Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite

1. WHO 2009 World Malaria Report 2009

2. BozdechZ

LlinásM

PulliamBL

WongED

ZhuJ

2003 The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1 E5

3. FlorensL

WashburnMP

RaineJD

AnthonyRM

GraingerM

2002 A proteomic view of the Plasmodium falciparum life cycle. Nature 419 520 526

4. HallN

KarrasM

RaineJD

CarltonJM

KooijTW

2005 A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307 82 86

5. LasonderE

IshihamaY

AndersenJS

VermuntAM

PainA

2002 Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature 419 537 542

6. Le RochKG

ZhouY

BlairPL

GraingerM

MochJK

2003 Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301 1503 1508

7. MikolajczakSA

Silva-RiveraH

PengX

TarunAS

CamargoN

2008 Distinct malaria parasite sporozoites reveal transcriptional changes that cause differential tissue infection competence in the mosquito vector and mammalian host. Mol Cell Biol 28 6196 6207

8. SilvestriniF

BozdechZ

LanfrancottiA

Di GiulioE

BultriniE

2005 Genome-wide identification of genes upregulated at the onset of gametocytogenesis in Plasmodium falciparum. Mol Biochem Parasitol 143 100 110

9. TarunAS

PengX

DumpitRF

OgataY

Silva-RiveraH

2008 A combined transcriptome and proteome survey of malaria parasite liver stages. Proc Natl Acad Sci U S A 105 305 310

10. YoungJA

FivelmanQL

BlairPL

de la VegaP

Le RochKG

2005 The Plasmodium falciparum sexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol 143 67 79

11. Le RochKG

JohnsonJR

FlorensL

ZhouY

SantrosyanA

2004 Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res 14 2308 2318

12. FothBJ

ZhangN

MokS

PreiserPR

BozdechZ

2008 Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites. Genome Biol 9 R177

13. CoulsonRM

HallN

OuzounisCA

2004 Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res 14 1548 1554

14. CallebautI

PratK

MeuriceE

MornonJP

TomavoS

2005 Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes. BMC Genomics 6 100

15. BischoffE

VaqueroC

2010 In silico and biological survey of transcription-associated proteins implicated in the transcriptional machinery during the erythrocytic development of Plasmodium falciparum. BMC Genomics 11 34

16. LanzerM

de BruinD

RavetchJV

1992 A sequence element associated with the Plasmodium falciparum KAHRP gene is the site of developmentally regulated protein-DNA interactions. Nucleic Acids Res 20 3051 3056

17. DecheringKJ

KaanAM

MbachamW

WirthDF

ElingW

1999 Isolation and functional characterization of two distinct sexual-stage-specific promoters of the human malaria parasite Plasmodium falciparum. Mol Cell Biol 19 967 978

18. HorrocksP

LanzerM

1999 Mutational analysis identifies a five base pair cis-acting sequence essential for GBP130 promoter activity in Plasmodium falciparum. Mol Biochem Parasitol 99 77 87

19. OstaM

Gannoun-ZakiL

BonnefoyS

RoyC

VialHJ

2002 A 24 bp cis-acting element essential for the transcriptional activity of Plasmodium falciparum CDP-diacylglycerol synthase gene promoter. Mol Biochem Parasitol 121 87 98

20. PorterME

2002 Positive and negative effects of deletions and mutations within the 5′ flanking sequences of Plasmodium falciparum DNA polymerase delta. Mol Biochem Parasitol 122 9 19

21. ChowCS

WirthDF

2003 Linker scanning mutagenesis of the Plasmodium gallinaceum sexual stage specific gene pgs28 reveals a novel downstream cis-control element. Mol Biochem Parasitol 129 199 208

22. MilitelloKT

DodgeM

BethkeL

WirthDF

2004 Identification of regulatory elements in the Plasmodium falciparum genome. Mol Biochem Parasitol 134 75 88

23. ThamWH

PaynePD

BrownGV

RogersonSJ

2007 Identification of basic transcriptional elements required for rif gene transcription. Int J Parasitol 37 605 615

24. SunilS

ChauhanVS

MalhotraP

2008 Distinct and stage specific nuclear factors regulate the expression of falcipains, Plasmodium falciparum cysteine proteases. BMC Mol Biol 9 47

25. VossTS

KaestliM

VogelD

BoppS

BeckHP

2003 Identification of nuclear proteins that interact differentially with Plasmodium falciparum var gene promoters. Mol Microbiol 48 1593 1607

26. VossTS

TonkinCJ

MartyAJ

ThompsonJK

HealerJ

2007 Alterations in local chromatin environment are involved in silencing and activation of subtelomeric var genes in Plasmodium falciparum. Mol Microbiol 66 139 150

27. ElementoO

SlonimN

TavazoieS

2007 A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28 337 350

28. JurgelenaiteR

DijkstraTM

KockenCH

HeskesT

2009 Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum. Bioinformatics 25 1484 1491

29. van NoortV

HuynenMA

2006 Combinatorial gene regulation in Plasmodium falciparum. Trends Genet 22 73 78

30. WuJ

SieglaffDH

GervinJ

XieXS

2008 Discovering regulatory motifs in the Plasmodium genome using comparative genomics. Bioinformatics 24 1843 1849

31. YoungJA

JohnsonJR

BennerC

YanSF

ChenK

2008 In silico discovery of transcription regulatory elements in Plasmodium falciparum. BMC Genomics 9 70

32. IengarP

JoshiNV

2009 Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum. BMC Genomics 10 18

33. EssienK

StoeckertCJJr

2010 Conservation and divergence of known apicomplexan transcriptional regulons. BMC Genomics 11 147

34. GunasekeraAM

MyrickA

Le RochK

WinzelerE

WirthDF

2007 Plasmodium falciparum: genome wide perturbations in transcript profiles among mixed stage cultures after chloroquine treatment. Exp Parasitol 117 87 92

35. GunasekeraAM

MyrickA

MilitelloKT

SimsJS

DongCK

2007 Regulatory motifs uncovered among gene expression clusters in Plasmodium falciparum. Mol Biochem Parasitol 153 19 30

36. MullapudiN

JosephSJ

KissingerJC

2009 Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii. Genome Biol 10 R34

37. AravindL

IyerLM

WellemsTE

MillerLH

2003 Plasmodium biology: genomic gleanings. Cell 115 771 785

38. TempletonTJ

IyerLM

AnantharamanV

EnomotoS

AbrahanteJE

2004 Comparative analysis of apicomplexa and genomic diversity in eukaryotes. Genome Res 14 1686 1695

39. BoschetC

GissotM

BriquetS

HamidZ

Claudel-RenardC

2004 Characterization of PfMyb1 transcription factor during erythrocytic development of 3D7 and F12 Plasmodium falciparum clones. Mol Biochem Parasitol 138 159 163

40. GissotM

BriquetS

RefourP

BoschetC

VaqueroC

2005 PfMyb1, a Plasmodium falciparum transcription factor, is required for intra-erythrocytic growth and controls key genes for cell cycle regulation. J Mol Biol 346 29 42

41. BriquetS

BoschetC

GissotM

TissandieE

SevillaE

2006 High-mobility-group box nuclear factors of Plasmodium falciparum. Eukaryot Cell 5 672 682

42. GissotM

TingLM

DalyTM

BergmanLW

SinnisP

2008 High mobility group protein HMGB2 is a critical regulator of Plasmodium oocyst development. J Biol Chem 283 17030 17038

43. BalajiS

BabuMM

IyerLM

AravindL

2005 Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res 33 3994 4006

44. JofukuKD

den BoerBG

Van MontaguM

OkamuroJK

1994 Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant Cell 6 1211 1225

45. Ohme-TakagiM

ShinshiH

1995 Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7 173 182

46. IyerLM

AnantharamanV

WolfMY

AravindL

2008 Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J Parasitol 38 1 31

47. FinnRD

TateJ

MistryJ

CoggillPC

SammutSJ

2008 The Pfam protein families database. Nucleic Acids Res 36 D281 288

48. De SilvaEK

GehrkeAR

OlszewskiK

LeonI

ChahalJS

2008 Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A 105 8393 8398

49. YudaM

IwanagaS

ShigenobuS

KatoT

KanekoI

2010 Transcription Factor AP2-Sp and its Target Genes in Malarial Sporozoites. Mol Microbiol 75 854 863

50. FlueckC

BartfaiR

NeiderwieserI

WitmerK

AlakoBTF

2010 A Major Role for the Plasmodium falciparum ApiAP2 Protein PFSIP2 in Chromosome End Biology. PLoS Pathog 6 e1000784

51. YudaM

IwanagaS

ShigenobuS

MairGR

JanseCJ

2009 Identification of a transcription factor in the mosquito-invasive stage of malaria parasites. Mol Microbiol 71 1402 1414

52. BergerMF

BulykML

2006 Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol Biol 338 245 260

53. BergerMF

PhilippakisAA

QureshiAM

HeFS

EstepPW3rd

2006 Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24 1429 1435

54. BergerMF

BadisG

GehrkeAR

TalukderS

PhilippakisAA

2008 Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133 1266 1276

55. BergerMF

BulykML

2009 Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 4 393 411

56. GarvieCW

WolbergerC

2001 Recognition of specific DNA sequences. Mol Cell 8 937 946

57. BadisG

BergerMF

PhilippakisAA

TalukderS

GehrkeAR

2009 Diversity and complexity in DNA recognition by transcription factors. Science 324 1720 1723

58. ZhouY

YoungJA

SantrosyanA

ChenK

YanSF

2005 In silico gene function prediction using ontology-based pattern identification. Bioinformatics 21 1237 1245

59. RothFP

HughesJD

EstepPW

ChurchGM

1998 Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16 939 945

60. BrickK

WatanabeJ

PizziE

2008 Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum. Genome Biol 9 R178

61. WakaguriH

SuzukiY

SasakiM

SuganoS

WatanabeJ

2009 Inconsistencies of genome annotations in apicomplexan parasites revealed by 5′-end-one-pass and full-length sequences of oligo-capped cDNAs. BMC Genomics 10 312

62. HarbisonCT

GordonDB

LeeTI

RinaldiNJ

MacisaacKD

2004 Transcriptional regulatory code of a eukaryotic genome. Nature 431 99 104

63. PontsN

HarrisEY

PrudhommeJ

WickI

Eckhardt-LudkaC

2010 Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res

64. AurrecoecheaC

BrestelliJ

BrunkBP

DommerJ

FischerS

2009 PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 37 D539 543

65. PlantaRJ

GoncalvesPM

MagerWH

1995 Global regulators of ribosome biosynthesis in yeast. Biochem Cell Biol 73 825 834

66. FoatBC

TepperRG

BussemakerHJ

2008 TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Res 36 D125 131

67. Huang daW

ShermanBT

LempickiRA

2009 Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4 44 57

68. HuG

CabreraA

KonoM

MokS

ChaalBK

Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol 28 91 98

69. ScherfA

Lopez-RubioJJ

RiviereL

2008 Antigenic variation in Plasmodium falciparum. Annu Rev Microbiol 62 445 470

70. LavstsenT

SalantiA

JensenAT

ArnotDE

TheanderTG

2003 Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions. Malar J 2 27

71. VossTS

HealerJ

MartyAJ

DuffyMF

ThompsonJK

2006 A var gene promoter controls allelic exclusion of virulence genes in Plasmodium falciparum malaria. Nature 439 1004 1008

72. BozdechZ

MokS

HuG

ImwongM

JaideeA

2008 The transcriptome of Plasmodium vivax reveals divergence and diversity of transcriptional regulation in malaria parasites. Proc Natl Acad Sci U S A 105 16290 16295

73. WestenbergerSJ

McCleanCM

ChattopadhyayR

DhariaNV

CarltonJM

2010 A systems-based analysis of Plasmodium vivax lifecycle transcription from human to mosquito. PLoS Negl Trop Dis 4 e653

74. GroveCA

De MasiF

BarrasaMI

NewburgerDE

AlkemaMJ

2009 A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 138 314 327

75. NoyesMB

ChristensenRG

WakabayashiA

StormoGD

BrodskyMH

2008 Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 133 1277 1289

76. ZhuC

ByersKJ

McCordRP

ShiZ

BergerMF

2009 High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19 556 566

77. LindnerSE

De SilvaEK

KeckJL

LlinásM

2010 Structural determinants of DNA binding by a P. falciparum ApiAP2 transcriptional regulator. J Mol Biol 395 558 567

78. BougdourA

BraunL

CannellaD

HakimiMA

2010 Chromatin modifications: implications in the regulation of gene expression in Toxoplasma gondii. Cell Microbiol 12 413 423

79. LaCountDJ

VignaliM

ChettierR

PhansalkarA

BellR

2005 A protein interaction network of the malaria parasite Plasmodium falciparum. Nature 438 103 107

80. BornemanAR

GianoulisTA

ZhangZD

YuH

RozowskyJ

2007 Divergence of transcription factor binding sites across related yeast species. Science 317 815 819

81. MosesAM

PollardDA

NixDA

IyerVN

LiXY

2006 Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol 2 e130

82. OdomDT

DowellRD

JacobsenES

GordonW

DanfordTW

2007 Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39 730 732

83. SchmidtD

WilsonMD

BallesterB

SchwaliePC

BrownGD

2010 Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding. Science

84. WilsonMD

Barbosa-MoraisNL

SchmidtD

ConboyCM

VanesL

2008 Species-specific transcription in mice carrying human chromosome 21. Science 322 434 438

85. ElementoO

TavazoieS

2005 Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 6 R18

86. CohnB

ManqueP

LaraAM

SerranoM

ShethN

2010 Putative cis-Regulatory Elements Associated with Heat Shock Genes Activated During Excystation of Cryptosporidium parvum. PLoS One 5 e9512

87. CarltonJM

AdamsJH

SilvaJC

BidwellSL

LorenziH

2008 Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455 757 763

88. PfeiferK

PrezantT

GuarenteL

1987 Yeast HAP1 activator binds to two upstream activation sites of different sequence. Cell 49 19 27

89. ColeC

BarberJD

BartonGJ

2008 The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36 W197 201

90. NewburgerDE

BulykML

2009 UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res 37 D77 82

91. HughesJD

EstepPW

TavazoieS

ChurchGM

2000 Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 296 1205 1214

92. WorkmanCT

YinY

CorcoranDL

IdekerT

StormoGD

2005 enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res 33 W389 392