Molecular Parasitology
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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:

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:

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:


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:

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:

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