Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum.

Nucleic Acids Research
José L RuizElena Gómez-Díaz

Abstract

Human malaria is a devastating disease and a major cause of poverty in resource-limited countries. To develop and adapt within hosts Plasmodium falciparum undergoes drastic switches in gene expression. To identify regulatory regions in the parasite genome, we performed genome-wide profiling of chromatin accessibility in two culture-adapted isogenic subclones at four developmental stages during the intraerythrocytic cycle by using the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). Tn5 transposase hypersensitivity sites (THSSs) localize preferentially at transcriptional start sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3. Our assay allows the identification of novel regulatory regions including TSS and enhancer-like elements. We show that the dynamics in the accessible chromatin profile matches temporal transcription during development. Motif analysis of stage-specific ATAC-seq sites predicts the in vivo binding sites and function of multiple ApiAP2 transcription factors. At last, the alternative expression states of some clonally variant genes (CVGs), including eba, phist, var and clag genes, associate with a dif...Continue Reading

References

Oct 9, 2002·Nature·Malcolm J GardnerBart Barrell
Oct 9, 2002·Nature·Laurence FlorensDaniel J Carucci
Jan 30, 2004·Molecular and Biochemical Parasitology·Kevin T MilitelloDyann F Wirth
Nov 3, 2004·Genome Research·Karine G Le RochElizabeth A Winzeler
Feb 16, 2005·International Journal for Parasitology·Alfred Cortés
Feb 27, 2007·Cell·Bing LiJerry L Workman
Aug 7, 2007·PLoS Pathogens·Alfred CortésAnthony A Holder
Oct 30, 2007·Molecular Cell·Olivier ElementoSaeed Tavazoie
Dec 18, 2007·Bioinformation·Lokesh Kumar, Matthias E Futschik
Sep 6, 2008·Trends in Parasitology·Thanat ChookajornLiwang Cui
Sep 13, 2008·Annual Review of Microbiology·Artur ScherfLoïc Riviere
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Feb 27, 2009·Current Genetics·Ron Dzikowski, Kirk W Deitsch
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 31, 2009·Cold Spring Harbor Symposia on Quantitative Biology·R A MartienssenM Tanurdzić
Nov 6, 2009·Nature·Hubertus J E BeaumontPaul B Rainey
Dec 23, 2009·Molecular Microbiology·Masao YudaIzumi Kaneko
Jan 8, 2010·Genome Research·Nadia PontsKarine G Le Roch
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
Feb 10, 2010·Molecular Microbiology·Thomas D OttoManuel Llinás
Jul 16, 2010·Nature Reviews. Genetics·Sayyed K ZaidiGary S Stein
Dec 1, 2010·Nature Reviews. Genetics·Vicky W ZhouBradley E Bernstein
Dec 4, 2010·Molecular and Biochemical Parasitology·Heather J PainterManuel Llinás
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg

❮ Previous
Next ❯

Citations

May 23, 2019·Briefings in Functional Genomics·Oriol Llorà-BatlleAlfred Cortés
Aug 1, 2019·Briefings in Functional Genomics·Marcus C S LeeManuel Llinás
Jun 21, 2019·Briefings in Functional Genomics·Christa G Toenhake, Richárd Bártfai
Aug 21, 2020·Molecular Systems Biology·Jessica M BryantArtur Scherf
Apr 10, 2019·Pathogens·Myriam D JeningaMichaela Petter
Nov 5, 2019·Frontiers in Immunology·Kelvin M KimenyiLynette Isabella Ochola-Oyier
Apr 16, 2020·Alzheimer's Research & Therapy·Yaqi WangPeichang Wang
Jun 21, 2019·Briefings in Functional Genomics·Steven Abel, Karine G Le Roch
Feb 11, 2020·Frontiers in Cell and Developmental Biology·Marta Silvia MagriJosé Luis Gómez-Skarmeta
May 7, 2019·Briefings in Functional Genomics·José L Ruiz, Elena Gómez-Díaz
Dec 5, 2020·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Chengqi WangRays H Y Jiang
Nov 26, 2019·Developmental Cell·Lacey J LuenseShelley L Berger
Jan 12, 2021·Frontiers in Cellular and Infection Microbiology·Thomas Hollin, Karine G Le Roch
Apr 17, 2021·PLoS Computational Biology·Christophe MenichelliLaurent Bréhélin
Jun 3, 2021·International Journal of Molecular Sciences·Maria Theresia WatzlowikGernot Längst
Sep 17, 2021·PeerJ·Philip J ShawSissades Tongsima

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE23787
GSE63369
GSE66185
GSE109599

Methods Mentioned

BETA
Assay
PCR
RNA-seq
ChIP-seq
ATAC-seq

Software Mentioned

plot
DESeq2 ’ R
deepTools2
ggplot2
Hmisc ’ R
HOMER
R
QualiMap
Cytoscape
ngs

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.

CREs: Gene & Cell Therapy

Gene and cell therapy advances have shown promising outcomes for several diseases. The role of cis-regulatory elements (CREs) is crucial in the design of gene therapy vectors. Here is the latest research on CREs in gene and cell therapy.

Antimalarial Agents

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

Allergy and Asthma

Allergy and asthma are inflammatory disorders that are triggered by the activation of an allergen-specific regulatory t cell. These t cells become activated when allergens are recognized by allergen-presenting cells. Here is the latest research on allergy and asthma.