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Genome organization and DNA accessibility control antigenic variation in trypanosomes.
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.
Nature 563 2018; 121–125

Exploiting CRISPR-Cas9 technology to investigate individual histone modifications.
Vasquez JJ, Wedel C, Cosentino RO, Siegel TN.
Nucleic Acids Research 46(18), 2018: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 doi: 10.15252/embj.201695323. [Epub ahead of print]

Wedel C, Siegel TN (2017)
Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq
Experimental Parasitology doi: 10.1016/j.exppara.2017.03.003. [Epub ahead of print]

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 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

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(16):8013-32

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(19):9939-45

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(7518):431-35

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(15):9717-29

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

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(6):3623-37
News & Analysis: Chappell L. Found in translation. Nat Rev Microbiol. 12(4):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

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(5):3164-76

Lopez-Rubio JJ, Siegel TN, Scherf A (2013)
Genome-wide chromatin immunoprecipitation-sequencing in Plasmodium
Methods in Molecular Biology 923:321-33

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(17):3066-77

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(10):434-41

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(15):4946-57

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(11):434-50

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(12):3923-35

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(9):1063-76
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(9):2119-30

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(4):1054-68

Siegel TN, Hekstra DR, Cross GAM (2008)
Analysis of the Trypanosoma brucei cell cycle by quantitative DAPI imaging
Molecular and Biochemical Parasitology 160(2):171-74

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(4):762-71

Siegel TN, Tan KSW, Cross GAM (2005)
Systematic study of sequencing motifs for RNA trans-splicing in Trypanosoma brucei
Molecular and Cellular Biology 25(21):9586-94