This guest post is a commentary by Carlo Artieri on “Transcript length mediates developmental timing of gene expression across Drosophila” by Artieri, C.G. and H.B. Fraser. The preprint is arXived here.

We have recently posted a preprint manuscript to arXiv that tests a decades-old hypothesis about how biological aspects of development constraint gene structure using several genome-scale transcriptional timecourses and interpret its effects in the context of Drosophila evolution. The paper may be of particular interest to researchers using genomic data in evo-devo studies.

During the early stages of identification and characterization of homeobox
domain (HOX) genes and their related regulators, it was noted that they activated in a temporally sequential manner roughly correlated to their pre-mRNA transcript length (i.e., short genes express early, followed by longer genes.) This led to the hypothesis that this pattern was produced by a purely physical mechanism (Gubb 1986): genes with long pre-mRNAs cannot complete transcription in the interval between the rapid cell cycles taking place during early insect development, leading to abortive, non-functional transcripts. As long pre-mRNAs result primarily from long introns, this was termed ‘Intron Delay’.

We explored patterns of expression of genes in D. melanogaster over two embryonic timescales: eight time points spanning the latter part of the early embryonic ‘syncytial cycles’, during which the most rapid cell cycles take place, and 12 time points spanning the ~24 hours of embryogenesis. Long genes (≥ 5 kb long pre-mRNA transcripts) expressed from the zygotic genome showed a lag in the time required to reach stable levels of expression relative to short genes (< 5 kb) in both timecourses; in fact, stable expression of long genes did not occur until ~12 hours into embryogenesis, or midway between fertilization and emergence of larva from the egg. No such pattern was observed among long or short genes that are maternally deposited in the embryo, as is expected if inability to terminate transcription is the driving mechanism behind this delay. Additional embryonic timecourse data from RNA-Seq libraries generated from non poly-A selected total RNA, and therefore not biased towards capture of processed RNAs, showed that only long zygotic
genes expressed during the earliest developmental time points show a marked deficiency in 3’ relative to 5’ derived reads. This is consistent with their inability to terminate transcription, but not with transcriptional delay due to reduced transcriptional activation during early development.

The analysis was extended using developmental expression data from 3 additional Drosophila species spanning ~60 million years of evolution and showed that this pattern of delayed expression of long zygotically expressed genes is conserved across the phylogeny. This led us to predict that short zygotically expressed genes that are conserved in their ability to escape intron delay would be under substantial evolutionary pressure to maintain their compact lengths, and found that this was the case when compared to long zygotic or either short or long maternally deposited genes.

We suggest that intron delay is an underappreciated mechanism affecting the expression level of a substantial fraction of the Drosophila embryonic transcriptome (~10%) and acts as a source of significant constraint on the structural evolution of important developmental genes.

References:
Gubb D. 1986. Intron‐delay and the precision of expression of homoeotic gene products in Drosophila. Developmental Genetics 7: 119–131