Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silentVSGgene arrays inTrypanosoma brucei.
The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific nucleosome positions to modulate accessibility to the DNA molecule.Trypanosoma brucei, a member of the Excavates supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization of chromatin in early genomes.



We have mapped nucleosome positions inT. bruceiand identified important differences compared to other eukaryotes: The RNA polymerase II initiation regions inT. bruceido not exhibit pronounced nucleosome depletion, and show little evidence for defined -1 and +1 nucleosomes. In contrast, a well-positioned nucleosome is present directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were depleted of nucleosomes, with a single well-positioned nucleosome present immediately downstream of the predicted sites. The regions flanking the silent variant surface glycoprotein (VSG) gene cassettes showed extensive arrays of well-positioned nucleosomes, which may repress cryptic transcription initiation. The silent VSG genes themselves exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within silent VSG gene cassettes, displayed a defined nucleosomal organization compared with replication origins in other chromosomal core regions.



Our results indicate that some organizational features of chromatin are evolutionarily ancient, and may already have been present in the last eukaryotic common ancestor.
Department of Biochemistry, Stellenbosch University, Matieland, 7602 South Africa.
Johannes Petrus
JP
Maree
Department of Biology, Pennsylvania State University (Brandywine Campus), Media, PA 19063 USA.
Megan Lindsay
ML
Povelones
Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD USA.
David Johannes
DJ
Clark
Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ UK.
Gloria
G
Rudenko
Department of Biochemistry, Stellenbosch University, Matieland, 7602 South Africa.
Hugh-George
0000-0003-2550-0493
HG
Patterton
D002843:Chromatin / Q000378:metabolism; D018503:Genome, Protozoan; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism*; D051738:Origin Recognition Complex / Q000235:genetics / Q000378:metabolism; D015800:Protozoan Proteins / Q000235:genetics* / Q000378:metabolism; D012319:RNA Polymerase II / Q000235:genetics* / Q000378:metabolism; D012341:RNA, Ribosomal, 5S / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D013728:Terminator Regions, Genetic; D024363:Transcription Initiation Site; D014346:Trypanosoma brucei brucei / Q000235:genetics*; D014643:Variant Surface Glycoproteins, Trypanosoma / Q000235:genetics* / Q000378:metabolism
D002843:Chromatin; D008562:Membrane Glycoproteins; D009707:Nucleosomes; D051738:Origin Recognition Complex; D015800:Protozoan Proteins; D012341:RNA, Ribosomal, 5S; D014643:Variant Surface Glycoproteins, Trypanosoma; C053277:procyclic acidic repetitive protein, Trypanosoma; D012343:RNA, Transfer; D012319:RNA Polymerase II
Bloodstream expression sites; Evolution; Genome-wide nucleosome positions; MNase-seq; Polycistronic transcription units; Silent variant surface glycoproteins; Trypanosoma brucei; VSG