Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life forms

Trypanosoma cruzi alternates between replicative and nonreplicative life forms, accompanied by a shift in global transcription levels and by changes in the nuclear architecture, the chromatin proteome and histone posttranslational modifications. To gain further insights into the epigenetic regulation that accompanies life form changes, we performed genome-wide high-resolution nucleosome mapping using two T. cruzi life forms (epimastigotes and cellular trypomastigotes). By combining a powerful pipeline that allowed us to faithfully compare nucleosome positioning and occupancy, more than 125 thousand nucleosomes were mapped, and approximately 20% of them differed between replicative and nonreplicative forms. The nonreplicative forms have less dynamic nucleosomes, possibly reflecting their lower global transcription levels and DNA replication arrest. However, dynamic nucleosomes are enriched at nonreplicative regulatory transcription initiation regions and at multigenic family members, which are associated with infective-stage and virulence factors. Strikingly, dynamic nucleosome regions are associated with GO terms related to nuclear division, translation, gene regulation and metabolism and, notably, associated with transcripts with different expression levels among life forms. Finally, the nucleosome landscape reflects the steady-state transcription expression: more abundant genes have a more deeply nucleosome-depleted region at putative 5’ splice sites, likely associated with trans-splicing efficiency. Taken together, our results indicate that chromatin architecture, defined primarily by nucleosome positioning and occupancy, reflects the phenotypic differences found among T. cruzi life forms despite the lack of a canonical transcriptional control context.

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Histone H2B.V demarcates strategic regions in the Trypanosoma cruzi genome, associates with a bromodomain factor and affects parasite differentiation and host cell invasion

10.1101/2021.06.08.447515 ◽

2021 ◽

Author(s):

Juliana Nunes Rosón ◽

Marcela Oliveira Vitarelli ◽

Héllida Marina Costa-Silva ◽

Kamille Schmitt Pereira ◽

David da Silva Pires ◽

...

Keyword(s):

Trypanosoma Cruzi ◽

Chromatin Structure ◽

Life Forms ◽

Histone Variants ◽

Parasite Life Cycle ◽

Nucleolar Proteins ◽

Genome Wide ◽

Switch Regions ◽

Chromatin Proteins ◽

Genomic Regions

Histone variants play a crucial role in chromatin structure organization and gene expression. Trypanosomatids have an unusual H2B variant (H2B.V) that is known to dimerize with the variant H2A.Z generating unstable nucleosomes. Previously, we found that H2B.V protein is enriched in nonreplicative life forms of Trypanosoma cruzi , suggesting that this variant may contribute to the differences in chromatin structure and global transcription rates observed among parasite life forms. Here, we performed the first genome-wide profiling of histone localization in T. cruzi using replicative and nonreplicative life forms, and we found that H2B.V was preferentially located at the edges of divergent switch regions, which encompass putative transcriptional start regions; at some tDNA loci; and between the conserved and disrupted genome compartments, mainly at trans-sialidase, mucin and MASP genes. Remarkably, the chromatin of nonreplicative forms was depleted of H2B.V-enriched peaks in comparison to replicative forms. Interactome assays indicated that H2B.V associated specifically with H2A.Z, bromodomain factor 2, nucleolar proteins and a histone chaperone, among others. Parasites expressing reduced H2B.V levels were associated with higher rates of parasite differentiation and mammalian cell infectivity. Taken together, H2B.V demarcates critical genomic regions and associates with regulatory chromatin proteins, suggesting a scenario wherein local chromatin structures associated with parasite differentiation and invasion are regulated during the parasite life cycle.

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Identification of Novel Interspersed DNA Repetitive Elements in the Trypanosoma cruzi Genome Associated with the 3′UTRs of Surface Multigenic Families

Genes ◽

10.3390/genes11101235 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1235

Author(s):

Simone Guedes Calderano ◽

Milton Yutaka Nishiyama Junior ◽

Marjorie Marini ◽

Nathan de Oliveira Nunes ◽

Marcelo da Silva Reis ◽

...

Keyword(s):

Trypanosoma Cruzi ◽

Genome Sequence ◽

Posttranscriptional Regulation ◽

Transcriptional Control ◽

Surface Protein ◽

Repetitive Elements ◽

Surface Proteins ◽

Control Of Gene Expression ◽

Intergenic Regions ◽

Multigenic Family

Trypanosoma cruzi is the etiological agent of Chagas disease, which affects millions of people in Latin America. No transcriptional control of gene expression has been demonstrated in this organism, and 50% of its genome consists of repetitive elements and members of multigenic families. In this study, we applied a novel bioinformatics approach to predict new repetitive elements in the genome sequence of T. cruzi. A new repetitive sequence measuring 241 nt was identified and found to be interspersed along the genome sequence from strains of different DTUs. This new repeat was mostly on intergenic regions, and upstream and downstream regions of the 241 nt repeat were enriched in surface protein genes. RNAseq analysis revealed that the repeat was part of processed mRNAs and was predominantly found in the 3′ untranslated regions (UTRs) of genes of multigenic families encoding surface proteins. Moreover, we detected a correlation between the presence of the repeat in the 3′UTR of multigenic family genes and the level of differential expression of these genes when comparing epimastigote and trypomastigote transcriptomes. These data suggest that this sequence plays a role in the posttranscriptional regulation of the expression of multigenic families.

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Nucleosome Positioning

ISRN Molecular Biology ◽

10.5402/2012/245706 ◽

2012 ◽

Vol 2012 ◽

pp. 1-5 ◽

Cited By ~ 7

Author(s):

Hiromi Nishida

Keyword(s):

Transcription Initiation ◽

Genomic Dna ◽

Cytosine Methylation ◽

Nucleosome Positioning ◽

Micrococcal Nuclease ◽

Gene Splicing ◽

Nucleosomal Dna ◽

Genome Wide ◽

Wide Range ◽

High Level

Nucleosome positioning is not only related to genomic DNA compaction but also to other biological functions. After the chromatin is digested by micrococcal nuclease, nucleosomal (nucleosome-bound) DNA fragments can be sequenced and mapped on the genomic DNA sequence. Due to the development of modern DNA sequencing technology, genome-wide nucleosome mapping has been performed in a wide range of eukaryotic species. Comparative analyses of the nucleosome positions have revealed that the nucleosome is more frequently formed in exonic than intronic regions, and that most of transcription start and translation (or transcription) end sites are located in nucleosome linker DNA regions, indicating that nucleosome positioning influences transcription initiation, transcription termination, and gene splicing. In addition, nucleosomal DNA contains guanine and cytosine (G + C)-rich sequences and a high level of cytosine methylation. Thus, the nucleosome positioning system has been conserved during eukaryotic evolution.

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Faculty Opinions recommendation of Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717347864.792702914 ◽

2012 ◽

Author(s):

Remy Bosselut

Keyword(s):

T Cell ◽

Transcriptional Control ◽

Cell Identity ◽

Genome Wide

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A deformation energy model reveals sequence-dependent property of nucleosome positioning

Chromosoma ◽

10.1007/s00412-020-00750-9 ◽

2021 ◽

Vol 130 (1) ◽

pp. 27-40

Author(s):

Guoqing Liu ◽

Hongyu Zhao ◽

Hu Meng ◽

Yongqiang Xing ◽

Lu Cai

Keyword(s):

Budding Yeast ◽

Nucleosome Occupancy ◽

Nucleosome Positioning ◽

Deformation Energy ◽

Energy Model ◽

Structural Parameter ◽

High Deformation ◽

Dna Deformation ◽

Genome Wide ◽

Genomic Regions

AbstractWe present a deformation energy model for predicting nucleosome positioning, in which a position-dependent structural parameter set derived from crystal structures of nucleosomes was used to calculate the DNA deformation energy. The model is successful in predicting nucleosome occupancy genome-wide in budding yeast, nucleosome free energy, and rotational positioning of nucleosomes. Our model also indicates that the genomic regions underlying the MNase-sensitive nucleosomes in budding yeast have high deformation energy and, consequently, low nucleosome-forming ability, while the MNase-sensitive non-histone particles are characterized by much lower DNA deformation energy and high nucleosome preference. In addition, we also revealed that remodelers, SNF2 and RSC8, are likely to act in chromatin remodeling by binding to broad nucleosome-depleted regions that are intrinsically favorable for nucleosome positioning. Our data support the important role of position-dependent physical properties of DNA in nucleosome positioning.

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Genome-wide discovery of G-quadruplexes in barley

Scientific Reports ◽

10.1038/s41598-021-86838-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

H. Busra Cagirici ◽

Hikmet Budak ◽

Taner Z. Sen

Keyword(s):

Transcription Initiation ◽

Large Window ◽

First Intron ◽

Domain Sequence ◽

Genome Wide ◽

Square Planar ◽

Peak Points ◽

Molecular Functions ◽

Nucleic Acid Structures ◽

Provided Examples

AbstractG-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.

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Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines.

Molecular and Cellular Biology ◽

10.1128/mcb.11.4.1854 ◽

1991 ◽

Vol 11 (4) ◽

pp. 1854-1860 ◽

Cited By ~ 18

Author(s):

N P Shah ◽

O N Witte ◽

C T Denny

Keyword(s):

Transcription Factor ◽

Cell Lines ◽

Transcription Initiation ◽

Transcriptional Control ◽

Philadelphia Chromosome ◽

Gc Content ◽

Cellular Transformation ◽

Nucleotide Sequence Analysis ◽

Coding Sequences ◽

Gene Assay

The t(9;22) Philadelphia chromosome translocation fuses 5' regulatory and coding sequences of the BCR gene to the c-ABL proto-oncogene. This results in the formation of hybrid BCR-ABL mRNAs and proteins. The shift in ABL transcriptional control to the BCR promoter may play a role in cellular transformation mediated by this rearrangement. We have functionally localized the BCR promoter to a region 1 kb 5' of BCR exon 1 coding sequences by using a chloramphenicol acetyltransferase reporter gene assay. Nucleotide sequence analysis of this region revealed many consensus binding sequences for transcription factor SP1 as well as two potential CCAAT box binding factor sites and one putative helix-loop-helix transcription factor binding site. No TATA-like or "initiator" element sequences were found. Because of low steady-state levels of BCR mRNA and the high GC content (78%) of the promoter region, definitive mapping of transcription start sites required artificial amplification of BCR promoter-directed transcripts. Overexpression from the BCR promoter in a COS cell system was effective in demonstrating multiple transcription initiation sites. In order to assess the effects of chromosomal translocation on the transcriptional control of the BCR gene, we determined S1 nuclease protection patterns of poly(A)+ RNA from tumor cell lines. No differences were observed in the locations and levels of BCR transcription initiation sites between those lines that harbored the t(9;22) translocation and those that did not. This demonstrates that BCR promoter function remains intact in spite of genomic rearrangement. The BCR promoter is structurally similar to the ABL promoters. Together, this suggests that the structural fusion of BCR-ABL and not its transcriptional deregulation is primarily responsible for the transforming effect of the t(9;22) translocation.

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