Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs

Puechberty, Jacques; Blaineau, Christine; Meghamla, Sabrina; Crobu, Lucien; Pagès, Michel; Bastien, Patrick

doi:10.1186/1471-2164-8-57

Cited by 11 publications

(10 citation statements)

References 26 publications

(52 reference statements)

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“…The only identifiable motif found in a majority of the isolated sequences was a G-tract (or C-tract) longer than 10 nucleotides. Similar elements were found within the transcription-enhancing 73-bp sequence derived from the L. major chr1 strand-switch region [ 4 ] which is conserved across Leishmania species [ 45 ]. However, because of their ubiquitous presence in regions devoid of TBP and acetylated H3 peaks, it is unlikely that these elements are sufficient to direct transcription initiation.…”

Section: Discussionmentioning

confidence: 75%

“…A single motif was identified from the presumed initiation sites for protein-coding gene transcription: a long G-tract (or C-tract in the complement). Two such G-tracts were found within the 73-bp sequence from the chr1 strand-switch region [ 3 , 4 ] and they are conserved across a range of Leishmania species [ 45 ]. While G-tracts were associated with TBP/SNAP 50 -binding sites upstream of most acetyl-H3 peaks, G-tracts of similar or longer (≥10 nucleotides) length are peppered throughout the genome, and almost half of the predicted sites of transcription initiation lack such G-tracts (data not shown).…”

Section: Resultsmentioning

confidence: 99%

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Histone acetylations mark origins of polycistronic transcription in Leishmania major

et al. 2009

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Background: Many components of the RNA polymerase II transcription machinery have been identified in kinetoplastid protozoa, but they diverge substantially from other eukaryotes. Furthermore, protein-coding genes in these organisms lack individual transcriptional regulation, since they are transcribed as long polycistronic units. The transcription initiation sites are assumed to lie within the 'divergent strand-switch' regions at the junction between opposing polycistronic gene clusters. However, the mechanism by which Kinetoplastidae initiate transcription is unclear, and promoter sequences are undefined.

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Section: Discussionmentioning

confidence: 75%

Section: Resultsmentioning

confidence: 99%

Histone acetylations mark origins of polycistronic transcription in Leishmania major

et al. 2009

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“…Interestingly, these features also occur at other specific regions putatively related to transcription initiation [18]. Although a high G+C content of SSRs has been observed, no signals such as TATA box or other typical RNA polymerase II core promoter elements have been detected [19]. Transcription termination signals have not been clearly defined for RNA polymerase II transcription of protein-coding genes, although a tract of Ts seems to be required in the case of the spliced leader genes in Leishmania tarentolae [20].The analysis of the regions between convergent DGCs, where termination signals may occur, reveals the presence of tRNA genes as well as other genes transcribed by RNA polymerase III [21], [22].…”

Section: Introductionmentioning

confidence: 98%

Genomic Analysis of Sequence-Dependent DNA Curvature in Leishmania

Smircich

Forteza²,

El-Sayed

et al. 2013

PLoS ONE

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Leishmania major is a flagellated protozoan parasite of medical importance. Like other members of the Trypanosomatidae family, it possesses unique mechanisms of gene expression such as constitutive polycistronic transcription of directional gene clusters, gene amplification, mRNA trans-splicing, and extensive editing of mitochondrial transcripts. The molecular signals underlying most of these processes remain under investigation. In order to investigate the role of DNA secondary structure signals in gene expression, we carried out a genome-wide in silico analysis of the intrinsic DNA curvature. The L. major genome revealed a lower frequency of high intrinsic curvature regions as well as inter- and intra- chromosomal distribution heterogeneity, when compared to prokaryotic and eukaryotic organisms. Using a novel method aimed at detecting region-integrated intrinsic curvature (RIIC), high DNA curvature was found to be associated with regions implicated in transcription initiation. Those include divergent strand-switch regions between directional gene clusters and regions linked to markers of active transcription initiation such as acetylated H3 histone, TRF4 and SNAP50. These findings suggest a role for DNA curvature in transcription initiation in Leishmania supporting the relevance of DNA secondary structures signals.

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“…This polycistronic transcription is followed by trans-splicing of a short leader sequence and a poly(A) tail onto the 5′ and 3′ ends of the individual protein-coding units ( 58 – 60 ). No consensus sequences have been identified at the dSSRs, although a poly(C) tract at the region where transcription initiates in the chromosome 1 dSSR is conserved across 15 Leishmania species ( 61 ). In the absence of defined regulatory sequence elements at the transcription start sites (TSSs) as well as the apparent absence of canonical transcription factors that are generally conserved across eukaryotes, epigenetic control mechanisms may play a major role in modulating gene expression.…”

Section: Epigenetic Processes Modulating Trypanosomatid Gene Expressimentioning

confidence: 99%

Histone Modifications and Other Facets of Epigenetic Regulation in Trypanosomatids: Leaving Their Mark

Saha

2020

mBio

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Histone posttranslational modifications (PTMs) modulate several eukaryotic cellular processes, including transcription, replication, and repair. Vast arrays of modifications have been identified in conventional eukaryotes over the last 20 to 25 years. While initial studies uncovered these primarily on histone tails, multiple modifications were subsequently found on the central globular domains as well. Histones are evolutionarily conserved across eukaryotes, and a large number of their PTMs and the functional relevance of these PTMs are largely conserved. Trypanosomatids, however, are early diverging eukaryotes. Although possessing all four canonical histones as well as several variants, their sequences diverge from those of other eukaryotes, particularly in the tails. Consequently, the modifications they carry also vary. Initial analyses almost 15 years ago suggested that trypanosomatids possessed a smaller collection of histone modifications. However, exhaustive high resolution mass spectrometry analyses in the last few years have overturned this belief, and it is now evident that the “histone code” proposed by Allis and coworkers in the early years of this century is as complex in these organisms as in other eukaryotes. Trypanosomatids cause several diseases, and the members of this group of organisms have varied lifestyles, evolving diverse mechanisms to evade the host immune system, some of which have been found to be principally controlled by epigenetic mechanisms. This minireview aims to acquaint the reader with the impact of histone PTMs on trypanosomatid cellular processes, as well as other facets of trypanosomatid epigenetic regulation, including the influence of three-dimensional (3D) genome architecture, and discusses avenues for future investigations.

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Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs

Cited by 11 publications

References 26 publications

Histone acetylations mark origins of polycistronic transcription in Leishmania major

Histone acetylations mark origins of polycistronic transcription in Leishmania major

Genomic Analysis of Sequence-Dependent DNA Curvature in Leishmania

Histone Modifications and Other Facets of Epigenetic Regulation in Trypanosomatids: Leaving Their Mark

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