Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting.
Journal
PLoS neglected tropical diseases
ISSN: 1935-2735
Titre abrégé: PLoS Negl Trop Dis
Pays: United States
ID NLM: 101291488
Informations de publication
Date de publication:
06 2020
06 2020
Historique:
received:
14
11
2019
accepted:
07
04
2020
revised:
06
07
2020
pubmed:
24
6
2020
medline:
11
8
2020
entrez:
24
6
2020
Statut:
epublish
Résumé
Filarial nematodes can cause debilitating diseases in humans. They have complicated life cycles involving an insect vector and mammalian hosts, and they go through a number of developmental molts. While whole genome sequences of parasitic worms are now available, very little is known about transcription factor (TF) binding sites and their cognate transcription factors that play a role in regulating development. To address this gap, we developed a novel motif prediction pipeline, Emotif Alpha, that integrates ten different motif discovery algorithms, multiple statistical tests, and a comparative analysis of conserved elements between the filarial worms Brugia malayi and Onchocerca volvulus, and the free-living nematode Caenorhabditis elegans. We identified stage-specific TF binding motifs in B. malayi, with a particular focus on those potentially involved in the L3-L4 molt, a stage important for the establishment of infection in the mammalian host. Using an in vitro molting system, we tested and validated three of these motifs demonstrating the accuracy of the motif prediction pipeline.
Identifiants
pubmed: 32574217
doi: 10.1371/journal.pntd.0008275
pii: PNTD-D-19-01897
pmc: PMC7337397
doi:
Substances chimiques
RNA, Helminth
0
Transcription Factors
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0008275Subventions
Organisme : NIAID NIH HHS
ID : R56 AI101372
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI126466
Pays : United States
Organisme : NIAID NIH HHS
ID : T32 AI007180
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI135172
Pays : United States
Organisme : NIAID NIH HHS
ID : F31 AI131527
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Bioinformatics. 2011 Jan 15;27(2):270-1
pubmed: 21081511
Nucleic Acids Res. 2016 Jun 20;44(11):e107
pubmed: 27084946
PLoS One. 2011;6(9):e24576
pubmed: 21931761
Nucleic Acids Res. 2016 Jan 4;44(D1):D110-5
pubmed: 26531826
Genome Biol. 2010;11(10):R106
pubmed: 20979621
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
J Mol Biol. 2005 Oct 14;353(1):1-13
pubmed: 16154590
Int J Parasitol. 2016 May;46(5-6):333-41
pubmed: 26896576
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W199-203
pubmed: 15215380
Mol Biochem Parasitol. 2012 Nov;186(1):38-43
pubmed: 23017214
Bioinformatics. 2011 Sep 1;27(17):2361-7
pubmed: 21752801
PLoS Negl Trop Dis. 2016 Jun 14;10(6):e0004772
pubmed: 27300294
Parasitol Res. 1991;77(1):65-71
pubmed: 1994372
Bioinformatics. 2007 Nov 1;23(21):2947-8
pubmed: 17846036
BMC Genomics. 2012 May 14;13:184
pubmed: 22583769
Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1560-5
pubmed: 15668401
PLoS Negl Trop Dis. 2018 May 21;12(5):e0006509
pubmed: 29782496
Mol Biochem Parasitol. 2003 Apr 25;128(1):67-75
pubmed: 12706798
Pac Symp Biocomput. 2001;:127-38
pubmed: 11262934
Nat Biotechnol. 2013 Jan;31(1):46-53
pubmed: 23222703
Bioinformatics. 2011 Apr 1;27(7):1017-8
pubmed: 21330290
Mol Biochem Parasitol. 2011 Dec;180(2):106-11
pubmed: 21944995
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Nucleic Acids Res. 2009 Jan;37(Database issue):D77-82
pubmed: 18842628
J Comput Biol. 2002;9(2):447-64
pubmed: 12015892
Dev Growth Differ. 2011 Jun;53(5):697-703
pubmed: 21671917
Trop Med Infect Dis. 2018 Jun 04;3(2):
pubmed: 30274454
BMC Genomics. 2008 Jan 23;9:30
pubmed: 18215260
Science. 2007 Sep 21;317(5845):1756-60
pubmed: 17885136
Mol Biochem Parasitol. 2004 Aug;136(2):227-42
pubmed: 15478801
Bioinformatics. 2009 Dec 1;25(23):3191-3
pubmed: 19797408
Science. 2004 Sep 17;305(5691):1743-6
pubmed: 15375261
mBio. 2016 Nov 23;7(6):
pubmed: 27881553
Parasitol Res. 2014 May;113(5):1827-35
pubmed: 24664084
Cell. 2008 Jul 25;134(2):291-303
pubmed: 18662544
PLoS Negl Trop Dis. 2017 Mar 30;11(3):e0005357
pubmed: 28358880
Cell. 2014 Sep 11;158(6):1431-1443
pubmed: 25215497
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W369-73
pubmed: 16845028
PLoS Negl Trop Dis. 2011 Dec;5(12):e1409
pubmed: 22180794
BMC Dev Biol. 2011 Nov 03;11:66
pubmed: 22050674
Parasitology. 1993 Nov;107 ( Pt 4):459-63
pubmed: 8278225
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
BMC Genomics. 2010 Apr 07;11:225
pubmed: 20370932
Genome Res. 2013 Jun;23(6):1039-50
pubmed: 23640720
Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3339-44
pubmed: 12626739
Nat Genet. 2013 May;45(5):495-500
pubmed: 23525074
J Comput Biol. 2009 Feb;16(2):317-29
pubmed: 19193149
Trends Biochem Sci. 2001 Mar;26(3):191-7
pubmed: 11246026
Int J Parasitol. 2008 Aug;38(10):1111-9
pubmed: 18364245
Mol Biochem Parasitol. 2009 Jul;166(1):15-21
pubmed: 19428668
J Immunol. 1998 Aug 1;161(3):1428-32
pubmed: 9686607
Genome Biol. 2013 Apr 25;14(4):R36
pubmed: 23618408
Mol Biochem Parasitol. 2004 Dec;138(2):165-70
pubmed: 15555728
Genome Biol. 2007;8(2):R24
pubmed: 17324271
Mol Biochem Parasitol. 2017 Jul;215:2-10
pubmed: 27899279
Mol Biochem Parasitol. 2011 Mar;176(1):37-41
pubmed: 21111761
Nat Microbiol. 2016 Nov 21;2:16216
pubmed: 27869790