(Q45963302)

8 January 2018

title

Nascent RNA sequencing reveals mechanisms of gene regulation in the human malaria parasite Plasmodium falciparum. (English)

1 reference

8 January 2018

main subject

Plasmodium falciparum

0 references

0 references

Evelien M Bunnik

5

0 references

Gayani Batugedara

2

object named as

Gayani Batugedara

1 reference

8 January 2018

Xueqing Maggie Lu

1

1 reference

8 January 2018

Michael Lee

3

1 reference

8 January 2018

Jacques Prudhomme

4

1 reference

8 January 2018

Karine G Le Roch

6

1 reference

8 January 2018

language of work or name

English

0 references

publication date

22 May 2017

1 reference

8 January 2018

published in

Nucleic Acids Research

1 reference

8 January 2018

volume

45

1 reference

8 January 2018

issue

13

1 reference

8 January 2018

page(s)

7825-7840

1 reference

8 January 2018

Creative Commons Attribution-NonCommercial 4.0 International

copyright license

start time

22 May 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum

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RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases

24 May 2018

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Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

24 May 2018

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Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

24 May 2018

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Plasmodium falciparum erythrocyte invasion: combining function with immune evasion

24 May 2018

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Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase

24 May 2018

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RNA polymerase II pausing during development

24 May 2018

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A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium

24 May 2018

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Dynamic regulation of transcriptional states by chromatin and transcription factors.

24 May 2018

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Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum

24 May 2018

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Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals

24 May 2018

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Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

24 May 2018

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

24 May 2018

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Precise maps of RNA polymerase reveal how promoters direct initiation and pausing

24 May 2018

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Poised RNA polymerase II changes over developmental time and prepares genes for future expression

24 May 2018

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Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

24 May 2018

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Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

24 May 2018

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RNA polymerase II elongation control

24 May 2018

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Fast gapped-read alignment with Bowtie 2

24 May 2018

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GC-content normalization for RNA-Seq data

24 May 2018

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Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

24 May 2018

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Quantitative time-course profiling of parasite and host cell proteins in the human malaria parasite Plasmodium falciparum

24 May 2018

1 reference

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3D nuclear architecture reveals coupled cell cycle dynamics of chromatin and nuclear pores in the malaria parasite Plasmodium falciparum.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

The Apicomplexan AP2 family: integral factors regulating Plasmodium development

24 May 2018

1 reference

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Identification and genome-wide prediction of DNA binding specificities for the ApiAP2 family of regulators from the malaria parasite

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Nucleosome occupancy at transcription start sites in the human malaria parasite: a hard-wired evolution of virulence?

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

c-Myc regulates transcriptional pause release

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Conservation and divergence of known apicomplexan transcriptional regulons

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Gene ontology analysis for RNA-seq: accounting for selection bias

24 May 2018

1 reference

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BEDTools: a flexible suite of utilities for comparing genomic features

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Nucleosome landscape and control of transcription in the human malaria parasite

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila

24 May 2018

1 reference

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The Sequence Alignment/Map format and SAMtools

24 May 2018

1 reference

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An unusual recent expansion of the C-terminal domain of RNA polymerase II in primate malaria parasites features a motif otherwise found only in mammalian polymerases.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Patterns of gene-specific and total transcriptional activity during the Plasmodium falciparum intraerythrocytic developmental cycle

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Specific DNA-binding by apicomplexan AP2 transcription factors

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Transcription regulation through promoter-proximal pausing of RNA polymerase II.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

In silico discovery of transcription regulatory elements in Plasmodium falciparum.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Differential regulation of NF-kappaB by elongation factors is determined by core promoter type

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Regulation of sexual development of Plasmodium by translational repression

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Controlling the elongation phase of transcription with P-TEFb

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Dynamic nucleosomes and gene transcription

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Discovery of gene function by expression profiling of the malaria parasite life cycle

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Identification and initial characterization of three novel cyclin-related proteins of the human malaria parasite Plasmodium falciparum

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

P-TEFb kinase recruitment and function at heat shock loci

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Activation of a Plasmodium falciparum cdc2-related kinase by heterologous p25 and cyclin H. Functional characterization of a P. falciparum cyclin homologue

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Human malaria parasites in continuous culture

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Enhancer loops appear stable during development and are associated with paused polymerase.

24 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Plasmodium falciparum: Preinitiation complex occupancy of active and inactive promoters during erythrocytic stage.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Transcriptional pausing in vivo: a nascent RNA hairpin restricts lateral movements of RNA polymerase in both forward and reverse directions.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Transcriptome of 3D7 and its gametocyte-less derivative F12 Plasmodium falciparum clones during erythrocytic development using a gene-specific microarray assigned to gene regulation, cell cycle and transcription factors

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737683

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

15 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX464

Complete in vitro maturation of Plasmodium falciparum gametocytes

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKX464

21 January 2018

Identifiers

DOI

10.1093/NAR/GKX464

1 reference

8 January 2018

release_ek6urgtlv5hxtm3rpp2cygcoa4

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ek6urgtlv5hxtm3rpp2cygcoa4

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

5737683

1 reference

8 January 2018

PubMed publication ID

28531310

1 reference

8 January 2018