Multiple transcripts of a gene for a leucine-rich repeat receptor kinase from morning glory (Ipomoea nil) originate from different TATA boxes in a tissue-specific manner

Abstract

TATA boxes are the most common regulatory elements found in the promoters of eukaryotic genes because they are associated with basal transcription initiation by RNA polymerase II. Often only a single TATA element is found in a given promoter, and tissue-, stage-and/or stimulus-specific expression occurs because the TATA box is associated with other cis -acting elements that enhance or repress transcription. We used software tools for gene analysis to assist in locating potential TATA box(es) in an AT-rich region of the promoter of a gene, inrpk1, which codes for a leucinerich receptor protein kinase in morning glory (Ipomoea nil). Through the use of RT-PCR and various combinations of forward primers bracketing most of the promoter region we were able to define the 5¢-ends of transcripts in this region. The region was then targeted for analysis by RNA Ligase-Mediated-5¢ Rapid Amplification of cDNA Ends (RLM-5¢ RACE) to identify the transcript initiation site(s). Positioning of initiation sites with respect to TATA boxes identified by gene analysis tools allowed us to identify three operational TATA elements which regulate basal transcription from this gene. Two TATA boxes were responsible for all of the inrpk1 transcripts found in leaves and cotyledons, and about 25-30% of the transcripts in roots. A third TATA box was involved only in expression in roots and accounted for the remaining 50-70% of root transcripts. RNAs expressed from this element lack two potentially functional upstream AUG codons, and may be translated more efficiently than transcripts originating from the other TATA boxes.

Expression of the myostatin gene in the adductor muscle of the Pacific lion‐paw scallop Nodipecten subnodosus in association with growth and environmental conditions

“…Today it is known that even if no consensus TATA‐box is identified in a promoter, TATA‐like boxes are found in many gene promoters that are associated with transcription initiation sites (Rhee and Pugh, ). Furthermore, different transcription initiation sites have been found associated with the presence of more than one TATA‐box in gene promoters that have several transcripts (Struhl, ; Yamada et al, ; Bassett et al, ; Grace et al, ; Farrell and Bassett, ; Bassett et al, ). The presence of more than one transcript for myostatin agrees with Gonzalez‐Cadavid et al (1998) who found the human myostatin gene produces three transcripts.…”

“…Also, a longer 5′UTR sequence is inferred to be transcribed from the reported promoter region of the Chlamys farreri myostatin gene sequence in which three transcription initiation sites were reported by Hu et al (); but only one TATA‐box was identified 29 bp before the start site of the NCBI reported mRNA transcript (EU563852.2). Transcription of one or another transcript when more than one TATA‐box is present has been associated with gene expression regulation, either in a tissue specific form (Kumar et al, ; Yamada et al, ; Bassett et al, ), in response to stress (Struhl, ), or during specific developmental stages (Grace et al, ). In addition to the TATA‐box found in the 5′UTR of the long N. subnodosus myostatin transcript, the in silico analysis identified a uORF.…”

Transcriptional regulation of the grape cytochrome P450 monooxygenase gene CYP736B expression in response to Xylella fastidiosa infection

“…Our study revealed that two TATA boxes, one P-box and one I-box were located at the far upstream region of CYP736B transcripts, whereas two CAAT boxes and a G-box were located at the TSS1-containing region, and one W-box was located at the TSS2-containing region. Previous studies indicated that TATA boxes are the most common regulatory elements found in promoters of eukaryotic genes because they are associated with basal transcription initiation by RNA polymerase II, especially with cis -acting elements that enhance or repress transcription [ 26 ]. I-box (core sequence GATAA) and P-box (core sequence TGTAAAG) were associated with light and ABA responsiveness in tobacco and Arabidopsis respectively [ 27 , 28 ].…”

Rice LGD1 containing RNA binding activity affects growth and development through alternative promoters

“…, 2001). Plants are not uncommon to this phenomenon, because multiple transcripts were alternatively transcribed from multiple TATA boxes in a tissue‐specific manner for a gene encoding leucine‐rich repeat receptor kinase in Ipomoea nil (Bassett et al. , 2004).…”