Single-stranded DNA binding proteins influence APOBEC3A substrate preference.
Single-stranded DNA binding proteins influence APOBEC3A substrate preference.
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DOI：
10.1038/s41598-021-00435-y
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发表时间：
2021-10-25
影响因子：
4.6
通讯作者：
Roberts SA
中科院分区：
文献类型：
--
作者：
Brown AL;Collins CD;Thompson S;Coxon M;Mertz TM;Roberts SA
胞苷脱氨酶APOBEC3A(A3A)是多种癌症类型突变的重要来源。这些APOBEC特征突变在癌症基因组中分布不均匀，与DNA复制和发夹形成序列形成的单链DNA有关。影响这些特异性的生化和细胞因素尚不清楚。我们在模拟细胞内单链DNA潜在来源的底物上测量了A3A的体外胞苷脱氨酶活性，发现A3A在含有4个NT单链DNA环的发夹上比具有更大环、气泡结构、复制叉状结构、单链DNA缺口或线形DNA的发夹更活跃。尽管预弯的单链DNA预计会更好地适合A3A活性部位，但我们确定A3A只支持4个核苷酸的发夹底物，是线性单链DNA底物的2-5倍。与发夹底物相比，在胞苷脱氨酶检测中加入全细胞裂解物或纯化的RPA可以更严重地降低线状单链DNA(45nt)上的A3A活性。这些结果表明，肿瘤基因组中发夹形成序列中A3A驱动的突变的大量丰富可能部分是由其他蛋白质驱动的，这些蛋白质优先结合更长的单链DNA区域，这限制了A3A的访问。此外，与停滞的T7RNA聚合酶相关的单链DNA上的A3A活性降低，这表明RNA聚合酶潜在的蛋白质阻断也限制了A3A的活性。这些结果有助于解释癌症基因组中APOBEC突变特征的小转录链偏见，以及在DNA复制过程中滞后链模板中发夹形成序列的一般靶向。
The cytidine deaminase, APOBEC3A (A3A), is a prominent source of mutations in multiple cancer types. These APOBEC-signature mutations are non-uniformly distributed across cancer genomes, associating with single-stranded (ss) DNA formed during DNA replication and hairpin-forming sequences. The biochemical and cellular factors that influence these specificities are unclear. We measured A3A’s cytidine deaminase activity in vitro on substrates that model potential sources of ssDNA in the cell and found that A3A is more active on hairpins containing 4 nt ssDNA loops compared to hairpins with larger loops, bubble structures, replication fork mimics, ssDNA gaps, or linear DNA. Despite pre-bent ssDNAs being expected to fit better in the A3A active site, we determined A3A favors a 4 nt hairpin substrate only 2- to fivefold over linear ssDNA substrates. Addition of whole cell lysates or purified RPA to cytidine deaminase assays more severely reduced A3A activity on linear ssDNA (45 nt) compared to hairpin substrates. These results indicate that the large enrichment of A3A-driven mutations in hairpin-forming sequences in tumor genomes is likely driven in part by other proteins that preferentially bind longer ssDNA regions, which limit A3A’s access. Furthermore, A3A activity is reduced at ssDNA associated with a stalled T7 RNA polymerase, suggesting that potential protein occlusion by RNA polymerase also limits A3A activity. These results help explain the small transcriptional strand bias for APOBEC mutation signatures in cancer genomes and the general targeting of hairpin-forming sequences in the lagging strand template during DNA replication.
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影响因子：
30.8
作者：
Burns, Michael B.;Temiz, Nuri A.;Harris, Reuben S.
通讯作者：
Harris, Reuben S.
影响因子：
64.5
作者：
Haradhvala NJ;Polak P;Stojanov P;Covington KR;Shinbrot E;Hess JM;Rheinbay E;Kim J;Maruvka YE;Braunstein LZ;Kamburov A;Hanawalt PC;Wheeler DA;Koren A;Lawrence MS;Getz G
通讯作者：
Getz G
影响因子：
30.8
作者：
Chan K;Roberts SA;Klimczak LJ;Sterling JF;Saini N;Malc EP;Kim J;Kwiatkowski DJ;Fargo DC;Mieczkowski PA;Getz G;Gordenin DA
通讯作者：
Gordenin DA
影响因子：
5.3
作者：
BLACKWELL, LJ;BOROWIEC, JA
通讯作者：
BOROWIEC, JA
DOI：
10.1016/j.bbagen.2019.129415
发表时间：
2019-11-01
影响因子：
3
作者：
Diamond, Cody P.;Im, Junbum;Larijani, Mani
通讯作者：
Larijani, Mani