MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites-Reference-Cited by-同舟云学术

MalariaSED: a deep learning framework to decipher the regulatory contributions of noncoding variants in malaria parasites

Published:2023-10-16 Issue:1 Volume:24 Page:
ISSN:1474-760X
Container-title:Genome Biology
language:en
Short-container-title:Genome Biol

Author:

Wang Chengqi,Dong Yibo,Li Chang,Oberstaller Jenna,Zhang Min,Gibbons Justin,Pires Camilla Valente,Xiao Mianli,Zhu Lei,Jiang Rays H. Y.,Kim Kami,Miao Jun,Otto Thomas D.,Cui Liwang,Adams John H.,Liu Xiaoming

Abstract

AbstractMalaria remains one of the deadliest infectious diseases. Transcriptional regulation effects of noncoding variants in this unusual genome of malaria parasites remain elusive. We developed a sequence-based, ab initio deep learning framework, MalariaSED, for predicting chromatin profiles in malaria parasites. The MalariaSED performance was validated by published ChIP-qPCR and TF motifs results. Applying MalariaSED to ~ 1.3 million variants shows that geographically differentiated noncoding variants are associated with parasite invasion and drug resistance. Further analysis reveals chromatin accessibility changes at Plasmodium falciparum rings are partly associated with artemisinin resistance. MalariaSED illuminates the potential functional roles of noncoding variants in malaria parasites.

Funder

National Institute of Health

National Institutes of Health

Publisher

Springer Science and Business Media LLC

Link

https://link.springer.com/content/pdf/10.1186/s13059-023-03063-z.pdf

Reference48 articles.

1. Zhu L, Tripathi J, Rocamora FM, Miotto O, van der Pluijm R, Voss TS, Mok S, Kwiatkowski DP, Nosten F, Day NPJ, et al. The origins of malaria artemisinin resistance defined by a genetic and transcriptomic background. Nat Commun. 2018;9:5158.

2. Gibbons J, Button-Simons KA, Adapa SR, Li S, Pietsch M, Zhang M, Liao X, Adams JH, Ferdig MT, Jiang RHY. Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum. BMC Genomics. 2018;19:849.

3. Wang C, Adapa SR, Gibbons J, Sutton S, Jiang RH. Punctuated chromatin states regulate Plasmodium falciparum antigenic variation at the intron and 2 kb upstream regions. BMC Genomics. 2016;17:652.

4. Swamy L, Amulic B, Deitsch KW. Plasmodium falciparum var gene silencing is determined by cis DNA elements that form stable and heritable interactions. Eukaryot Cell. 2011;10:530–9.

5. Santos JM, Josling G, Ross P, Joshi P, Orchard L, Campbell T, Schieler A, Cristea IM, Llinas M. Red blood cell invasion by the malaria parasite is coordinated by the PfAP2-I transcription factor. Cell Host Microbe. 2017;21:731–741 e710.