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Recent advances in malaria genomics and epigenomics

View Article: PubMed Central - PubMed

ABSTRACT

Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.

No MeSH data available.


Related in: MedlinePlus

Malaria parasite genomic components involved in pathogenesis. a The expression of invasion-related genes is regulated through epigenetic and post-transcriptional mechanisms. Bromodomain protein 2 (BDP2) binds to H3K9ac marks within the promoter region of genes associated with red blood cell (RBC) invasion (as well as other gene families not depicted here [31]), enabling their transcription. This is likely achieved through the recruitment of BDP1 and transcription factors (TFs) of the ApiAP2 family. Following transcription during the trophozoite stage, mRNAs encoding invasion-related proteins are bound by ALBA1 functioning as translation repressor. After progression to the schizont stage, ALBA1 is released, allowing the timely synthesis of proteins required for merozoite invasion of RBCs. b Experimental findings either directly from studies on ap2-g or from epigenetically regulated var genes are suggestive of an epigenetically controlled mechanism regulating ap2-g transcription. In sexually committed parasites, ap2-g is characterized by H3K4me2/3 and H3K9ac histone marks and most likely contains histone variants H2A.Z and H2B.Z located in its promoter region. BDPs are believed to bind to H3K9ac, facilitating ap2-g transcription. ApiAP2-G drives expression of genes required for sexual development through binding to a 6/8-mer upstream DNA motif. ap2-g expression itself is believed to be multiplied through an autoregulatory feedback loop where ApiAP2-G binds to its own promoter that also contains ApiAP2-G motifs. In asexual blood-stage parasites, ap2-g is transcriptionally silenced by heterochromatin protein 1 (HP1) binding to H3K9me3 histone marks (located in repressive loci in the nuclear periphery). Histone deacetylase 2 (HDA2) catalyzes the removal of H3K9ac from active ap2-g, facilitating ap2-g silencing. c Monoallelic expression of one of the approximately 60 members of the erythrocyte membrane protein 1 (EMP1)-encoding var genes is regulated through epigenetic silencing of all but one var gene copy. The active var is marked by euchromatin post-translational modifications H3K4me2/3 and H3K9ac and histone variants H2A.Z/H2B.Z located in its promoter region, as well as H3K36me3 covering the whole var gene body but absent from the promoter region. Transcription of noncoding RNAs associated with the active var gene is facilitated by upstream as well as intronic promoters. All other silenced var genes cluster into perinuclear repressive loci and are characterized by HP1 binding to H3K9me3 marks. var gene silencing also involves SET2/vs-dependent placing of H3K36me3 histone marks in promoter regions and is marked by the absence of non-coding RNAs, likely safeguarded through RNaseII exonuclease activity. In addition, other histone code modulators such as HDA2, SET10, and SIR2A/B are likely involved in epigenetic var gene regulation. d Mutations in kelch13 (K13) were found to be the major contributors to artemisinin (ART) resistance identified in drug-resistant parasites in the laboratory as well as in field isolates. kelch13 mutations appear to arise in a complex array of background mutations (that is, mutations in genes encoding ferredoxin (FD), apicomplast ribosomal protein S10 (ARPS10), multidrug resistance protein 2 (MDR2), and chloroquine resistance transporter (CRT)), not yet detected in African parasites. In addition, elevated phosphatidylinositol-3-kinase (PI3K) levels have been observed in ART-resistant parasites and PI3K signaling has been implicated to impact on the unfolded protein response observed in ART-resistant parasites. H2A.Z/H2B.Z, orange/yellow-paired quarter circles; H3K4me2/3, light green circles; H3K9ac, dark green circles; H3K9me3, red circles; H3K36me3, blue circles; canonical nucleosomes, grey globes; ApiAP2-G binding motif; light blue line; ncRNAs, wobbly red lines; mRNAs, wobbly black lines. AP2n other TFs belonging to the ApiAP2 DNA binding protein family, ncRNA non-coding RNA, TFs transcription factors
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Fig3: Malaria parasite genomic components involved in pathogenesis. a The expression of invasion-related genes is regulated through epigenetic and post-transcriptional mechanisms. Bromodomain protein 2 (BDP2) binds to H3K9ac marks within the promoter region of genes associated with red blood cell (RBC) invasion (as well as other gene families not depicted here [31]), enabling their transcription. This is likely achieved through the recruitment of BDP1 and transcription factors (TFs) of the ApiAP2 family. Following transcription during the trophozoite stage, mRNAs encoding invasion-related proteins are bound by ALBA1 functioning as translation repressor. After progression to the schizont stage, ALBA1 is released, allowing the timely synthesis of proteins required for merozoite invasion of RBCs. b Experimental findings either directly from studies on ap2-g or from epigenetically regulated var genes are suggestive of an epigenetically controlled mechanism regulating ap2-g transcription. In sexually committed parasites, ap2-g is characterized by H3K4me2/3 and H3K9ac histone marks and most likely contains histone variants H2A.Z and H2B.Z located in its promoter region. BDPs are believed to bind to H3K9ac, facilitating ap2-g transcription. ApiAP2-G drives expression of genes required for sexual development through binding to a 6/8-mer upstream DNA motif. ap2-g expression itself is believed to be multiplied through an autoregulatory feedback loop where ApiAP2-G binds to its own promoter that also contains ApiAP2-G motifs. In asexual blood-stage parasites, ap2-g is transcriptionally silenced by heterochromatin protein 1 (HP1) binding to H3K9me3 histone marks (located in repressive loci in the nuclear periphery). Histone deacetylase 2 (HDA2) catalyzes the removal of H3K9ac from active ap2-g, facilitating ap2-g silencing. c Monoallelic expression of one of the approximately 60 members of the erythrocyte membrane protein 1 (EMP1)-encoding var genes is regulated through epigenetic silencing of all but one var gene copy. The active var is marked by euchromatin post-translational modifications H3K4me2/3 and H3K9ac and histone variants H2A.Z/H2B.Z located in its promoter region, as well as H3K36me3 covering the whole var gene body but absent from the promoter region. Transcription of noncoding RNAs associated with the active var gene is facilitated by upstream as well as intronic promoters. All other silenced var genes cluster into perinuclear repressive loci and are characterized by HP1 binding to H3K9me3 marks. var gene silencing also involves SET2/vs-dependent placing of H3K36me3 histone marks in promoter regions and is marked by the absence of non-coding RNAs, likely safeguarded through RNaseII exonuclease activity. In addition, other histone code modulators such as HDA2, SET10, and SIR2A/B are likely involved in epigenetic var gene regulation. d Mutations in kelch13 (K13) were found to be the major contributors to artemisinin (ART) resistance identified in drug-resistant parasites in the laboratory as well as in field isolates. kelch13 mutations appear to arise in a complex array of background mutations (that is, mutations in genes encoding ferredoxin (FD), apicomplast ribosomal protein S10 (ARPS10), multidrug resistance protein 2 (MDR2), and chloroquine resistance transporter (CRT)), not yet detected in African parasites. In addition, elevated phosphatidylinositol-3-kinase (PI3K) levels have been observed in ART-resistant parasites and PI3K signaling has been implicated to impact on the unfolded protein response observed in ART-resistant parasites. H2A.Z/H2B.Z, orange/yellow-paired quarter circles; H3K4me2/3, light green circles; H3K9ac, dark green circles; H3K9me3, red circles; H3K36me3, blue circles; canonical nucleosomes, grey globes; ApiAP2-G binding motif; light blue line; ncRNAs, wobbly red lines; mRNAs, wobbly black lines. AP2n other TFs belonging to the ApiAP2 DNA binding protein family, ncRNA non-coding RNA, TFs transcription factors

Mentions: Epigenetics lies at the very heart of gene expression, regulating access of the transcriptional machinery to chromatin [20] via (1) post-translational modifications (PTMs) of histones, (2) nucleosome occupancy, and (3) global chromatin architecture. In the past decade, various histone PTMs have been identified throughout the Plasmodium lifecycle (reviewed in [21]) and the existing catalog of modifications in Pf was recently extended to 232 distinct PTMs, 88 unique to Plasmodium [22]. The majority of detected PTMs show dynamic changes across the intra-erythrocytic development cycle (IDC), likely mirroring changes within chromatin organization linked to its transcriptional status. Methylation and acetylation of N-terminal histone tails are by far the most studied regulatory PTMs, linked either to a transcriptionally active chromatin structure (that is, euchromatin) or to transcriptionally inert heterochromatin. In Pf, various genes encoding putative epigenetic modulators (that is, proteins catalyzing either the addition or removal of histone PTM marks) have been identified [23], but only a few have been subjected to more detailed investigation [24, 25]. Many of the histone modifiers are essential for Plasmodium development, making them a promising target for antimalarial drugs [26]. In Pf, conditional knockdown of HDA2, a histone lysine deacetylase (HDAC) catalyzing the removal of acetyl groups from acetylated histone 3 lysine 9 (H3K9ac), resulted in elevated H3K9ac levels in previously defined heterochromatin regions [27]. H3K9ac is an epigenetic mark associated with transcriptionally active euchromatin [28] and HDA2 depletion resulted in the transcriptional activation of genes located in heterochromatin regions, leading to impaired asexual growth and an increased gametocyte conversion [27]. Interestingly, genes found to be dysregulated by HDA2 knockdown are also known to be associated with HP1, a key epigenetic player binding to tri-methylated H3K9 (H3K9me3), linked to transcriptionally repressed chromatin. Strikingly, conditional knockdown of PfHP1 recapitulated, to a much greater extent, the phenotype observed in HDA2-knockdown mutants [29]. HP1 is believed to act as a recruitment platform for histone lysine methyltransferases (HKMTs), required for maintenance and spreading of H3K9me3 marks [30], which is consistent with the reduction of H3K9me3 observed in HP1 knockdown cells [29]. In addition, bromodomain protein 1 (BDP1) was found to bind to H3K9ac and H3K14ac marks within transcription start sites (TSSs) in Pf, among them predominantly invasion-related genes (Fig. 3a), and BDP1-knockdown parasites consistently failed to invade new erythrocytes. BDP1 also appears to act as a recruitment platform for other effector proteins such as BDP2 and members of the apicomplexan AP2 (ApiAP2) transcription factor family [31].Fig. 3


Recent advances in malaria genomics and epigenomics
Malaria parasite genomic components involved in pathogenesis. a The expression of invasion-related genes is regulated through epigenetic and post-transcriptional mechanisms. Bromodomain protein 2 (BDP2) binds to H3K9ac marks within the promoter region of genes associated with red blood cell (RBC) invasion (as well as other gene families not depicted here [31]), enabling their transcription. This is likely achieved through the recruitment of BDP1 and transcription factors (TFs) of the ApiAP2 family. Following transcription during the trophozoite stage, mRNAs encoding invasion-related proteins are bound by ALBA1 functioning as translation repressor. After progression to the schizont stage, ALBA1 is released, allowing the timely synthesis of proteins required for merozoite invasion of RBCs. b Experimental findings either directly from studies on ap2-g or from epigenetically regulated var genes are suggestive of an epigenetically controlled mechanism regulating ap2-g transcription. In sexually committed parasites, ap2-g is characterized by H3K4me2/3 and H3K9ac histone marks and most likely contains histone variants H2A.Z and H2B.Z located in its promoter region. BDPs are believed to bind to H3K9ac, facilitating ap2-g transcription. ApiAP2-G drives expression of genes required for sexual development through binding to a 6/8-mer upstream DNA motif. ap2-g expression itself is believed to be multiplied through an autoregulatory feedback loop where ApiAP2-G binds to its own promoter that also contains ApiAP2-G motifs. In asexual blood-stage parasites, ap2-g is transcriptionally silenced by heterochromatin protein 1 (HP1) binding to H3K9me3 histone marks (located in repressive loci in the nuclear periphery). Histone deacetylase 2 (HDA2) catalyzes the removal of H3K9ac from active ap2-g, facilitating ap2-g silencing. c Monoallelic expression of one of the approximately 60 members of the erythrocyte membrane protein 1 (EMP1)-encoding var genes is regulated through epigenetic silencing of all but one var gene copy. The active var is marked by euchromatin post-translational modifications H3K4me2/3 and H3K9ac and histone variants H2A.Z/H2B.Z located in its promoter region, as well as H3K36me3 covering the whole var gene body but absent from the promoter region. Transcription of noncoding RNAs associated with the active var gene is facilitated by upstream as well as intronic promoters. All other silenced var genes cluster into perinuclear repressive loci and are characterized by HP1 binding to H3K9me3 marks. var gene silencing also involves SET2/vs-dependent placing of H3K36me3 histone marks in promoter regions and is marked by the absence of non-coding RNAs, likely safeguarded through RNaseII exonuclease activity. In addition, other histone code modulators such as HDA2, SET10, and SIR2A/B are likely involved in epigenetic var gene regulation. d Mutations in kelch13 (K13) were found to be the major contributors to artemisinin (ART) resistance identified in drug-resistant parasites in the laboratory as well as in field isolates. kelch13 mutations appear to arise in a complex array of background mutations (that is, mutations in genes encoding ferredoxin (FD), apicomplast ribosomal protein S10 (ARPS10), multidrug resistance protein 2 (MDR2), and chloroquine resistance transporter (CRT)), not yet detected in African parasites. In addition, elevated phosphatidylinositol-3-kinase (PI3K) levels have been observed in ART-resistant parasites and PI3K signaling has been implicated to impact on the unfolded protein response observed in ART-resistant parasites. H2A.Z/H2B.Z, orange/yellow-paired quarter circles; H3K4me2/3, light green circles; H3K9ac, dark green circles; H3K9me3, red circles; H3K36me3, blue circles; canonical nucleosomes, grey globes; ApiAP2-G binding motif; light blue line; ncRNAs, wobbly red lines; mRNAs, wobbly black lines. AP2n other TFs belonging to the ApiAP2 DNA binding protein family, ncRNA non-coding RNA, TFs transcription factors
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Fig3: Malaria parasite genomic components involved in pathogenesis. a The expression of invasion-related genes is regulated through epigenetic and post-transcriptional mechanisms. Bromodomain protein 2 (BDP2) binds to H3K9ac marks within the promoter region of genes associated with red blood cell (RBC) invasion (as well as other gene families not depicted here [31]), enabling their transcription. This is likely achieved through the recruitment of BDP1 and transcription factors (TFs) of the ApiAP2 family. Following transcription during the trophozoite stage, mRNAs encoding invasion-related proteins are bound by ALBA1 functioning as translation repressor. After progression to the schizont stage, ALBA1 is released, allowing the timely synthesis of proteins required for merozoite invasion of RBCs. b Experimental findings either directly from studies on ap2-g or from epigenetically regulated var genes are suggestive of an epigenetically controlled mechanism regulating ap2-g transcription. In sexually committed parasites, ap2-g is characterized by H3K4me2/3 and H3K9ac histone marks and most likely contains histone variants H2A.Z and H2B.Z located in its promoter region. BDPs are believed to bind to H3K9ac, facilitating ap2-g transcription. ApiAP2-G drives expression of genes required for sexual development through binding to a 6/8-mer upstream DNA motif. ap2-g expression itself is believed to be multiplied through an autoregulatory feedback loop where ApiAP2-G binds to its own promoter that also contains ApiAP2-G motifs. In asexual blood-stage parasites, ap2-g is transcriptionally silenced by heterochromatin protein 1 (HP1) binding to H3K9me3 histone marks (located in repressive loci in the nuclear periphery). Histone deacetylase 2 (HDA2) catalyzes the removal of H3K9ac from active ap2-g, facilitating ap2-g silencing. c Monoallelic expression of one of the approximately 60 members of the erythrocyte membrane protein 1 (EMP1)-encoding var genes is regulated through epigenetic silencing of all but one var gene copy. The active var is marked by euchromatin post-translational modifications H3K4me2/3 and H3K9ac and histone variants H2A.Z/H2B.Z located in its promoter region, as well as H3K36me3 covering the whole var gene body but absent from the promoter region. Transcription of noncoding RNAs associated with the active var gene is facilitated by upstream as well as intronic promoters. All other silenced var genes cluster into perinuclear repressive loci and are characterized by HP1 binding to H3K9me3 marks. var gene silencing also involves SET2/vs-dependent placing of H3K36me3 histone marks in promoter regions and is marked by the absence of non-coding RNAs, likely safeguarded through RNaseII exonuclease activity. In addition, other histone code modulators such as HDA2, SET10, and SIR2A/B are likely involved in epigenetic var gene regulation. d Mutations in kelch13 (K13) were found to be the major contributors to artemisinin (ART) resistance identified in drug-resistant parasites in the laboratory as well as in field isolates. kelch13 mutations appear to arise in a complex array of background mutations (that is, mutations in genes encoding ferredoxin (FD), apicomplast ribosomal protein S10 (ARPS10), multidrug resistance protein 2 (MDR2), and chloroquine resistance transporter (CRT)), not yet detected in African parasites. In addition, elevated phosphatidylinositol-3-kinase (PI3K) levels have been observed in ART-resistant parasites and PI3K signaling has been implicated to impact on the unfolded protein response observed in ART-resistant parasites. H2A.Z/H2B.Z, orange/yellow-paired quarter circles; H3K4me2/3, light green circles; H3K9ac, dark green circles; H3K9me3, red circles; H3K36me3, blue circles; canonical nucleosomes, grey globes; ApiAP2-G binding motif; light blue line; ncRNAs, wobbly red lines; mRNAs, wobbly black lines. AP2n other TFs belonging to the ApiAP2 DNA binding protein family, ncRNA non-coding RNA, TFs transcription factors
Mentions: Epigenetics lies at the very heart of gene expression, regulating access of the transcriptional machinery to chromatin [20] via (1) post-translational modifications (PTMs) of histones, (2) nucleosome occupancy, and (3) global chromatin architecture. In the past decade, various histone PTMs have been identified throughout the Plasmodium lifecycle (reviewed in [21]) and the existing catalog of modifications in Pf was recently extended to 232 distinct PTMs, 88 unique to Plasmodium [22]. The majority of detected PTMs show dynamic changes across the intra-erythrocytic development cycle (IDC), likely mirroring changes within chromatin organization linked to its transcriptional status. Methylation and acetylation of N-terminal histone tails are by far the most studied regulatory PTMs, linked either to a transcriptionally active chromatin structure (that is, euchromatin) or to transcriptionally inert heterochromatin. In Pf, various genes encoding putative epigenetic modulators (that is, proteins catalyzing either the addition or removal of histone PTM marks) have been identified [23], but only a few have been subjected to more detailed investigation [24, 25]. Many of the histone modifiers are essential for Plasmodium development, making them a promising target for antimalarial drugs [26]. In Pf, conditional knockdown of HDA2, a histone lysine deacetylase (HDAC) catalyzing the removal of acetyl groups from acetylated histone 3 lysine 9 (H3K9ac), resulted in elevated H3K9ac levels in previously defined heterochromatin regions [27]. H3K9ac is an epigenetic mark associated with transcriptionally active euchromatin [28] and HDA2 depletion resulted in the transcriptional activation of genes located in heterochromatin regions, leading to impaired asexual growth and an increased gametocyte conversion [27]. Interestingly, genes found to be dysregulated by HDA2 knockdown are also known to be associated with HP1, a key epigenetic player binding to tri-methylated H3K9 (H3K9me3), linked to transcriptionally repressed chromatin. Strikingly, conditional knockdown of PfHP1 recapitulated, to a much greater extent, the phenotype observed in HDA2-knockdown mutants [29]. HP1 is believed to act as a recruitment platform for histone lysine methyltransferases (HKMTs), required for maintenance and spreading of H3K9me3 marks [30], which is consistent with the reduction of H3K9me3 observed in HP1 knockdown cells [29]. In addition, bromodomain protein 1 (BDP1) was found to bind to H3K9ac and H3K14ac marks within transcription start sites (TSSs) in Pf, among them predominantly invasion-related genes (Fig. 3a), and BDP1-knockdown parasites consistently failed to invade new erythrocytes. BDP1 also appears to act as a recruitment platform for other effector proteins such as BDP2 and members of the apicomplexan AP2 (ApiAP2) transcription factor family [31].Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Malaria continues to impose a significant disease burden on low- and middle-income countries in the tropics. However, revolutionary progress over the last 3 years in nucleic acid sequencing, reverse genetics, and post-genome analyses has generated step changes in our understanding of malaria parasite (Plasmodium spp.) biology and its interactions with its host and vector. Driven by the availability of vast amounts of genome sequence data from Plasmodium species strains, relevant human populations of different ethnicities, and mosquito vectors, researchers can consider any biological component of the malarial process in isolation or in the interactive setting that is infection. In particular, considerable progress has been made in the area of population genomics, with Plasmodium falciparum serving as a highly relevant model. Such studies have demonstrated that genome evolution under strong selective pressure can be detected. These data, combined with reverse genetics, have enabled the identification of the region of the P. falciparum genome that is under selective pressure and the confirmation of the functionality of the mutations in the kelch13 gene that accompany resistance to the major frontline antimalarial, artemisinin. Furthermore, the central role of epigenetic regulation of gene expression and antigenic variation and developmental fate in P. falciparum is becoming ever clearer. This review summarizes recent exciting discoveries that genome technologies have enabled in malaria research and highlights some of their applications to healthcare. The knowledge gained will help to develop surveillance approaches for the emergence or spread of drug resistance and to identify new targets for the development of antimalarial drugs and perhaps vaccines.

No MeSH data available.


Related in: MedlinePlus