Molecular and Biochemical Parasitology 84 (1997) 189–201 Analysis of Trypanosoma brucei 6sg expression site switching in vitro David Horn, George A.M. Cross* Laboratory of Molecular Parasitology, The Rockefeller Uni6ersity, 1230 York A6enue, New York, NY 10021-6399, USA Received 19 August 1996; accepted 7 November 1996 Abstract Trypanosoma brucei can undergo antigenic variation by switching between distinct telomeric variant surface glycoprotein gene (6sg) expression sites (ESs) or by replacing the active 6sg. DNA rearrangements have often been associated with ES switching, but it is unclear if such rearrangements are necessary or whether ES inactivation always accompanies ES activation. To explore these issues, we derived ten independent clones, from the same parent, that had undergone a similar 6sg activation event. This was achieved in the absence of an immune response, in vitro, using cells with selectable markers integrated into an ES. Nine of the ten clones had undergone ES switching. Such heritable changes in transcription state occurred at a frequency of approximately 6×10−7. Comparison of switched and un-switched clones highlighted the dynamic nature of T. brucei telomeres, but changes in telomere length were not specifically associated with ES switching. Mapping within and beyond the ESs revealed no detectable DNA rearrangements, indicating that rearrangements are not necessary for ES activation/inactivation. Examination of individual cells indicated that ES activation consistently accompanied inactivation of the previously active ES. In some cases, however, we found cells that appeared to have efficiently established the switched state but which subsequently, at a frequency of approximately 2×10−3, generated cells expressing both pre- and post-switch 6sgs. These results show that ES activation/inactivation is usually a coupled process but that cells can inherit a propensity to uncouple these events. © 1997 Elsevier Science B.V. Keywords: Antigenic variation; Expression site; Telomere; Trypanosoma brucei; Variant surface glycoprotein 1. Introduction In the blood and tissue spaces of the mam- Abbre iations: ES, expression site; TRF, telomere restriction 6 malian host, Trypanosoma brucei escapes elimina- fragment; Vsg (6sg), variant surface glycoprotein (gene). * Corresponding author. Tel.: +1 212 3277571; fax: +1 tion by the host immune response by a process of 212 3277845; e-mail: [email protected] antigenic variation (reviewed in [1,2]). Antigenic 0166-6851/97/$17.00 © 1997 Elsevier Science B.V. All rights reserved PII S0166-6851(96)02794-6 190 D. Horn, G.A.M. Cross / Molecular and Biochemical Parasitology 84 (1997) 189–201 variation involves the mutually exclusive and se- T. equiperdum [14], suggesting that ESs can switch quential expression of individual variant surface on and off independently. glycoprotein (Vsg) genes (6sg) derived from a In T. brucei clone 118a, a single copy of 6sg221 repertoire of approximately 1000 6sgs and is present at a transcriptionally repressed ES. This pseudo-6sgs [3]. The expressed 6sg is invariably 6sg can be activated via duplication or ES switch- located at the telomere-proximal end of a poly- ing [15]. Activation of the 6sg221 ES occurred cistronic transcription unit known as an expres- with no detectable rearrangement up to 55 kb sion site (ES). A number of ES-associated genes upstream of 6sg221 [15] and inactivation occurred are also present in these polycistronic transcrip- without a single point mutation within 3.4 kb tion units and the ES promoter is located approx- spanning the ES promoter [10]. The active ES in imately 50 kb upstream of the 6sg. Antigenic clone 118a can also undergo inactivation and variation is spontaneous and can occur by a num- subsequent reactivation [16]. To capture and ber of mechanisms, but most commonly involves study multiple examples of activation of the replacement of the active 6sg, by gene conversion 6sg221 ES, we inserted genes encoding resistance at the active ES, or by switching transcription to phleomycin and G418 into the silent 6sg221 ES from one ES to another (reviewed in [1,2]). The in 118a cells [5]. Acquisition of drug-resistance 6sgs at silent telomeric ESs are more likely to can consequently be exploited to capture clones in become expressed and can be activated by either which the 6sg221 ES has become transcriptionally of these mechanisms [4]. active, or the marker cassette has been duplicated We [5] and others [6] have recently shown that to a transcriptionally active locus. Activation events can be captured immediately while mini- position effects repress transcription at a silent T. mizing sub-culturing or other procedures that brucei ES. We wish to discover how ES domains could allow unrelated DNA rearrangements to faithfully and heritably maintain their transcrip- accumulate. Also, because drug selection, as op- tional status over many generations, yet infre- posed to immune selection, does not require inac- quently allow alterations of state. DNA tivation of the previously active 6sg for survival, rearrangements can alter gene expression in a our approach allows the isolation of cells that number of organisms [7] and rearrangements activate a second ES without inactivating the within an ES, or upstream of the promoter region, previously active ES. have been found after ES switching, (reviewed in In this study, we show that detectable DNA [8]), but it is unclear if any of these changes are rearrangements are not necessary for ES switching necessary for ES switching. We wanted to deter- and that ES activation usually accompanies inac- mine, using more stringent experimental protocols tivation of the previously active ES. Our switched than hitherto possible, whether any DNA rear- clones, however, inherited different phenotypes. rangements are necessary for ES switching, or Some of these clones inherited a propensity to whether ES switching can be attributed solely to uncouple ES activation and inactivation leading epigenetic phenomena. We also wanted to deter- to the generation of cells expressing two 6sgs. mine if ES inactivation invariably accompanies ES activation. There are estimated to be approxi- mately 20 bloodstream-form ESs in the T. brucei 2. Materials and methods genome [9–12]. Usually, only one ES is active at a time in individual bloodstream-form cells and 2.1. Cells ES activity is controlled at or near transcription initiation [10], with notable exceptions. In a Cells were maintained and cloned as previously switch associated with a large insertion upstream described [5]. T. brucei Mitat 1.5 clone 118a was of the silenced 6sg, the region upstream of the derived from stabilate 049 and Mitat 1.2 clone insertion continued to be transcribed [13]. Fur- 221a was derived in culture from stabilate 052 thermore, stable expression of two 6sgs from dif- [17,18]. G418 was purchased from Gibco and ferent ESs in individual cells has been reported in phleomycin from Cayla. D. Horn, G.A.M. Cross / Molecular and Biochemical Parasitology 84 (1997) 189–201 191 2.2. DNA analysis and Schizosaccharomyces pombe chromosome markers were from Bio-Rad and low-range pulsed Genomic DNA was isolated and Southern blot- field gel electrophoresis markers were from New ting was carried out as previously described [5]. England Biolabs. Large DNA fragments were vi- Agarose blocks containing intact T. brucei chro- sualized and transferred to membrane as de- mosomes were prepared as described for mam- scribed [19]. All post-hybridization washes were at malian cells [19]. Restriction enzyme digestion of 65°C in 0.2×SSC and 0.2% SDS. DNA in agarose was carried out according to the manufacturer (New England Biolabs). DNA em- 2.3. Protein analysis bedded in agarose was size-fractionated using a Rotating Agarose Gel Electrophoresis apparatus Western blotting and immunofluorescence anal- (Stratagene). Gels were prepared from SeaKem ysis were carried out as previously described [5]. LE agarose (FMC) in 0.5×TBE and the elec- For detection of Neo or Ble, protein from 3×105 trophoresis temperature was kept constant at cells was loaded per lane. For detection of Vsg, 12°C. Hansenula wingei, Saccharomyces cere6isiae protein from 1.5×105 cells was loaded per lane. Vsg, Neo or Ble proteins were separated in 10, 12.5 and 17.5% polyacrylamide gels, respectively. The antiserum to Vsg221 was depleted of anti- body to the cross-reacting determinant [20]. Fig. 1. Selection of switched cells in vitro. (A) Physical maps of the 6sg118 and 6sg221 ES loci in 118+/bRn cells, which express 6sg118 [5]. The endogenous ES promoters and the inserted rRNA promoter are indicated as open and filled arrowheads respectively. The telomere is indicated down- stream of each 6sg.×70 represents imperfect ‘70 bp’ repeats, and some relevant restriction sites are shown. Abbreviations used for restriction enzymes are E, EcoRI; N, NarI. Probes used for Southern analysis are indicated as bars below the maps; 6sg118 probe a contains 730 bp directly upstream of the EcoRI site; 6sg118 probe b contains 200 bp directly down- stream of the EcoRI site; the ble probe contains the entire coding region from pUT-56 [26] and the 6sg221 probe is a 770-bp fragment containing the first 520 bp of the coding region. (B) Selection of drug-resistant cells from 118+/bRn cultures. 106 118+/bRn cells were transferred to medium containing 1 mgml−1phleomycin (O). As a control, approxi- mately 104 cells were grown in medium without phleomycin ( ). Cell density was determined in both cultures after6hand every day for ten days. (C) Western analysis of ten indepen- dent drug-resistant clones. 221+/bRn cells act as a positive control for cells that have activated the linked ble, neo and 6sg221 genes. This strain was generated by inserting selectable markers directly into an active 6sg221 ES [5]. Protein was isolated from 221+/bRn cells (lane+), 118+/bRn parental cells (lane P), four independent clones derived by phleomycin selection (selection for activation of ble, lanes B1–B4) and six independent clones derived by G418 selection (selection for activation of neo, lanes N1–N6).