Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals

Abstract

Alternative splicing (AS), alternative transcription initiation (ATI) and alternative transcription termination (ATT) create the extraordinary complexity of transcriptomes and make key contributions to the structural and functional diversity of mammalian proteomes. Analysis of mammalian genomic and transcriptomic data shows that contrary to the traditional view, the joint contribution of ATI and ATT to the transcriptome and proteome diversity is quantitatively greater than the contribution of AS. Although the mean numbers of protein-coding constitutive and alternative nucleotides in gene loci are nearly identical, their distribution along the transcripts is highly non-uniform. On average, coding exons in the variable 5' and 3' transcript ends that are created by ATI and ATT contain approximately four times more alternative nucleotides than core protein-coding regions that diversify exclusively via AS. Short upstream exons that encompass alternative 5'-untranslated regions and N-termini of proteins evolve under strong nucleotide-level selection whereas in 3'-terminal exons that encode protein C-termini, protein-level selection is significantly stronger. The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns.

Figure 1.

Anatomy of mammalian transcripts: functional domains, constitutive and alternative nucleotides and alternative events. TI, transcription initiation site; AUG, translation initiation site; TT, transcription termination site; translation termination site; ATI, alternative transcription initiation; AS, alternative splicing; ATT, alternative transcription termination. Protein-coding regions are filled by black (in cCDSs) or by dark grey (in grey areas). UTRs are shown in white (for UTRs) and in light grey (for grey areas).

Figure 2.

Distributions of introns in longest isoforms transcribed from polymorphic and monomorphic gene loci (A) and in their protein coding regions (B).

Figure 3.

Mean numbers of introns in different functional regions of AS, ATI and ATT genes.

Figure 4.

Predominant extension of alternative transcripts in the 5′- and 3′-terminal regions. Mean lengths of functional regions (x-axis) and mean numbers of introns (y-axis) are shown. (A) ATI gene group; (B) ATT gene group; (C) ATI + ATT gene group; (D) AS gene group. Zero on the x-axis is the distal (most downstream) start codon in the respective locus.

Figure 5.

Distributions of RNA/nucleotide selection pressure ratio values, RNSP (A) and Protein Selection Pressure ratio values, PSP (B) in the 5′ grey area, cCDS and the 3′ grey area.