scholarly journals A 5700 year-old human genome and oral microbiome from chewed birch pitch

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Theis Z. T. Jensen ◽  
Jonas Niemann ◽  
Katrine Højholt Iversen ◽  
Anna K. Fotakis ◽  
Shyam Gopalakrishnan ◽  
...  
Keyword(s):  
Human Genome ◽  
Epstein Barr Virus ◽  
Oral Microbiome ◽  
Dark Skin ◽  
Hunter Gatherers ◽  
Barr Virus ◽  
Brown Hair ◽  
Epstein Barr ◽  
The Individual ◽  
Blue Eyes

AbstractThe rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.

scholarly journals Stone Age "chewing gum" yields 5,700 year-old human genome and oral microbiome

2018 ◽  
Author(s):  
Theis ZT Jensen ◽  
Jonas Niemann ◽  
Katrine Hoejholt Iversen ◽  
Anna K Fotakis ◽  
Shyam Gopalakrishnan ◽  
...  
Keyword(s):  
Human Genome ◽  
Oral Microbiome ◽  
Chewing Gum ◽  
Average Depth ◽  
Stone Age ◽  
Dark Skin ◽  
Hunter Gatherers ◽  
The Individual ◽  
Blue Eyes ◽  
Microbial Dna

We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous "chewing gum" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,858-5,661 cal. BP (GrM-13305; 5,007+/-11). We sequenced the genome to an average depth-of-coverage of 2.3x and find that the individual who chewed the resin was female and genetically more closely related to western hunter-gatherers from mainland Europe, than hunter-gatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

scholarly journals Epstein-Barr virus nuclear antigen 2 (EBNA2) extensively rewires the human chromatin landscape at autoimmune risk loci

2020 ◽  
Author(s):  
Ted Hong ◽  
Omer Donmez ◽  
Daniel Miller ◽  
Carmy Forney ◽  
Michael Lape ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Human Genome ◽  
Genetic Risk ◽  
Epstein Barr Virus ◽  
Critical Role ◽  
Chromatin Accessibility ◽  
Nuclear Antigen ◽  
Barr Virus ◽  
Chromatin Looping ◽  
Epstein Barr

AbstractThe interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein-Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we demonstrated that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding, in a B cell line that was 1) uninfected, 2) infected with a strain of EBV lacking EBNA2, or 3) infected with a strain that expresses EBNA2. We identified >400 EBNA2-dependent differentially expressed human genes and >4,000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed >3,000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP-seq data revealed >2,000 regions where EBNA2 altered chromatin looping interactions. Importantly, autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events. We present examples of autoimmune risk genotype-dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1 and CD80. Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.

scholarly journals Intron Retention May Regulate Expression of Epstein-Barr Virus Nuclear Antigen 3 Family Genes

1999 ◽  
Vol 73 (2) ◽  
pp. 1195-1204 ◽  
Author(s):  
Norbert Kienzle ◽  
David B. Young ◽  
Daphne Liaskou ◽  
Marion Buck ◽  
Sonia Greco ◽  
...  
Keyword(s):  
Protein Expression ◽  
Epstein Barr Virus ◽  
Intron Retention ◽  
Fine Tuning ◽  
Nuclear Antigen ◽  
Cell Fractionation ◽  
Flag Epitope ◽  
Barr Virus ◽  
Epstein Barr ◽  
The Individual

ABSTRACT The nuclear antigen 3 family genes (EBNA-3, EBNA-4, and EBNA-6) of Epstein-Barr virus (EBV) are important for EBV-induced immortalization and survival of B lymphocytes. However, little is known about how the expression of these genes is regulated. Each of the EBNA-3, EBNA-4, and EBNA-6 genes consists of two exons separated by a small intron. Reverse transcriptase PCR assays revealed that the vast majority of the EBNA-3, EBNA-4, and EBNA-6 mRNA, expressed in transfected and EBV-infected B cells, retained intron sequences. Northern blot and S1 protection assays confirmed that most of the EBNA-3 mRNA contained intron. Examination of deletion mutants of EBNA-3 indicated that the EBNA-3 protein was not necessary for intron retention and that there was no splicing silencing element encoded in the EBNA-3 mRNA. Cell fractionation and RNA gradient analysis revealed that the unspliced EBNA 3 family mRNAs were transported into the cytoplasm and associated with the polysomes. However, Western blot analysis of FLAG-epitope tagged EBNA-3 gave no indication of the presence of splice variant protein forms of EBNA-3. In contrast, transiently transfected cells expressing EBNA-3 revealed a sixfold increase in EBNA-3 protein expression from the genomic EBNA-3 gene compared to EBNA-3 cDNA. These data show that the intronic sequences can influence EBNA-3 protein expression and suggest that intron retention may provide a means for the fine-tuning of expression of the individual EBNA 3 family genes.

scholarly journals Epstein–Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci

2021 ◽  
Author(s):  
Ted Hong ◽  
Sreeja Parameswaran ◽  
Omer A. Donmez ◽  
Daniel Miller ◽  
Carmy Forney ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Human Genome ◽  
Genetic Risk ◽  
Epstein Barr Virus ◽  
Chromatin Accessibility ◽  
Nuclear Antigen ◽  
Barr Virus ◽  
Chromatin Looping ◽  
A Genome ◽  
Epstein Barr

The interplay between environmental and genetic factors plays a key role in the development of many autoimmune diseases. In particular, the Epstein–Barr virus (EBV) is an established contributor to multiple sclerosis, lupus, and other disorders. Previously, we showed that the EBV nuclear antigen 2 (EBNA2) transactivating protein occupies up to half of the risk loci for a set of seven autoimmune disorders. To further examine the mechanistic roles played by EBNA2 at these loci on a genome-wide scale, we globally examined gene expression, chromatin accessibility, chromatin looping, and EBNA2 binding in a B cell line that was (1) uninfected, (2) infected with a strain of EBV lacking EBNA2, or (3) infected with a strain that expresses EBNA2. We identified more than 400 EBNA2-dependent differentially expressed human genes and more than 5000 EBNA2 binding events in the human genome. ATAC-seq analysis revealed more than 2000 regions in the human genome with EBNA2-dependent chromatin accessibility, and HiChIP data revealed more than 1700 regions where EBNA2 altered chromatin looping interactions. Autoimmune genetic risk loci were highly enriched at the sites of these EBNA2-dependent chromatin-altering events. We present examples of autoimmune risk genotype–dependent EBNA2 events, nominating genetic risk mechanisms for autoimmune risk loci such as ZMIZ1. Taken together, our results reveal important interactions between host genetic variation and EBNA2-driven disease mechanisms. Further, our study highlights a critical role for EBNA2 in rewiring human gene regulatory programs through rearrangement of the chromatin landscape and nominates these interactions as components of genetic mechanisms that influence the risk of multiple autoimmune diseases.

scholarly journals Genetic analysis of the Epstein–Barr virus-coded leader protein EBNA-LP as a co-activator of EBNA2 function

2001 ◽  
Vol 82 (12) ◽  
pp. 3067-3079 ◽  
Author(s):  
Eamon M. McCann ◽  
Gemma L. Kelly ◽  
Alan B. Rickinson ◽  
Andrew I. Bell
Keyword(s):  
Genetic Analysis ◽  
Epstein Barr Virus ◽  
Cell Transformation ◽  
Nuclear Antigen ◽  
Barr Virus ◽  
Lmp1 Expression ◽  
Leader Protein ◽  
Epstein Barr ◽  
The Individual ◽  
Unique Domain

Co-operation between the Epstein–Barr virus (EBV)-coded leader protein EBNA-LP and the nuclear antigen EBNA2 appears to be critical for efficient virus-induced B cell transformation. Here we report the genetic analysis of EBNA-LP function using two transient co-transfection assays of co-operativity, activation of latent membrane protein 1 (LMP1) expression from a resident EBV genome in Akata-BL cells and activation of an EBNA2-responsive reporter construct. Small deletions were introduced into each of five conserved regions (CRs) of EBNA-LP sequence present in type 1 and type 2 EBV strains and in several primate lymphocryptovirus EBNA-LP homologues. Deletions within all three CRs in the EBNA-LP W1W2 repeat domain completely abrogated function, through inhibition of nuclear localization in the cases of CR1 and CR2 but not of CR3; deletions within CR4 and CR5 in the Y1Y2 unique domain had relatively little effect, yet loss of the whole Y2 sequence blocked activity. Alanine substitution of serine residues within potential phosphorylation sites identified two mutants of particular interest. Substitution of three such residues (S34,36,63) within W1W2 not only abrogated EBNA-LP activity but was associated with a complete loss of EBNA2 detectability in co-transfected cells, implying possible destabilization of the co-expressed EBNA2 protein. More importantly the individual substitution of S36 completely blocked EBNA-LP/EBNA2 co-operativity while retaining EBNA2 expression. We infer critical roles for the CR3 domain and for the S36 residue in EBNA-LP’s co-operative function.

scholarly journals Identifying Sites Bound by Epstein-Barr Virus Nuclear Antigen 1 (EBNA1) in the Human Genome: Defining a Position-Weighted Matrix To Predict Sites Bound by EBNA1 in Viral Genomes

2009 ◽  
Vol 83 (7) ◽  
pp. 2930-2940 ◽  
Author(s):  
Lindsay R. Dresang ◽  
David T. Vereide ◽  
Bill Sugden
Keyword(s):  
Dna Binding ◽  
Human Genome ◽  
Binding Sites ◽  
Epstein Barr Virus ◽  
Consensus Sequence ◽  
Nuclear Antigen ◽  
Barr Virus ◽  
Dna Binding Sites ◽  
Weighted Matrix ◽  
Epstein Barr

ABSTRACT We identified binding sites for Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) in the human genome using chromatin immunoprecipitation and microarrays. The sequences for these newly identified sites were used to generate a position-weighted matrix (PWM) for EBNA1's DNA-binding sites. This PWM helped identify additional DNA-binding sites for EBNA1 in the genomes of EBV, Kaposi's sarcoma-associated herpesvirus, and cercopithecine herpesvirus 15 (CeHV-15) (also called herpesvirus papio 15). In particular, a homologue of the Rep* locus in EBV was predicted in the genome of CeHV-15, which is notable because Rep* of EBV was not predicted by the previously developed consensus sequence for EBNA1's binding DNA. The Rep* of CeHV-15 functions as an origin of DNA synthesis in the EBV-positive cell line Raji; this finding thus builds on a set of DNA-binding sites for EBNA1 predicted in silico.

scholarly journals Epstein-Barr Virus BART MicroRNAs Are Produced from a Large Intron prior to Splicing

2008 ◽  
Vol 82 (18) ◽  
pp. 9094-9106 ◽  
Author(s):  
Rachel Hood Edwards ◽  
Aron R. Marquitz ◽  
Nancy Raab-Traub
Keyword(s):  
Epstein Barr Virus ◽  
Barr Virus ◽  
Individual Mirnas ◽  
Sequence Variations ◽  
Large Intron ◽  
Exon 1 ◽  
Alternatively Spliced ◽  
Epstein Barr ◽  
The Individual ◽  
Bart Mirnas

ABSTRACT Latent Epstein-Barr virus (EBV) infection is associated with several lymphoproliferative disorders, including posttransplant lymphoma, Hodgkin's disease, and Burkitt's lymphoma, as well as nasopharyngeal carcinoma (NPC). Twenty-nine microRNAs (miRNAs) have been identified that are transcribed during latent infection from three clusters in the EBV genome. Two of the three clusters of miRNAs are made from the BamHI A rightward transcripts (BARTs), a set of alternatively spliced transcripts that are highly abundant in NPC but have not been shown to produce a detectable protein. This study indicates that while the BART miRNAs are located in the first four introns of the transcripts, processing of the pre-miRNAs from the primary transcript occurs prior to completion of the splicing reaction. Additionally, production of the BART miRNAs correlates with accumulation of a spliced mRNA in which exon 1 is joined directly to exon 3, suggesting that this form of the transcript may favor production of miRNAs. Sequence variations and processing of pre-miRNAs to the mature form also may account for various differences in miRNA abundance. Importantly, residual intronic pieces that result from processing of the pre-miRNAs were detected in the nucleus. The predicted structures of these pieces suggest there is a bias or temporal pattern to the production of the individual pre-miRNAs. These findings indicate that multiple factors contribute to the production of the BART miRNAs and to the apparent differences in abundance between the individual miRNAs of the cluster.

scholarly journals Epstein-Barr Virus Episome Physically Interacts with Active Regions of the Host Genome in Lymphoblastoid Cells

2020 ◽  
Vol 94 (24) ◽  
Author(s):  
Luopin Wang ◽  
Jun Laing ◽  
Bingyu Yan ◽  
Hufeng Zhou ◽  
Liangru Ke ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Growth ◽  
Human Genome ◽  
Epstein Barr Virus ◽  
Active Regions ◽  
Host Genome ◽  
Lymphoblastoid Cells ◽  
Barr Virus ◽  
Interphase Cells ◽  
Epstein Barr

ABSTRACT The Epstein-Barr virus (EBV) episome is known to interact with the three-dimensional structure of the human genome in infected cells. However, the exact locations of these interactions and their potential functional consequences remain unclear. Recently, high-resolution chromatin conformation capture (Hi-C) assays in lymphoblastoid cells have become available, enabling us to precisely map the contacts between the EBV episome(s) and the human host genome. Using available Hi-C data at a 10-kb resolution, we have identified 15,000 reproducible contacts between EBV episome(s) and the human genome. These contacts are highly enriched in chromatin regions denoted by typical or super enhancers and active markers, including histone H3K27ac and H3K4me1. Additionally, these contacts are highly enriched at loci bound by host transcription factors that regulate B cell growth (e.g., IKZF1 and RUNX3), factors that enhance cell proliferation (e.g., HDGF), or factors that promote viral replication (e.g., NBS1 and NFIC). EBV contacts show nearly 2-fold enrichment in host regions bound by EBV nuclear antigen 2 (EBNA2) and EBNA3 transcription factors. Circular chromosome conformation capture followed by sequencing (4C-seq) using the EBV origin of plasmid replication (oriP) as a “bait” in lymphoblastoid cells further confirmed contacts with active chromatin regions. Collectively, our analysis supports interactions between EBV episome(s) and active regions of the human genome in lymphoblastoid cells. IMPORTANCE EBV is associated with ∼200,000 cancers each year. In vitro, EBV can transform primary human B lymphocytes into immortalized cell lines. EBV-encoded proteins, along with noncoding RNAs and microRNAs, hijack cellular proteins and pathways to control cell growth. EBV nuclear proteins usurp normal transcriptional programs to activate the expression of key oncogenes, including MYC, to provide a proliferation signal. EBV nuclear antigens also repress CDKN2A to suppress senescence. EBV membrane protein activates NF-κB to provide survival signals. EBV genomes are maintained by EBNA1, which tethers EBV episomes to the host chromosomes during mitosis. However, little is known about where EBV episomes are located in interphase cells. In interphase cells, EBV promoters drive the expression of latency genes, while oriP functions as an enhancer for these promoters. In this study, integrative analyses of published lymphoblastoid cell line (LCL) Hi-C data and our 4C-seq experiments position EBV episomes to host genomes with active epigenetic marks. These contact points were significantly enriched for super enhancers. The close proximity of EBV episomes and the super enhancers that are enriched for transcription cofactors or mediators in lymphoblasts may benefit EBV gene expression, suggesting a novel mechanism of transcriptional activation.

scholarly journals The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation

2017 ◽  
Vol 92 (3) ◽  
Author(s):  
Stephanie A. Moquin ◽  
Sean Thomas ◽  
Sean Whalen ◽  
Alix Warburton ◽  
Samantha G. Fernandez ◽  
...  
Keyword(s):  
Human Genome ◽  
Epstein Barr Virus ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Transcription Start Sites ◽  
Barr Virus ◽  
Molecular Events ◽  
Epstein Barr ◽  
Human Side ◽  
Three Dimensional Space

ABSTRACT The human genome is structurally organized in three-dimensional space to facilitate functional partitioning of transcription. We learned that the latent episome of the human Epstein-Barr virus (EBV) preferentially associates with gene-poor chromosomes and avoids gene-rich chromosomes. Kaposi's sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not. Contacts on the EBV side localize to OriP, the latent origin of replication. This genetic element and the EBNA1 protein that binds there are sufficient to reconstitute chromosome association preferences of the entire episome. Contacts on the human side localize to gene-poor and AT-rich regions of chromatin distant from transcription start sites. Upon reactivation from latency, however, the episome moves away from repressive heterochromatin and toward active euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during reactivation. Involvement of myriad interchromosomal associations also suggests a role for this type of long-range association in gene regulation. IMPORTANCE The human genome is structurally organized in three-dimensional space, and this structure functionally affects transcriptional activity. We set out to investigate whether a double-stranded DNA virus, Epstein-Barr virus (EBV), uses mechanisms similar to those of the human genome to regulate transcription. We found that the EBV genome associates with repressive compartments of the nucleus during latency and with active compartments during reactivation. This study advances our knowledge of the EBV life cycle, adding three-dimensional relocalization as a novel component to the molecular events that occur during reactivation. Furthermore, the data add to our understanding of nuclear compartments, showing that disperse interchromosomal interactions may be important for regulating transcription.

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