Addendum: Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites.
Addendum: Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites.
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附录：转录组学和蛋白质组学揭示了疟原虫子孢子成熟过程中的两波翻译抑制。
DOI：
10.1038/s41467-021-27767-7
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发表时间：
2022-01-06
影响因子：
16.6
通讯作者：
Kappe SHI
中科院分区：
文献类型：
--
作者：
Lindner SE;Swearingen KE;Shears MJ;Sebastian A;Walker MP;Vrana EN;Hart KJ;Minns AM;Albert I;Sinnis P;Moritz RL;Kappe SHI
在文章的原始版本中，无意的操作员错误导致我们对RNA-seq数据的处理无法解释映射读数的正确链型（例如，单个切换未从默认值更改）。在我们的生物信息学家同事（现在作为共同作者加入）的关键贡献下，我们重新分析了这些RNA-seq数据（如下所述），并在本附录中提供了基于它们的下游解释。重要的是，在比较有义和反义映射读段的秩丰度时，我们观察到恶性疟原虫和约氏疟原虫在子孢子发育的两个阶段中的强相关性（补充图1）。也许正因为如此，原条款的主要结论仍然有效，不需要修改。然而，新的分析需要修改一些基因列表的组成。此外，我们现在还通过应用转录完整性编号（TIN）度量来识别和解释导入转录，该度量适用于所有转录本，以使这些数据集更加强大。首先，使用约氏疟原虫17 XNL株寄生虫，我们现在已经鉴定了2795和2402个RNA，其具有通过所有包含阈值的可检测和明确的序列读段（包括最小读段计数> 20），（与先前鉴定的4195和3887个RNA相比）（补充数据1）。类似地，对于恶性疟原虫NF 54株寄生虫，我们在卵囊子孢子和唾液腺子孢子阶段分别鉴定了2408和2166个RNA（相对于先前鉴定的3535和3575个RNA）。在这些阶段中最丰富的mRNAs基本上与以前报道的一样，并且在卵囊子孢子和唾液腺子孢子阶段的mRNA丰度的极端波动对于一些转录物是明显的（例如，py17x_0514800，> 90倍; py17x_1354300，297倍），包括在感染性子孢子（UIS）家族中上调的那些（例如，pyluis 4，丰度增加约1900倍）（图1，补充数据2和补充数据3）。如上所述，我们还观察到疟原虫子孢子中的大量反义转录。即使在应用严格过滤以解释当相邻基因转录成注释的基因特征时发生的导入转录之后，我们在恶性疟原虫卵囊子孢子和唾液腺子孢子中分别检测到306和327个反义转录物，以及在约氏疟原虫卵囊子孢子和唾液腺子孢子中分别检测到479和410个反义转录物。反义转录物的排序丰度和有义转录物的排序丰度的比较揭示了强的统计学显著相关性（补充图1）。此外，这些反义转录物中的一些在子孢子阶段和物种之间差异表达，这当然需要进一步研究以了解这些是否以及如何影响生物学上重要的过程（补充图2和补充数据3）。
In the original version of the Article, an inadvertent operator error resulted in our processing of the RNA-seq data to not account for the correct strandedness of the mapped reads (eg, a single toggle was not changed from the default). Here with the key contributions of our bioinformatician colleagues (now added as co-authors), we have thus reanalyzed these RNA-seq data (described below) and we provide the downstream interpretations based upon them in this Addendum. Importantly, upon a comparison of the rank abundance of the sense and antisense mapped reads, we observed strong correlations for both P. falciparum and P. yoelii in both stages of sporozoite development (Supplementary Fig. 1). Perhaps due to this, the major conclusions of the original Article still are valid and do not require modification. However, the new analyses required modification of the composition of some gene lists. In addition, we have now also identified and accounted for run-in transcription through the application of a Transcript Integrity Number (TIN) metric that is applied to all transcripts to make these datasets more robust 1. We provide those corrections to the gene lists and relevant figures and Supplementary Files here.First, using P. yoelii 17XNL strain parasites we have now identified 2795 and 2402 RNAs with detectable and unambiguous sequence reads that pass all inclusion thresholds (including minimum read count> 20) that are present in oocyst sporozoites and salivary gland sporozoites, respectively (versus 4195 and 3887 RNAs previously identified)(Supplementary Data 1). Similarly, with P. falciparum NF54 strain parasites, we identified 2408 and 2166 RNAs in oocyst sporozoite and salivary gland sporozoite stages, respectively (versus 3535 and 3575 RNAs previously identified). The most abundant mRNAs in these stages remain largely as previously reported, and the same extreme swings in mRNA abundance across oocyst sporozoite and salivary gland sporozoite stages are evident for some transcripts (eg, py17x_0514800,> 90-fold; py17x_1354300, 297-fold) including those of the upregulated in infectious sporozoites (UIS) family (eg, pyuis4,~ 1900-fold increase in abundance)(Fig. 1, Supplementary Data 2, and Supplementary Data 3). As noted above, we also observed substantial antisense transcription in Plasmodium sporozoites. Even after stringent filtering was applied to account for run-in transcription that occurs when a neighboring gene is transcribed into the annotated gene feature, we detected 306 and 327 antisense transcripts in P. falciparum oocyst sporozoites and salivary gland sporozoites respectively, as well as 479 and 410 antisense transcripts in P. yoelii oocyst sporozoites and salivary gland sporozoites, respectively. A comparison of the ranked abundance of antisense transcripts and the ranked abundance of sense transcripts revealed a strong statistically significant correlation (Supplementary Fig. 1). Moreover, some of these antisense transcripts are differentially expressed across sporozoite stages and across species, which certainly warrants further study to understand if and how these affect biologically important processes (Supplementary Fig. 2 and Supplementary Data 3).
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3
作者：
Wang L;Nie J;Sicotte H;Li Y;Eckel-Passow JE;Dasari S;Vedell PT;Barman P;Wang L;Weinshiboum R;Jen J;Huang H;Kohli M;Kocher JP
通讯作者：
Kocher JP
影响因子：
48
作者：
Kim D;Langmead B;Salzberg SL
通讯作者：
Salzberg SL