Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum

Nucleic Acids Research
Xueqing Maggie LuKarine G Le Roch

Abstract

Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (IDC); however, the just-in-time transcriptional model has recently been challenged by findings that show the importance of post-transcriptional regulation. To further explore the role of transcriptional regulation, we performed the first genome-wide nascent RNA profiling in P. falciparum. Our findings indicate that the majority of genes are transcribed simultaneously during the trophozoite stage of the IDC and that only a small subset of genes is subject to differential transcriptional timing. RNA polymerase II is engaged with promoter regions prior to this transcriptional burst, suggesting that Pol II pausing plays a dominant role in gene regulation. In addition, we found that the overall transcriptional program during gametocyte differentiation is surprisingly similar to the IDC, with the exception of relatively small subsets of genes. Results from this study suggest that further characterization of the molecular ...Continue Reading

References

Aug 20, 1976·Science·W Trager, J B Jensen
Nov 26, 1981·Nature·T Ifediba, J P Vanderberg
Jun 22, 2000·Proceedings of the National Academy of Sciences of the United States of America·I Artsimovitch, R Landick
Aug 2, 2003·Science·Karine G Le RochElizabeth A Winzeler
Jul 17, 2004·Genome Research·Richard M R CoulsonChristos A Ouzounis
Nov 3, 2004·Genome Research·Karine G Le RochElizabeth A Winzeler
Apr 25, 2006·Trends in Genetics : TIG·Jane Mellor
Aug 4, 2006·Molecular Cell·B Matija Peterlin, David H Price
Aug 5, 2006·Science·Gunnar R MairAndrew P Waters
May 16, 2007·Molecular and Cellular Biology·Liat Amir-ZilbersteinRivka Dikstein
Feb 9, 2008·BMC Genomics·Jason A YoungElizabeth A Winzeler
Mar 12, 2008·Molecular and Cellular Biology·Chanhyo LeeDavid S Gilmour
May 29, 2008·Proceedings of the National Academy of Sciences of the United States of America·David A HendrixMichael S Levine
Jun 11, 2008·Proceedings of the National Academy of Sciences of the United States of America·Erandi K De SilvaManuel Llinás
Oct 28, 2008·Experimental Parasitology·Anusha M GopalakrishnanCarlos López-Estraño
Apr 22, 2009·Nucleic Acids Research·Jake BaumTania F de Koning-Ward
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 8, 2010·Genome Research·Nadia PontsKarine G Le Roch
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 6, 2010·Genome Biology·Matthew D YoungAlicia Oshlack
Feb 10, 2010·Molecular Microbiology·Thomas D OttoManuel Llinás
Mar 5, 2010·BMC Genomics·Kobby Essien, Christian J Stoeckert
May 4, 2010·Cell·Peter B RahlRichard A Young
Aug 17, 2010·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Nadia PontsKarine G Le Roch
Nov 26, 2010·Molecular Cell·Fernando Carrillo OesterreichKarla M Neugebauer
Dec 4, 2010·Molecular and Biochemical Parasitology·Heather J PainterManuel Llinás
May 12, 2011·Molecular & Cellular Proteomics : MCP·Bernardo Javier FothZbynek Bozdech
Dec 20, 2011·BMC Bioinformatics·Davide RissoSandrine Dudoit
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Mar 13, 2012·Annual Review of Biochemistry·Qiang ZhouDavid H Price

❮ Previous
Next ❯

Citations

Apr 18, 2018·The Journal of Eukaryotic Microbiology·Ning JiangQijun Chen
Aug 18, 2018·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Priscila M HiraiwaAndréa R Ávila
Jul 6, 2018·Annual Review of Microbiology·Gabrielle A JoslingManuel Llinás
May 22, 2019·Antimicrobial Agents and Chemotherapy·Lais Pessanha de CarvalhoJana Held
Oct 6, 2018·Molecular Systems Biology·Chee Sheng NgPeter R Preiser
Dec 5, 2019·BMC Genomics·Riëtte van BiljonLyn-Marie Birkholtz
May 30, 2020·ELife·Slavica Pavlovic DjuranovicSergej Djuranovic
Jan 30, 2019·Frontiers in Cellular and Infection Microbiology·Monica Ararat-SarriaHernando Curtidor
Jun 21, 2019·Briefings in Functional Genomics·Steven Abel, Karine G Le Roch
May 7, 2019·Briefings in Functional Genomics·José L Ruiz, Elena Gómez-Díaz
Jun 27, 2019·Briefings in Functional Genomics·Mary R Galinski
Nov 19, 2019·Frontiers in Cell and Developmental Biology·Meng LiuQingfeng Zhang
Jan 12, 2021·Frontiers in Cellular and Infection Microbiology·Thomas Hollin, Karine G Le Roch
Apr 17, 2021·PLoS Computational Biology·Christophe MenichelliLaurent Bréhélin
Apr 27, 2021·Frontiers in Cellular and Infection Microbiology·Marta MachadoMarkus Ganter
May 8, 2021·RNA Biology·Diana Renteria AlvarezKausik Chakrabarti
Sep 17, 2021·PeerJ·Philip J ShawSissades Tongsima

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE85478

Methods Mentioned

BETA
environmental stress
immunoprecipitation
PCRs
PCR
electrophoresis
ChIP
ChIP-Seq
in vitro transcription
Illumina sequencing
RNA-seq

Software Mentioned

MarkDuplicates
Bowtie
CentriMo
Picard Tools
FASTX
ChIP
GRO
seq
Blastp
BEDtools

Related Concepts

Related Feeds

Antimalarial Agents (ASM)

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.

Cardiomyopathy

Cardiomyopathy is a disease of the heart muscle, that can lead to muscular or electrical dysfunction of the heart. It is often an irreversible disease that is associated with a poor prognosis. There are different causes and classifications of cardiomyopathies. Here are the latest discoveries pertaining to this disease.

Antimalarial Agents

Antimalarial agents, also known as antimalarials, are designed to prevent or cure malaria. Discover the latest research on antimalarial agents here.