Two Thymidine Hydroxylases Differentially Regulate the Formation of Glucosylated DNA at Regions Flanking Polymerase II Polycistronic Transcription Units Throughout the Genome of Trypanosoma Brucei

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2010 Mar 11

PMID 20215442

Citations 50

Authors

Laura J Cliffe

T Nicolai Siegel

Marion Marshall

George A M Cross

Robert Sabatini

Affiliations

Soon will be listed here.

Abstract

Base J is a hypermodified DNA base localized primarily to telomeric regions of the genome of Trypanosoma brucei. We have previously characterized two thymidine-hydroxylases (TH), JBP1 and JBP2, which regulate J-biosynthesis. JBP2 is a chromatin re-modeling protein that induces de novo J-synthesis, allowing JBP1, a J-DNA binding protein, to stimulate additional J-synthesis. Here, we show that both JBP2 and JBP1 are capable of stimulating de novo J-synthesis. We localized the JBP1- and JBP2-stimulated J by anti-J immunoprecipitation and high-throughput sequencing. This genome-wide analysis revealed an enrichment of base J at regions flanking polymerase II polycistronic transcription units (Pol II PTUs) throughout the T. brucei genome. Chromosome-internal J deposition is primarily mediated by JBP1, whereas JBP2-stimulated J deposition at the telomeric regions. However, the maintenance of J at JBP1-specific regions is dependent on JBP2 SWI/SNF and TH activity. That similar regions of Leishmania major also contain base J highlights the functional importance of the modified base at Pol II PTUs within members of the kinetoplastid family. The regulation of J synthesis/localization by two THs and potential biological function of J in regulating kinetoplastid gene expression is discussed.

Citing Articles

Mono-allelic epigenetic regulation of polycistronic transcription initiation by RNA polymerase II in .

Kieft R, Cliffe L, Yan H, Schmitz R, Hajduk S, Sabatini R mBio. 2024; 16(2):e0232824.

PMID: 39704500 PMC: 11796357. DOI: 10.1128/mbio.02328-24.

Protein phosphatase PP1 regulation of RNA polymerase II transcription termination and allelic exclusion of VSG genes in trypanosomes.

Kieft R, Zhang Y, Yan H, Schmitz R, Sabatini R Nucleic Acids Res. 2024; 52(12):6866-6885.

PMID: 38783162 PMC: 11229358. DOI: 10.1093/nar/gkae392.

Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome.

Marinov G, Chen X, Swaffer M, Xiang T, Grossman A, Greenleaf W Genome Biol. 2024; 25(1):115.

PMID: 38711126 PMC: 11071213. DOI: 10.1186/s13059-024-03261-3.

Kinetic Studies on the 2-Oxoglutarate/Fe(II)-Dependent Nucleic Acid Modifying Enzymes from the AlkB and TET Families.

Peng Z, Ma J, Christov C, Karabencheva-Christova T, Lehnert N, Li D DNA (Basel). 2024; 3(2):65-84.

PMID: 38698914 PMC: 11065319. DOI: 10.3390/dna3020005.

Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes.

Meng W, Wang Z, Zhang Y, Hou Y, Xue J J Biol Chem. 2024; 300(4):106791.

PMID: 38403247 PMC: 11065753. DOI: 10.1016/j.jbc.2024.106791.

References

Cross M, Kieft R, Sabatini R, Wilm M, de Kort M, van der Marel G . The modified base J is the target for a novel DNA-binding protein in kinetoplastid protozoans. EMBO J. 1999; 18(22):6573-81. PMC: 1171720. DOI: 10.1093/emboj/18.22.6573. View

Langmead B, Trapnell C, Pop M, Salzberg S . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10(3):R25. PMC: 2690996. DOI: 10.1186/gb-2009-10-3-r25. View

Sabatini R, Meeuwenoord N, van Boom J, Borst P . Recognition of base J in duplex DNA by J-binding protein. J Biol Chem. 2001; 277(2):958-66. DOI: 10.1074/jbc.M109000200. View

Cross M, Kieft R, Sabatini R, Dirks-Mulder A, Chaves I, Borst P . J-binding protein increases the level and retention of the unusual base J in trypanosome DNA. Mol Microbiol. 2002; 46(1):37-47. DOI: 10.1046/j.1365-2958.2002.03144.x. View

Liang X, Haritan A, Uliel S, Michaeli S . trans and cis splicing in trypanosomatids: mechanism, factors, and regulation. Eukaryot Cell. 2003; 2(5):830-40. PMC: 219355. DOI: 10.1128/EC.2.5.830-840.2003. View

Kapler G, Coburn C, Beverley S . Stable transfection of the human parasite Leishmania major delineates a 30-kilobase region sufficient for extrachromosomal replication and expression. Mol Cell Biol. 1990; 10(3):1084-94. PMC: 360971. DOI: 10.1128/mcb.10.3.1084-1094.1990. View

Bernards A, Van der Ploeg L, Frasch A, Borst P, Boothroyd J, Coleman S . Activation of trypanosome surface glycoprotein genes involves a duplication-transposition leading to an altered 3' end. Cell. 1981; 27(3 Pt 2):497-505. DOI: 10.1016/0092-8674(81)90391-3. View

Van Leeuwen F, Wijsman E, Kieft R, van der Marel G, VAN Boom J, Borst P . Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. Genes Dev. 1998; 11(23):3232-41. PMC: 316749. DOI: 10.1101/gad.11.23.3232. View

Van Leeuwen F, Taylor M, Mondragon A, Moreau H, Gibson W, Kieft R . beta-D-glucosyl-hydroxymethyluracil is a conserved DNA modification in kinetoplastid protozoans and is abundant in their telomeres. Proc Natl Acad Sci U S A. 1998; 95(5):2366-71. PMC: 19348. DOI: 10.1073/pnas.95.5.2366. View

10.

Lowell J, Cross G . A variant histone H3 is enriched at telomeres in Trypanosoma brucei. J Cell Sci. 2004; 117(Pt 24):5937-47. DOI: 10.1242/jcs.01515. View

11.

DiPaolo C, Kieft R, Cross M, Sabatini R . Regulation of trypanosome DNA glycosylation by a SWI2/SNF2-like protein. Mol Cell. 2005; 17(3):441-51. DOI: 10.1016/j.molcel.2004.12.022. View

12.

Genest P, Riet B, Dumas C, Papadopoulou B, van Luenen H, Borst P . Formation of linear inverted repeat amplicons following targeting of an essential gene in Leishmania. Nucleic Acids Res. 2005; 33(5):1699-709. PMC: 1069007. DOI: 10.1093/nar/gki304. View

13.

Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu D . The genome of the African trypanosome Trypanosoma brucei. Science. 2005; 309(5733):416-22. DOI: 10.1126/science.1112642. View

14.

Bentin Toaldo C, Kieft R, Dirks-Mulder A, Sabatini R, van Luenen H, Borst P . A minor fraction of base J in kinetoplastid nuclear DNA is bound by the J-binding protein 1. Mol Biochem Parasitol. 2005; 143(1):111-5. PMC: 10278234. DOI: 10.1016/j.molbiopara.2005.05.001. View

15.

Glover L, Horn D . Repression of polymerase I-mediated gene expression at Trypanosoma brucei telomeres. EMBO Rep. 2005; 7(1):93-9. PMC: 1369228. DOI: 10.1038/sj.embor.7400575. View

16.

Taylor J, Rudenko G . Switching trypanosome coats: what's in the wardrobe?. Trends Genet. 2006; 22(11):614-20. DOI: 10.1016/j.tig.2006.08.003. View

17.

Genest P, Riet B, Cijsouw T, van Luenen H, Borst P . Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania. Nucleic Acids Res. 2007; 35(7):2116-24. PMC: 1874636. DOI: 10.1093/nar/gkm050. View

18.

Yu Z, Genest P, Riet B, Sweeney K, DiPaolo C, Kieft R . The protein that binds to DNA base J in trypanosomatids has features of a thymidine hydroxylase. Nucleic Acids Res. 2007; 35(7):2107-15. PMC: 1874643. DOI: 10.1093/nar/gkm049. View

19.

Kieft R, Brand V, Ekanayake D, Sweeney K, DiPaolo C, Reznikoff W . JBP2, a SWI2/SNF2-like protein, regulates de novo telomeric DNA glycosylation in bloodstream form Trypanosoma brucei. Mol Biochem Parasitol. 2007; 156(1):24-31. PMC: 4735730. DOI: 10.1016/j.molbiopara.2007.06.010. View

20.

Ekanayake D, Cipriano M, Sabatini R . Telomeric co-localization of the modified base J and contingency genes in the protozoan parasite Trypanosoma cruzi. Nucleic Acids Res. 2007; 35(19):6367-77. PMC: 2095807. DOI: 10.1093/nar/gkm693. View