Publications

members of the Siegel lab are listed in bold
# equal contribution
* corresponding authors

Key publications

Keneskhanova Z#, McWilliam KR#, Cosentino RO#, Barcons-Simon A, Dobrynin A, Smith JE, Subota I, Mugnier MR, Colomé-Tatché M*, Siegel TN * (2025)
Genomic determinants of antigen expression hierarchy in African trypanosomes.
Nature https://doi.org/10.1038/s41586-025-08720-w

Luzak V, Osses E, Danese A, Odendaal C, Stricker SH, Haanstra JR, Erhard F, Siegel TN* (2025)
SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.
Nucleic Acids Research gkae1203 doi.org/10.1093/nar/gkae1203

Rabuffo C, Schmidt MR, Yadav P, Tong P, Carloni R, Barcons-Simon A, Cosentino RO, Krebs S, Matthews KR, Allshire RC, Siegel TN* (2024)
Inter-chromosomal transcription hubs shape the 3D genome architecture of African trypanosomes.
Nature Communications 15: 10716 doi: 10.1038/s41467-024-55285-9

McWilliam KR#, Keneskhanova Z#, Cosentino RO#, Dobrynin A, Smith JE, Subota I, Mugnier MR, Colome-Tatche M*, Siegel TN* (2024)
High-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes.
bioRxiv 2024.03 doi: 10.1101/2024.03.22.586247

Beaver AK, Keneskhanova Z, Cosentino RO, Weiss BL, Awuoche EO, Smallenberger GM, Buenconsejo GY, Crilly NP, Smith JE, Hakim JMC, Zhang B, Bobb B, Rijo-Ferreira F, Figueiredo LM, Aksoy S, Siegel TN, Mugnier MR* (2024)
Tissue spaces are reservoirs of antigenic diversity for Trypanosoma brucei.
Nature 636: 430-437 doi: 10.1038/s41586-024-08151-z

Schmidt MR*, Barcons-Simon A, Rabuffo C, Siegel TN* (2024)
Smoother: on-the-fly processing of interactome data using prefix sums.
Nucleic Acids Research 52: e23 doi: 10.1093/nar/gkae008

Barcons-Simon A, Carrington M, Siegel TN* (2023)
Decoding the impact of nuclear organization on antigenic variation in parasites
Nature Microbiology 8: 1408-1418 doi: 10.1038/s41564-023-01424-9

Cosentino RO*, Brink BG, Siegel TN* (2021)
Allele-specific assembly of a eukaryotic genome corrects apparent frameshifts and reveals a lack of nonsense-mediated mRNA decay.
NAR Genomics and Bioinformatics doi.org/10.1093/nargab/lqab082

Faria J#, Luzak V#, Müller LSM, Brink BG, Hutchinson S, Glover L, Horn D*, Siegel TN* (2021)
Spatial integration of transcription and splicing in a dedicated compartment sustains monogenic antigen expression in African trypanosomes.
Nature Microbiology 6: 289-300 doi: 10.1038/s41564-020-00833-4

commentaries:

preLights: Mariana De Niz. Antigenic variation by switching inter-chromosomal interactions with an RNA splicing locus in trypanosomes
Nature Microbiolgy Behind the Paper: Luzak V and Faria J. A nuclear enterprise drives immune evasion.

Kraus AJ, Vanselow JT, Lamer S, Brink BG, Schlosser A, Siegel TN* (2020)
Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes.
Nature Communications 11: 1498 doi.org/10.1038/s41467-020-15274-0

Müller LSM#, Cosentino RO#, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba A-E, Sebra RP, Siegel TN* (2018)
Genome organization and DNA accessibility control antigenic variation in trypanosomes.
Nature 563: 121–125 doi.org/10.1038/s41586-018-0619-8

commentaries:

News and Views: Kelly S and Carrington M. Chromatin clues to the trypanosome parasite’s uniform coat. Nature 563: 40-42
Science Immunology Editors’ Choice: Griffin GK. Trypping up antigenic variation in sleeping sickness. Science Immunology 3: eaav7758
Nature Microbiology Behind the Paper: Siegel TN. Linking genome architecture and antigenic variation.

Vasquez JJ#, Wedel C#, Cosentino RO, Siegel TN* (2018)
Exploiting CRISPR-Cas9 technology to investigate individual histone modifications.
Nucleic Acids Research 46(18):e106 doi: org/10.1093/nar/gky517

Wedel C, Förstner KU, Derr R, Siegel TN* (2017)
GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes
EMBO Journal 36: 2581–2594 doi: 10.15252/embj.201695323

Vasquez JJ, Hon CH, Vanselow JT, Schlosser A, Siegel TN* (2014)
Comparative ribosome profiling reveals extensive translational complexity in different Trypanosoma brucei life cycle stages
Nucleic Acids Research 42: 3623-37 doi: 10.1093/nar/gkt1386

commentary:

News & Analysis: Chappell L. Found in translation. Nat Rev Microbiol. 12: 238

Siegel TN, Hekstra DR, Wang X, Dewell S, Cross GAM* (2010)
Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites
Nucleic Acids Research 38: 4946-57 doi: 10.1093/nar/gkq237

Siegel TN, Hekstra DR#, Kemp LE#, Figueiredo LM, Fenyo D, Wang X, Dewell S, Lowell JE, Cross GAM* (2009)
Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei
Genes and Development 23: 1063-76 doi: 10.1101/gad.1790409

commentaries:

Perspective: Talbert PB and Henikoff S. Chromatin-based transcription punctuation. Genes & Dev. 23: 1037-41
Science Editors’ Choice: Purnell BA. Start and Stop Signals. Science 324(5931)

Complete List of Publications

2023 - 2025

McWilliam KR, Keneskhanova Z, Cosentino RO, Dobrynin A, Smith JE, Subota I, Mugnier MR, Colome-Tatche M, Siegel TN (2024)
High-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes.
bioRxiv 2024.03. doi: 10.1101/2024.03.22.586247

Schmidt MR, Barcons-Simon A, Rabuffo C, Siegel TN (2024)
Smoother: on-the-fly processing of interactome data using prefix sums.
Nucleic Acids Research 52: e23 doi: 10.1093/nar/gkae008

Barcons-Simon A, Carrington M, Siegel TN (2023)
Decoding the impact of nuclear organization on antigenic variation in parasites
Nature Microbiology 8: 1408-1418 doi: 10.1038/s41564-023-01424-9

2020 - 2022

Rosón JN, Vitarelli MO, Costa-Silva HM, Pereira KS, Pires DDS, Lopes LS, Cordeiro B, Kraus AJ, Cruz KNT, Calderano SG, Fragoso SP, Siegel TN, Elias MC, da Cunha JPC* (2022)
H2B.V demarcates divergent strand-switch regions, some tDNA loci, and genome compartments in Trypanosoma cruzi and affects parasite differentiation and host cell invasion
PLoS Pathogens 18: e1009694 doi.org/10.1371/journal.ppat.1009694

Luzak V, López-Escobar L, Siegel TN*, Figueiredo LM* (2021)
Cell-to-Cell Heterogeneity in Trypanosomes
Annual Review of Microbiology 75: 107-128 doi.org/10.1146/annurev-micro-040821-012953

2016 - 2019

Kraus AJ, Brink BG, Siegel TN* (2019)
Efficient and specific oligo-based depletion of rRNA.
Scientific Reports doi: org/10.1038/s41598-019-48692-2

Bifeld E, Lorenzen S, Bartsch K, Vasquez JJ, Siegel TN, Clos J* (2018)
Ribosome Profiling Reveals HSP90 Inhibitor Effects on Stage-Specific Protein Synthesis in Leishmania donovani
mSystems 6: e00214-18 doi: 10.1128/mSystems.00214-18

Müller LSM#, Cosentino RO#, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba A-E, Sebra RP, Siegel TN* (2018)
Genome organization and DNA accessibility control antigenic variation in trypanosomes.
Nature 563: 121–125 doi.org/10.1038/s41586-018-0619-8

commentaries:

News and Views: Kelly S and Carrington M. Chromatin clues to the trypanosome parasite’s uniform coat. Nature 563: 40-42
Science Immunology Editors’ Choice: Griffin GK. Trypping up antigenic variation in sleeping sickness. Science Immunology 3: eaav7758
Nature Microbiology Behind the Paper: Siegel TN. Linking genome architecture and antigenic variation.

Hassan MA*, Vasquez JJ, Guo-Liang C, Meissner M, Siegel TN (2017)
Comparative ribosome profiling uncovers a dominant role for translational control in Toxoplasma gondii
BMC Genomics 18: 861 doi: 10.1186/s12864-017-4362-6

Wedel C, Siegel TN* (2017)
Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq
Experimental Parasitology 180: 2-12 doi: 10.1016/j.exppara.2017.03.003

Reynolds DL, Hofmeister BT, Cliffe L, Siegel TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R (2016)
Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination
Molecular Microbiology 101: 559-574 doi: 10.1111/mmi.13408

Reynolds D, Hofmeister B, Cliffe L, Siegel TN, Schmitz RJ, Sabatini R* (2016)
Histone H3 variant regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei
PLoS Genetics 12: e1005758 doi: 10.1371/journal.pgen.1005758

2013 - 2015

Fritz M, Vanselow J, Sauer N, Lamer S, Goos C, Siegel TN, Subota I, Schlosser A, Carrington M, Kramer S* (2015)
Novel insights into RNP granules by employing the trypanosome’s microtubule skeleton as a molecular sieve
Nucleic Acids Research 43: 8013-32 43: 8013-32 doi: 10.1093/nar/gkv731

ElBashir R, Vanselow JT, Kraus A, Janzen CJ, Siegel TN, Schlosser A* (2015)
Fragment ion patchwork quantification for measuring site-specific acetylation degrees
Analytical Chemistry 87: 9939-45 doi: 10.1021/acs.analchem.5b02517

Zhang Q, Siegel TN, Martins, RM, Wang F, Cao J, Gao Q, Cheng X, Jiang L, Hon CH, Scheidig-Benatar C, Sakamoto H,
Turner L, Jensen ATR, Claes A, Guizetti J, Malmquist NA, Scherf A* (2014)
Exonuclease-mediated degradation of nascent RNA silences genes linked to severe malaria
Nature 513: 431-35 513 doi: 10.1038/nature13468

Reynolds D, Cliffe LJ, Förstner KU, Hon CH, Siegel TN, Sabatini R* (2014)
Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in L. major and T. brucei
Nucleic Acids Research 42: 9717-29 doi: 10.1093/nar/gku714

Vembar SS, Scherf A, Siegel TN* (2014)
Noncoding RNAs as emerging regulators of Plasmodium falciparum virulence gene expression
Current Opinion in Microbiology, 20C: 153-161 doi: 101016/j.mib.2014.06.013

commentary:

News & Analysis: Chappell L. Found in translation. Nat Rev Microbiol. 12: 238

Siegel TN*, Hon CH, Zhang Q, Lopez Rubio JJ, Scheidig-Benatar C, Martins, RM, Sismeiro O, Coppée JY, Scherf A* (2014)
Strand-specific RNAseq reveals widespread occurrence and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum
BMC Genomics 15: 150 doi: 10.1186/1471-2164-15-150

Nguyen TN, Müller LSM, Park SH, Siegel TN, Günzl A* (2013)
Promoter occupancy of the basal class I transcription factor A differs strongly between active and silent VSG expression sites in Trypanosoma brucei
Nucleic Acids Research 42: 3164-76 doi: 10.1093/nar/gkt1301

Lopez-Rubio JJ, Siegel TN, Scherf A* (2013)
Genome-wide chromatin immunoprecipitation-sequencing in Plasmodium
Methods in Molecular Biology 923: 321-33 doi: 10.1007/978-1-62703-026-7_23

2010-2012

Chêne A, Vembar SS, Riviere L, Lopez-Rubio JJ, Claes A, Siegel TN, Sakamoto H, Scheidig-Benatar C, Hernandez-Rivas R, Scherf A* (2012)
PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites
Nucleic Acids Research 40: 3066-77 doi: 10.1093/nar/gkr1215

Siegel TN, Gunasekera K, Cross GAM, Ochsenreiter T* (2011)
Transcript processing and abundance in Trypanosoma brucei: lessons from high-throughput RNA sequencing
Trends in Parasitology 27: 434-41 doi: 10.1016/j.pt.2011.05.006

Wright JR, Siegel TN, Cross GAM* (2010)
Histone H3 trimethylated at lysine 4 is enriched at probable transcription start sites in Trypanosoma brucei
Molecular and Biochemical Parasitology 136: 434-50 doi: 10.1016/j.molbiopara.2010.03.013

Cliffe LJ, Siegel TN, Marshall M, Cross GAM, Sabatini R* (2010)
Two thymidine hydroxylases differentially regulate the formation of glucosylated DNA at regions flanking polymerase II polycistronic transcription units throughout the genome of Trypanosoma brucei
Nucleic Acids Research 38: 3923-35 doi: 10.1093/nar/gkq146

2009 and earlier

Siegel TN, Hekstra DR, Kemp LE, Figueiredo LM, Fenyo D, Wang X, Dewell S, Lowell JE, Cross GAM* (2009)
Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei
Genes and Development 23: 1063-76 doi: 10.1101/gad.1790409

commentaries:

Perspective: Talbert PB and Henikoff S. Chromatin-based transcription punctuation. Genes & Dev. 23(9):1037-41
Science Editors’ Choice: Purnell BA. Start and Stop Signals. Science 324(5931)

DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT* (2009)
Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor
Molecular and Cellular Proteomics 8: 2119-30 doi: 10.1074/mcp.M900038-MCP200

Kawahara T, Siegel TN, Ingram AK, Alsford S, Cross GAM, Horn D* (2008)
MYST family histone acetyltransferases in trypanosomes function in cell cycle progression and transcription control
Molecular Microbiology 69: 1054-68 doi: 10.1111/j.1365-2958.2008.06346.x

Siegel TN, Hekstra DR, Cross GAM* (2008)
Analysis of the Trypanosoma brucei cell cycle by quantitative DAPI imaging
Molecular and Biochemical Parasitology 160: 171-74 doi: 10.1016/j.molbiopara.2008.04.004

Siegel TN, Kawahara T, DeGrasse JA, Janzen CJ, Horn D, Cross GAM* (2008)
Acetylation of histone H4K4 is cell-cycle regulated and mediated by HAT3 in Trypanosoma brucei
Molecular Microbiology 67: 762-71 doi: 10.1111/j.1365-2958.2007.06079.x

Siegel TN, Tan KSW, Cross GAM* (2005)
Systematic study of sequencing motifs for RNA trans-splicing in Trypanosoma brucei
Molecular and Cellular Biology 25: 9586-94 doi: 10.1128/MCB.25.21.9586-9594.2005

Publications

Key publications

Complete List of Publications

2023 - 2025

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