Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes

Wenzhe Liu, Anish Das, Rachel Morales, Mahrukh Banday, Virginie Aris, David Lukac, Patricia Soteropoulos, David A. Wah, Jennifer Palenchar, Vivian Bellofatto

Research output: Contribution to journalArticle

Abstract

RNA polymerase II (RNAP-II) synthesizes the m7G-capped Spliced Leader (SL) RNA and most protein-coding mRNAs in trypanosomes. RNAP-II recruitment to DNA usually requires a set of transcription factors that make sequence-specific contacts near transcriptional start sites within chromosomes. In trypanosomes, the transcription factor TFIIB is necessary for RNAP-II-dependent SL RNA transcription. However, the trypanosomal TFIIB (tTFIIB) lacks the highly basic DNA binding region normally found in the C-terminal region of TFIIB proteins. To assess the precise pattern of tTFIIB binding within the SL RNA gene locus, as well as within several other loci, we performed chromatin immunoprecipitation/microarray analysis using a tiled gene array with a probe spacing of 10 nucleotides. We found that tTFIIB binds non-randomly within the SL RNA gene locus mainly within a 220-nt long region that straddles the transcription start site. tTFIIB does not bind within the small subunit (SSU) rRNA locus, indicating that trypanosomal TFIIB is not a component of an RNAP-I transcriptional complex. Interestingly, discrete binding sites were observed within the putative promoter regions of two loci on different chromosomes. These data suggest that although trypanosomal TFIIB lacks a highly basic DNA binding region, it nevertheless localizes to discrete regions of chromatin that include the SL RNA gene promoter.

Original languageEnglish (US)
Pages (from-to)139-142
Number of pages4
JournalMolecular and Biochemical Parasitology
Volume186
Issue number2
DOIs
StatePublished - Dec 1 2012

Fingerprint

Spliced Leader RNA
Trypanosoma brucei brucei
Chromatin Immunoprecipitation
Microarray Analysis
Genetic Promoter Regions
Transcription Factor TFIIB
Chromosomes
RNA Polymerase II
Trypanosomiasis
Genes
DNA
Transcription Factors
Transcription Initiation Site
Chromatin
Proteins
Nucleotides
Binding Sites
Messenger RNA

All Science Journal Classification (ASJC) codes

  • Parasitology
  • Molecular Biology

Keywords

  • Chromatin immunoprecipitation
  • RNA synthesis
  • SL RNA genes
  • TFIIB
  • Trypanosoma brucei
  • Trypanosomes

Cite this

Liu, Wenzhe ; Das, Anish ; Morales, Rachel ; Banday, Mahrukh ; Aris, Virginie ; Lukac, David ; Soteropoulos, Patricia ; Wah, David A. ; Palenchar, Jennifer ; Bellofatto, Vivian. / Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes. In: Molecular and Biochemical Parasitology. 2012 ; Vol. 186, No. 2. pp. 139-142.
@article{efbb5334a43a4ed1a7c0821f150d7c65,
title = "Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes",
abstract = "RNA polymerase II (RNAP-II) synthesizes the m7G-capped Spliced Leader (SL) RNA and most protein-coding mRNAs in trypanosomes. RNAP-II recruitment to DNA usually requires a set of transcription factors that make sequence-specific contacts near transcriptional start sites within chromosomes. In trypanosomes, the transcription factor TFIIB is necessary for RNAP-II-dependent SL RNA transcription. However, the trypanosomal TFIIB (tTFIIB) lacks the highly basic DNA binding region normally found in the C-terminal region of TFIIB proteins. To assess the precise pattern of tTFIIB binding within the SL RNA gene locus, as well as within several other loci, we performed chromatin immunoprecipitation/microarray analysis using a tiled gene array with a probe spacing of 10 nucleotides. We found that tTFIIB binds non-randomly within the SL RNA gene locus mainly within a 220-nt long region that straddles the transcription start site. tTFIIB does not bind within the small subunit (SSU) rRNA locus, indicating that trypanosomal TFIIB is not a component of an RNAP-I transcriptional complex. Interestingly, discrete binding sites were observed within the putative promoter regions of two loci on different chromosomes. These data suggest that although trypanosomal TFIIB lacks a highly basic DNA binding region, it nevertheless localizes to discrete regions of chromatin that include the SL RNA gene promoter.",
keywords = "Chromatin immunoprecipitation, RNA synthesis, SL RNA genes, TFIIB, Trypanosoma brucei, Trypanosomes",
author = "Wenzhe Liu and Anish Das and Rachel Morales and Mahrukh Banday and Virginie Aris and David Lukac and Patricia Soteropoulos and Wah, {David A.} and Jennifer Palenchar and Vivian Bellofatto",
year = "2012",
month = "12",
day = "1",
doi = "10.1016/j.molbiopara.2012.09.003",
language = "English (US)",
volume = "186",
pages = "139--142",
journal = "Molecular and Biochemical Parasitology",
issn = "0166-6851",
publisher = "Elsevier",
number = "2",

}

Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes. / Liu, Wenzhe; Das, Anish; Morales, Rachel; Banday, Mahrukh; Aris, Virginie; Lukac, David; Soteropoulos, Patricia; Wah, David A.; Palenchar, Jennifer; Bellofatto, Vivian.

In: Molecular and Biochemical Parasitology, Vol. 186, No. 2, 01.12.2012, p. 139-142.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Chromatin immunoprecipitation and microarray analysis reveal that TFIIB occupies the SL RNA gene promoter region in Trypanosoma brucei chromosomes

AU - Liu, Wenzhe

AU - Das, Anish

AU - Morales, Rachel

AU - Banday, Mahrukh

AU - Aris, Virginie

AU - Lukac, David

AU - Soteropoulos, Patricia

AU - Wah, David A.

AU - Palenchar, Jennifer

AU - Bellofatto, Vivian

PY - 2012/12/1

Y1 - 2012/12/1

N2 - RNA polymerase II (RNAP-II) synthesizes the m7G-capped Spliced Leader (SL) RNA and most protein-coding mRNAs in trypanosomes. RNAP-II recruitment to DNA usually requires a set of transcription factors that make sequence-specific contacts near transcriptional start sites within chromosomes. In trypanosomes, the transcription factor TFIIB is necessary for RNAP-II-dependent SL RNA transcription. However, the trypanosomal TFIIB (tTFIIB) lacks the highly basic DNA binding region normally found in the C-terminal region of TFIIB proteins. To assess the precise pattern of tTFIIB binding within the SL RNA gene locus, as well as within several other loci, we performed chromatin immunoprecipitation/microarray analysis using a tiled gene array with a probe spacing of 10 nucleotides. We found that tTFIIB binds non-randomly within the SL RNA gene locus mainly within a 220-nt long region that straddles the transcription start site. tTFIIB does not bind within the small subunit (SSU) rRNA locus, indicating that trypanosomal TFIIB is not a component of an RNAP-I transcriptional complex. Interestingly, discrete binding sites were observed within the putative promoter regions of two loci on different chromosomes. These data suggest that although trypanosomal TFIIB lacks a highly basic DNA binding region, it nevertheless localizes to discrete regions of chromatin that include the SL RNA gene promoter.

AB - RNA polymerase II (RNAP-II) synthesizes the m7G-capped Spliced Leader (SL) RNA and most protein-coding mRNAs in trypanosomes. RNAP-II recruitment to DNA usually requires a set of transcription factors that make sequence-specific contacts near transcriptional start sites within chromosomes. In trypanosomes, the transcription factor TFIIB is necessary for RNAP-II-dependent SL RNA transcription. However, the trypanosomal TFIIB (tTFIIB) lacks the highly basic DNA binding region normally found in the C-terminal region of TFIIB proteins. To assess the precise pattern of tTFIIB binding within the SL RNA gene locus, as well as within several other loci, we performed chromatin immunoprecipitation/microarray analysis using a tiled gene array with a probe spacing of 10 nucleotides. We found that tTFIIB binds non-randomly within the SL RNA gene locus mainly within a 220-nt long region that straddles the transcription start site. tTFIIB does not bind within the small subunit (SSU) rRNA locus, indicating that trypanosomal TFIIB is not a component of an RNAP-I transcriptional complex. Interestingly, discrete binding sites were observed within the putative promoter regions of two loci on different chromosomes. These data suggest that although trypanosomal TFIIB lacks a highly basic DNA binding region, it nevertheless localizes to discrete regions of chromatin that include the SL RNA gene promoter.

KW - Chromatin immunoprecipitation

KW - RNA synthesis

KW - SL RNA genes

KW - TFIIB

KW - Trypanosoma brucei

KW - Trypanosomes

UR - http://www.scopus.com/inward/record.url?scp=84870429461&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84870429461&partnerID=8YFLogxK

U2 - 10.1016/j.molbiopara.2012.09.003

DO - 10.1016/j.molbiopara.2012.09.003

M3 - Article

C2 - 22999857

AN - SCOPUS:84870429461

VL - 186

SP - 139

EP - 142

JO - Molecular and Biochemical Parasitology

JF - Molecular and Biochemical Parasitology

SN - 0166-6851

IS - 2

ER -