Mono-allelic VSG expression by RNA polymerase I in Trypanosoma brucei: Expression site control from both ends?

Günzl, Arthur; Kirkham, Justin K.; Nguyen, Tu N.; Badjatia, Nitika; Park, Sung Hee

doi:10.1016/j.gene.2014.09.047

Cited by 37 publications

(36 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Despite this early divergence, Trypanosoma brucei encodes an extensive repertoire of proteins associated with chromatin structure, modification, and functional regulation [3–6]. The presence of an epigenome in trypanosomes is perhaps expected, given the evolutionary origin of functional core histones in the ancestral Archaea [7], and the presence of linker histone homologs in evolutionarily distant bacteria [8].…”

Section: Introductionmentioning

confidence: 99%

Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

Maree

Povelones

Clark

et al. 2017

Epigenetics & Chromatin

View full text Add to dashboard Cite

BackgroundThe 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.ResultsWe have mapped nucleosome positions in T. brucei and identified important differences compared to other eukaryotes: The RNA polymerase II initiation regions in T. brucei do 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.ConclusionsOur results indicate that some organizational features of chromatin are evolutionarily ancient, and may already have been present in the last eukaryotic common ancestor.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-017-0121-9) contains supplementary material, which is available to authorized users.

show abstract

Section: Introductionmentioning

confidence: 99%

Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

Maree

Povelones

Clark

et al. 2017

Epigenetics & Chromatin

View full text Add to dashboard Cite

show abstract

“…Furthermore, the CITFA complex remained localized to the nucleolus and the ESB after depletion of CITFA1, which caused CITFA to dissociate from the RRNA and BES promoters (46). These results raised the possibility that sequestration of CITFA to the nucleolus and the ESB may be the trypanosomes' means to restrict productive RNA Pol I transcription to these compartments (75). Since LC8 has been implicated in subnuclear and subcellular localization of many of its binding partners (20), sequestration or spatially controlled formation of CITFA2-LC8 may be a mechanism for localizing CITFA function.…”

Section: Figmentioning

confidence: 99%

Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A

Kirkham

Park

Nguyen

et al. 2016

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

Dynein light chain LC8 is highly conserved among eukaryotes and has both dynein-dependent and dynein-independent functions. Interestingly, LC8 was identified as a subunit of the class I transcription factor A (CITFA), which is essential for transcription by RNA polymerase I (Pol I) in the parasite Trypanosoma brucei. Given that LC8 has never been identified with a basal transcription factor and that T. brucei relies on RNA Pol I for expressing the variant surface glycoprotein (VSG), the key protein in antigenic variation, we investigated the CITFA-specific role of LC8. Depletion of LC8 from mammalian-infective bloodstream trypanosomes affected cell cycle progression, reduced the abundances of rRNA and VSG mRNA, and resulted in rapid cell death. Sedimentation analysis, coimmunoprecipitation of recombinant proteins, and bioinformatic analysis revealed an LC8 binding site near the N terminus of the subunit CITFA2. Mutation of this site prevented the formation of a CITFA2-LC8 heterotetramer and, in vivo, was lethal, affecting assembly of a functional CITFA complex. Gel shift assays and UV cross-linking experiments identified CITFA2 as a promoter-binding CITFA subunit. Accordingly, silencing of LC8 or CITFA2 resulted in a loss of CITFA from RNA Pol I promoters. Hence, we discovered an LC8 interaction that, unprecedentedly, has a basal function in transcription. Dynein light chain LC8 was originally discovered as a component of the outer arm axonemal dynein in Chlamydomonas reinhardtii (1) but was later found to be present also in cytoplasmic dyneins 1 and 2 (2-4). LC8 is conserved throughout eukaryotic genomes (5). As a part of the dynein motor, LC8 is important for fundamental cellular processes, such as tubulin minus-enddirected intracellular transport, chromatid separation during mitosis, and nuclear migration (6), as well as flagellum-specific functions, namely, motility, intraflagellar transport (7), and ciliogenesis (8, 9). While not essential in Saccharomyces cerevisiae (10), mutation or knockdown of LC8 is embryonic lethal in animals (8,9,11,12). Given that LC8 is more conserved between species than other components of the dynein motor and that LC8 is present in organisms which lack a dynein motor, it was likely that LC8 had nondynein functions (3, 5). LC8 has since been shown to interact with several different proteins and to affect various cellular processes, including protein localization and stability, transcription regulation, and apoptosis (13-15).At physiological pH, LC8 exists almost exclusively as a dimer (16, 17), interacting with partner proteins via two identical sites generated at the dimer interface which bind to diverse short, linear motifs (16,18,19). LC8 promotes the dimerization of its binding partners through aligning dimerization domains present in the partner protein (13,(20)(21)(22). While it was previously hypothesized that LC8 functions as a linker, allowing attachment of the dynein motor to its cargo, the emerging view is that interaction with LC8 induces dimerization, imparting new s...

show abstract

“…What mediates this singularity of ES expression [20]? Using drug selection pressure, it is possible to force the trypanosome to simultaneously activate a second ES; however, this state is not well tolerated by the cell.…”

Section: How Is Vsg Expression Controlled In a Monoallelic Fashion?mentioning

confidence: 99%

“…Repressive chromatin domains or gradients appear to control ESs from both ends [20]. An inhibitory chromatin state appears to restrict transcription initiation and elongation at VSG ES promoters, as knockdown of chromatin remodellers including ISWI and FACT results in derepression of silent ESs [38,39].…”

Section: How Is Vsg Expression Controlled In a Monoallelic Fashion?mentioning

confidence: 99%

How to create coats for all seasons: elucidating antigenic variation in African trypanosomes

Ooi

Rudenko

2017

Emerging Topics in Life Sciences

View full text Add to dashboard Cite

Extracellular parasites of the mammalian bloodstream face considerable challenges including incessant assault by the immune system. African trypanosomes are consummate survivors in this inclement environment and are renowned for their supremely sophisticated strategy of antigenic variation of their protective surface coat during the course of chronic infections. Recent developments are making us realize how complex this antigenic machinery is and are allowing us to tackle previously intractable problems. However, many of the simplest (and arguably the most important) questions still remain unanswered! How is the extraordinary heterogeneity of variant surface glycoprotein variants during a chronic infection generated?The bloodstream form of Trypanosoma brucei is coated with a dense covering of ∼10 7 variant surface glycoprotein (VSG) molecules, which extend as antigenically variable rods connected to the cell surface via glycosylphosphatidylinositol (GPI) anchors [1]. This GPI attachment allows VSGs to move freely over the cell surface [2]. Tight packing of these VSGs produces a protective barrier shielding invariant surface proteins from recognition by host antibodies and preventing trypanosome lysis by the alternative pathway of the complement system [3]. Extraordinarily high rates of recycling of surface VSG allow selective removal of host cell molecules including antibodies and complement from the trypanosome surface, thereby functioning as a 'coat-cleaning ' machine [4]. This prolongs trypanosome survival in rising antibody titres and facilitates escape from macrophages [5].Each trypanosome has a vast repertoire of VSG genes [6], differing in number and content between different strains, presumably as a consequence of diversifying forces. For example, the 'VSGnome' of T. brucei 427 contains more than 2500 different VSG genes, of which more than 80% are not immediately functional [7]. Switching the active VSG can entail transcriptional switches between the ∼15 telomeric VSG expression site (ES) transcription units (Figure 1). More importantly, DNA rearrangements and predominantly gene conversions can copy new VSGs (or segments of VSGs) into the active ES, thereby resulting in an antigenic switch [8] (Figure 1). This extraordinary ability to construct novel patchwork, or mosaic, VSGs is key for trypanosome survival [9]. The continuous recombination of various permutations and combinations of sections of VSG genes (or pseudogenes) allows the trypanosome to construct an almost infinite number of antigenically distinct VSG coat types.A given wave of trypanosome parasitaemia is normally predominantly composed of a major VSG variant, although it has long been known that minor VSG variants are also present within each wave. However, there is possibly phenomenal heterogeneity within these infection waves, as next-generation RNA sequencing of RNA transcripts has documented an extraordinary variety of minor VSG variants [10]. These experiments argue that a considerable percentage of the available VSG repertoire is disp...

show abstract

Mono-allelic VSG expression by RNA polymerase I in Trypanosoma brucei: Expression site control from both ends?

Cited by 37 publications

References 67 publications

Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma brucei

Dynein Light Chain LC8 Is Required for RNA Polymerase I-Mediated Transcription in Trypanosoma brucei, Facilitating Assembly and Promoter Binding of Class I Transcription Factor A

How to create coats for all seasons: elucidating antigenic variation in African trypanosomes

Contact Info

Product

Resources

About