Publications
members of the Siegel lab are listed in bold
# equal contribution
* co-corresponding authors
Key Publications
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
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
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
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
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.
Vasquez JJ#, Wedel C#, Cosentino RO, Siegel TN (2018)
Exploiting CRISPR-Cas9 technology to investigate individual histone modifications.
Nucleic Acids Research 46: e106 doi: org/10.1093/nar/gky517
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, 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
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
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*, 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
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
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