Choi Jessica D, Del Pinto Lelani A, Sutter Nathan B
Department of Biology, La Sierra University, Riverside, CA, USA.
The Jackson Laboratory, Bar Harbor, ME, USA.
Mob DNA. 2025 Jan 4;16(1):1. doi: 10.1186/s13100-024-00338-5.
Messenger RNA 3' untranslated regions (3'UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA (AATAAA in DNA) is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3'UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy numbers. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands of Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may terminate transcript in some dog genes.
Each of the dog's nine Can-SINE consensus sequences carry an average of three AATAAA PASs on their sense strands but zero on their antisense strands. Consistent with the idea that Can-SINEs can terminate transcripts, we find that sense-oriented Can-SINEs are approximately ten times more frequent at 3' ends of 3'UTRs compared to further upstream within 3'UTRs. Furthermore, the count of AATAAA PASs on head-to-tail SINE sequences differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3'UTR ends are likely to carry an AATAAA motif on the mRNA sense strand while those further upstream are not. We identified loci where Can-SINE insertion has truncated or altered a 3'UTR of the dog genome (dog 3'UTR) compared to the human ortholog. Dog 3'UTRs have peaks of AATAAA PAS frequency at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp length for target site duplications (TSDs). All dog Can-SINE types favor integration at TSDs beginning with A(4).
Dog Can-SINE retrotransposition has imported AATAAA PASs into gene transcripts and led to alteration of 3'UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3'UTR regions but are retained at the far downstream end of 3'UTRs, which we infer reflects their role as termination sequences for these transcripts.
信使核糖核酸3'非翻译区（3'UTRs）控制基因表达的许多方面，并决定转录本的终止位置。聚腺苷酸化信号（PAS）AAUAAA（DNA中的AATAAA）是转录本终止的关键调节因子，这个六聚体或类似序列在3'UTR末端的30个碱基对范围内非常常见。短散在元件（SINE）反转录转座子以高拷贝数存在于整个基因组中。当插入基因时，它们会破坏表达、改变剪接或导致mRNA在细胞核内滞留。家犬和其他食肉动物的基因组携带数十万种Can-SINEs，这是一种与tRNA相关的具有转录终止潜力的SINE。因此，我们询问Can-SINEs是否可能在某些犬类基因中终止转录本。
犬类的9种Can-SINE共有序列中，每条正义链平均携带3个AATAAA PAS，而反义链上则为零。与Can-SINEs可终止转录本的观点一致，我们发现与3'UTR内更上游相比，正义方向的Can-SINEs在3'UTR的3'末端出现的频率大约高10倍。此外，转录本中头对头SINE序列上AATAAA PAS的数量在正义和反义方向的反转录转座子之间存在显著差异。3'UTR末端附近的Can-SINEs在mRNA正义链上可能携带AATAAA基序，而那些更上游的则没有。我们确定了一些位点，与人类直系同源基因相比，Can-SINE插入导致犬类基因组的3'UTR（犬3'UTR）被截断或改变。犬3'UTR在距末端28、32和36个碱基对处有AATAAA PAS频率峰值。这种周期性部分由Can-SINE富含AT的尾巴中的TAAA(n)重复序列解释。我们注释了拳师犬参考基因组中所有经过重复序列屏蔽的Can-SINE拷贝，发现年轻的SINEC_Cf类型的靶位点重复（TSD）长度模式为15个碱基对。所有犬类Can-SINE类型都倾向于整合到以A(4)开头的TSD处。
犬类Can-SINE反转录转座已将AATAAA PAS导入基因转录本并导致3'UTR改变。AATAAA序列在内含子和3'UTR上游区域的Can-SINEs中被选择性去除，但保留在3'UTR的最下游末端，我们推断这反映了它们作为这些转录本终止序列的作用。
