H2B.V demarcates divergent strand-switch regions, some tDNA loci, and genome compartments in Trypanosoma cruzi and affects parasite differentiation and host cell invasion.

T Nicolai Siegel,Stenio Perdigão Fragoso,Karin Navarro Tozzi Cruz,Leticia De Sousa Lopes,Juliana Nunes Rosón,Barbara Cordeiro,Julia Pinheiro Chagas Da Cunha,Simone Guedes Calderano,David Da Silva Pires,Kamille Schmitt Pereira,Maria Carolina Elias,Lyris Martins Franco De Godoy,Marcela De Oliveira Vitarelli,Héllida Marina Costa-Silva,Amelie J Kraus

doi:10.1371/journal.ppat.1009694

Abstract

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 tissue-derived trypomastigote (TCT) life forms, a nonreplicative stage 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 epimastigotes and TCT life forms, and we found that H2B.V was preferentially located at the edges of divergent transcriptional strand 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 TCT forms was depleted of H2B.V-enriched peaks in comparison to epimastigote 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.

Highlights

Chromatin is formed from the interactions among DNA, RNAs and proteins
In T. brucei, histone variants mark the start and ending sites of transcription; little is known about whether these proteins change their genome location, expression levels and interactors along life forms and what the impact is of these changes on parasite differentiation and infection
In T. cruzi, the causative agent of Chagas disease, we previously found that the histone variant of H2B is enriched in TCT forms, a nonreplicative and infective form, suggesting that this variant may contribute to the differences in chromatin structure and global transcription rates observed among these life forms

Summary

Introduction

Histones are responsible for establishing the folded chromatin structure, presented as nucleosomes, where each one contains two dimers of H2A-H2B and one tetramer of H3-H4. Changes in chromatin conformation caused by histone posttranslational modifications (PTMs) and variant histone deposition can affect interactions in chromatin structure and gene expression [1,2]. Aside from canonical histones, differ in primary structure and may be located in specific genomic regions and tissues. CENP-A is a histone variant of histone H3 that is located at centromeres [3]. H2A.Z is present in diverse organisms, destabilizes nucleosome structure and is implicated in transcription activation [4,5]. Few H2B variants have been identified in eukaryotes, including TH2B, which is involved in the cell cycle of germinative mouse male cells [6]; a H2B.Z involved in gene expression in apicomplexans [7], and a H2B.V in trypanosomatids [8], which will be further explored below

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