Reprogramming of 3′ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS One 4, e8419

The abstract:

BACKGROUND: The 3′ untranslated regions (3’UTRs) of mRNAs contain cis elements involved in post-transcriptional regulation of gene expression. Over half of all mammalian genes contain multiple polyadenylation sites that lead to different 3’UTRs for a gene. Studies have shown that the alternative polyadenylation (APA) pattern varies across tissues, and is dynamically regulated in proliferating or differentiating cells. Generation of induced pluripotent stem (iPS) cells, in which differentiated cells are reprogrammed to an embryonic stem (ES) cell-like state, has been intensively studied in recent years. However, it is not known how 3’UTRs are regulated during cell reprogramming. METHODS/MAIN FINDINGS: Using a computational method that robustly examines APA across DNA microarray data sets, we analyzed 3’UTR dynamics in generation of iPS cells from different cell types. We found that 3’UTRs shorten during reprogramming of somatic cells, the extent of which depends on the type of source cell. By contrast, reprogramming of spermatogonial cells involves 3’UTR lengthening. The alternative polyadenylation sites that are highly responsive to change of cell state in generation of iPS cells are also highly regulated during embryonic development in opposite directions. Compared with other sites, they are more conserved, can lead to longer alternative 3’UTRs, and are associated with more cis elements for polyadenylation. Consistently, reprogramming of somatic cells and germ cells involves significant upregulation and downregulation, respectively, of mRNAs encoding polyadenylation factors, and RNA processing is one of the most significantly regulated biological processes during cell reprogramming. Furthermore, genes containing target sites of ES cell-specific microRNAs (miRNAs) in different portions of 3’UTR are distinctively regulated during cell reprogramming, suggesting impact of APA on miRNA targeting. CONCLUSIONS/SIGNIFICANCE: Taken together, these findings indicate that reprogramming of 3’UTRs by APA, which result from regulation of both general polyadenylation activity and cell type-specific factors and can reset post-transcriptional gene regulatory programs in the cell, is an integral part of iPS cell generation, and the APA pattern can be a good biomarker for cell type and state, useful for sample classification. The results also suggest that perturbation of the mRNA polyadenylation machinery or RNA processing activity may facilitate generation of iPS cells.

Happy New Year to everyone!