Assessment of transcript polyadenylation by 3' RACE: the response of epidermal growth factor messenger ribonucleic acid to thyroid hormone in the thyroid and submaxillary glands.

The complementary DNA (cDNA) sequence of epidermal growth factor (EGF) indicates that its 3' untranslated region (3' UTR) is 745 bases long, with polyadenylation occurring at residue 4749. However, when we used reverse transcriptase-polymerase chain reaction (RT-PCR) with an anchored 3' primer [3'rapid amplification of cDNA ends (RACE)] to amplify the 3' ends of cDNA, we actually detected two major products [800 and 600 base pairs (bp)] and a minor product (400 bp) in the thyroid or submaxillary glands (SMGs) of male mice. Analysis of genomic DNA with a battery of primer pairs gave only the predicted PCR products from the 3' UTR, demonstrating the lack of introns in this region of genomic DNA and eliminating alternate splicing as the explanation of the transcript diversity we detected. We confirmed that two potential polyadenylation sites proximal to residue 4749 are used in vivo by hybridizing the same 3' RACE products with probes specific for the 5' end of the 3' UTR, and also for poly-A tails. To assess the distribution of poly-A tail lengths on transcripts using the terminal polyadenylation site (4749), we used several different approaches to analyze 3' RACE products. Solution hybridization with 3' UTR probes revealed a striking difference between transcripts in SMG and thyroid: SMG contained two large 3' RACE populations (approximately 770 and 870 bp), whereas thyroid only contained one (approximately 770 bp). EGF transcript heterogeneity due to different poly-A tail lengths was confirmed using an upstream primer 400 bases closer to the 3' end of the 3' UTR, and TaqI digestion. Again we found two major populations in SMG (approximately 380 and 480 bp), but only one (380 bp) in thyroid, which upon TaqI digestion showed tissue-specific heterogeneity only in the 3' fragment. T4 treatment of male mice (0.25 microgram T4/gm ip) increased the intensity of both populations in SMG and the smaller population in thyroid within 24 h. However, after a week of T4 injections, only the intensity of the population with the longer poly-A tails in the SMG remained elevated, a finding consistent with tissue-specific enhanced stability of transcripts due to polyadenylation. Finally, to resolve poly-A tail lengths more precisely, we used an upstream primer that was specific for the 3' end of murine 3' UTR. This approach revealed that the thyroid contains three major populations of EGF transcripts, with poly-A tail lengths of approximately 20, 50, and 70 A's. After T3 treatment for 24 h, the intensity of transcripts containing 20 A's increased 52% (P < 0.02) and those with 50 A's increased 130% (P < 0.01), whereas there was no change in transcripts with tails > or = 70 A's. On the other hand, there were no distinct bands in SMG samples, but rather a heterogeneous distribution of poly-A tail lengths from approximately 20-120 A's that showed an overall increase of approximately 60% in response to T3.