TY - JOUR
T1 - Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes
AU - Faria, Joana
AU - Luzak, Vanessa
AU - Müller, Laura S. M.
AU - Brink, Benedikt G.
AU - Hutchinson, Sebastian
AU - Glover, Lucy
AU - Horn, David
AU - Siegel, T. Nicolai
N1 - Funding Information:
We thank the Dundee Imaging Facility and J. Rouse for access to the Zeiss 880 Airyscan and Leica Confocal SP8 HyVolution microscope, respectively, and S. Alsford (London School of Hygiene and Tropical Medicine) for the SNAP42 tagging construct. We thank N. Jones (Oxford Instruments) for advice on image analysis using Imaris 9.5. We thank R. Cosentino and all members of the Siegel, Ladurner, Meissner and Boshart laboratories for valuable discussion, T. Straub (Bioinformatics Core Facility, BMC) for providing server space and help with data analysis, and the Core Unit Systems Medicine, University of Würzburg for next-generation sequencing. This work was funded by a Wellcome Trust Investigator Award to D.H. (100320/Z/12/Z), the German Research Foundation (SI 1610/3-1 and 213249687—SFB 1064), the Center for Integrative Protein Science (CIPSM) and an ERC Starting Grant (3D_Tryps 715466) to T.N.S. The University of Dundee Imaging Facility is supported by the MRC Next Generation Optical Microscopy award (MR/K015869/1). L.S.M.M. was supported by a grant of the German Excellence Initiative to the Graduate School of Life Science, University of Würzburg.
Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature Limited.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2021/1/11
Y1 - 2021/1/11
N2 - Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections1. African trypanosomes—parasites that cause lethal diseases in humans and livestock—employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2,600 antigen-coding genes2. In other eukaryotes, the expression of individual genes can be enhanced by mechanisms involving the juxtaposition of otherwise distal chromosomal loci in the three-dimensional nuclear space3–5. However, trypanosomes lack classical enhancer sequences or regulated transcription initiation6,7. In this context, it has remained unclear how genome architecture contributes to monogenic transcription elongation and transcript processing. Here, we show that the single expressed antigen-coding gene displays a specific inter-chromosomal interaction with a major messenger RNA splicing locus. Chromosome conformation capture (Hi-C) revealed a dynamic reconfiguration of this inter-chromosomal interaction upon activation of another antigen. Super-resolution microscopy showed the interaction to be heritable and splicing dependent. We found a specific association of the two genomic loci with the antigen exclusion complex, whereby VSG exclusion 1 (VEX1) occupied the splicing locus and VEX2 occupied the antigen-coding locus. Following VEX2 depletion, loss of monogenic antigen expression was accompanied by increased interactions between previously silent antigen genes and the splicing locus. Our results reveal a mechanism to ensure monogenic expression, where antigen transcription and messenger RNA splicing occur in a specific nuclear compartment. These findings suggest a new means of post-transcriptional gene regulation.
AB - Highly selective gene expression is a key requirement for antigenic variation in several pathogens, allowing evasion of host immune responses and maintenance of persistent infections1. African trypanosomes—parasites that cause lethal diseases in humans and livestock—employ an antigenic variation mechanism that involves monogenic antigen expression from a pool of >2,600 antigen-coding genes2. In other eukaryotes, the expression of individual genes can be enhanced by mechanisms involving the juxtaposition of otherwise distal chromosomal loci in the three-dimensional nuclear space3–5. However, trypanosomes lack classical enhancer sequences or regulated transcription initiation6,7. In this context, it has remained unclear how genome architecture contributes to monogenic transcription elongation and transcript processing. Here, we show that the single expressed antigen-coding gene displays a specific inter-chromosomal interaction with a major messenger RNA splicing locus. Chromosome conformation capture (Hi-C) revealed a dynamic reconfiguration of this inter-chromosomal interaction upon activation of another antigen. Super-resolution microscopy showed the interaction to be heritable and splicing dependent. We found a specific association of the two genomic loci with the antigen exclusion complex, whereby VSG exclusion 1 (VEX1) occupied the splicing locus and VEX2 occupied the antigen-coding locus. Following VEX2 depletion, loss of monogenic antigen expression was accompanied by increased interactions between previously silent antigen genes and the splicing locus. Our results reveal a mechanism to ensure monogenic expression, where antigen transcription and messenger RNA splicing occur in a specific nuclear compartment. These findings suggest a new means of post-transcriptional gene regulation.
KW - Epigenetics
KW - Next-generation sequencing
KW - Nuclear organization
KW - Parasite immune evasion
UR - http://www.scopus.com/inward/record.url?scp=85099113042&partnerID=8YFLogxK
U2 - 10.1038/s41564-020-00833-4
DO - 10.1038/s41564-020-00833-4
M3 - Article
C2 - 33432154
AN - SCOPUS:85099113042
JO - Nature Microbiology
JF - Nature Microbiology
SN - 2058-5276
ER -