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  1. Article ; Online: An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans.

    Wahba, Lamia / Hansen, Loren / Fire, Andrew Z

    Developmental cell

    2021  Volume 56, Issue 16, Page(s) 2295–2312.e6

    Abstract: Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and ... ...

    Abstract Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and their ability to silence transcripts with imperfect complementarity have raised several (non-exclusive) models for the underlying drivers of sterility. Here, we report the extranuclear and transferable nature of the sterility driver, its suppression via mutations disrupting the endogenous RNAi and poly-uridylation machinery, and copy-number amplification at the ribosomal DNA locus. In piRNA-deficient animals, several small interfering RNA (siRNA) populations become increasingly overabundant in the generations preceding loss of germline function, including ribosomal siRNAs (risiRNAs). A concomitant increase in uridylated sense rRNA fragments suggests that poly-uridylation may potentiate RNAi-mediated gene silencing of rRNAs. We conclude that loss of the piRNA machinery allows for unchecked amplification of siRNA populations, originating from abundant highly structured RNAs, to deleterious levels.
    MeSH term(s) Animals ; Caenorhabditis elegans ; Epigenesis, Genetic ; Female ; Fertility/genetics ; Oogonial Stem Cells/cytology ; Oogonial Stem Cells/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Ribosomal/genetics ; RNA, Ribosomal/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism
    Chemical Substances RNA, Ribosomal ; RNA, Small Interfering
    Language English
    Publishing date 2021-08-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2021.07.014
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  2. Article ; Online: PLP-1 is essential for germ cell development and germline gene silencing in

    Vishnupriya, Rajaram / Thomas, Linitha / Wahba, Lamia / Fire, Andrew / Subramaniam, Kuppuswamy

    Development (Cambridge, England)

    2020  Volume 147, Issue 22

    Abstract: The germline genome is guarded against invading foreign genetic elements by small RNA-dependent gene-silencing pathways. Components of these pathways localize to, or form distinct aggregates in the vicinity of, germ granules. These components and their ... ...

    Abstract The germline genome is guarded against invading foreign genetic elements by small RNA-dependent gene-silencing pathways. Components of these pathways localize to, or form distinct aggregates in the vicinity of, germ granules. These components and their dynamics in and out of granules are currently being intensively studied. Here, we report the identification of PLP-1, a
    MeSH term(s) Animals ; Animals, Genetically Modified/genetics ; Animals, Genetically Modified/metabolism ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Silencing ; Germ Cells/cytology ; Germ Cells/metabolism ; Male
    Chemical Substances Caenorhabditis elegans Proteins ; DNA-Binding Proteins
    Language English
    Publishing date 2020-11-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.195578
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  3. Article ; Online: The Rs of biology: R-loops and the regulation of regulators.

    Wahba, Lamia / Koshland, Douglas

    Molecular cell

    2013  Volume 50, Issue 5, Page(s) 611–612

    Abstract: Work by Sun et al. (2013) in Arabidopsis reveals an additional function for R-loops in suppressing the expression of a long noncoding RNA and sheds light on the single-stranded DNA binding protein AtNDX that promotes persistence of the R-loop. ...

    Abstract Work by Sun et al. (2013) in Arabidopsis reveals an additional function for R-loops in suppressing the expression of a long noncoding RNA and sheds light on the single-stranded DNA binding protein AtNDX that promotes persistence of the R-loop.
    MeSH term(s) Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Homeodomain Proteins/metabolism ; MADS Domain Proteins/genetics ; RNA, Antisense/genetics ; RNA, Long Noncoding/genetics ; RNA, Plant/genetics ; Transcription, Genetic
    Chemical Substances Arabidopsis Proteins ; Homeodomain Proteins ; MADS Domain Proteins ; RNA, Antisense ; RNA, Long Noncoding ; RNA, Plant
    Language English
    Publishing date 2013-06-06
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2013.05.024
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  4. Article ; Online: An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes.

    Wahba, Lamia / Jain, Nimit / Fire, Andrew Z / Shoura, Massa J / Artiles, Karen L / McCoy, Matthew J / Jeong, Dae-Eun

    mSphere

    2020  Volume 5, Issue 3

    Abstract: In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with ... ...

    Abstract In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the "virome" keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265-269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270-273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.
    MeSH term(s) Animals ; Base Sequence ; Betacoronavirus/genetics ; Chiroptera/virology ; Coronavirus Infections/veterinary ; Coronavirus Infections/virology ; Eutheria/virology ; Lung/virology ; Lung Diseases/veterinary ; Lung Diseases/virology ; Metagenomics/methods ; SARS-CoV-2 ; Sequence Alignment
    Keywords covid19
    Language English
    Publishing date 2020-05-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2379-5042
    ISSN (online) 2379-5042
    DOI 10.1128/mSphere.00160-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

    Lamia Wahba / Nimit Jain / Andrew Z. Fire / Massa J. Shoura / Karen L. Artiles / Matthew J. McCoy / Dae-Eun Jeong

    mSphere, Vol 5, Iss 3, p e00160-

    2020  Volume 20

    Abstract: Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through ...

    Abstract Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the “virome” keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265–269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270–273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.
    Keywords covid ; sars-ncov-2 ; bioinformatics ; coronavirus ; metagenomics ; pangolin ; Microbiology ; QR1-502 ; covid19
    Subject code 612
    Language English
    Publishing date 2020-05-01T00:00:00Z
    Publisher American Society for Microbiology
    Document type Article ; Online
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  6. Article: The homologous recombination machinery modulates the formation of RNA-DNA hybrids and associated chromosome instability.

    Wahba, Lamia / Gore, Steven K / Koshland, Douglas

    eLife

    2013  Volume 2, Page(s) e00505

    Abstract: Genome instability in yeast and mammals is caused by RNA-DNA hybrids that form as a result of defects in different aspects of RNA biogenesis. We report that in yeast mutants defective for transcription repression and RNA degradation, hybrid formation ... ...

    Abstract Genome instability in yeast and mammals is caused by RNA-DNA hybrids that form as a result of defects in different aspects of RNA biogenesis. We report that in yeast mutants defective for transcription repression and RNA degradation, hybrid formation requires Rad51p and Rad52p. These proteins normally promote DNA-DNA strand exchange in homologous recombination. We suggest they also directly promote the DNA-RNA strand exchange necessary for hybrid formation since we observed accumulation of Rad51p at a model hybrid-forming locus. Furthermore, we provide evidence that Rad51p mediates hybridization of transcripts to homologous chromosomal loci distinct from their site of synthesis. This hybrid formation in trans amplifies the genome-destabilizing potential of RNA and broadens the exclusive co-transcriptional models that pervade the field. The deleterious hybrid-forming activity of Rad51p is counteracted by Srs2p, a known Rad51p antagonist. Thus Srs2p serves as a novel anti-hybrid mechanism in vivo. DOI:http://dx.doi.org/10.7554/eLife.00505.001.
    MeSH term(s) Chromosomal Instability ; Chromosomes, Artificial, Yeast ; DNA/genetics ; Homologous Recombination ; Humans ; Nucleic Acid Hybridization ; Polymerase Chain Reaction ; RNA/genetics ; Rad51 Recombinase/metabolism
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2) ; RAD51 protein, human (EC 2.7.7.-) ; Rad51 Recombinase (EC 2.7.7.-)
    Language English
    Publishing date 2013-06-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.00505
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  7. Article ; Online: Recompleting the

    Yoshimura, Jun / Ichikawa, Kazuki / Shoura, Massa J / Artiles, Karen L / Gabdank, Idan / Wahba, Lamia / Smith, Cheryl L / Edgley, Mark L / Rougvie, Ann E / Fire, Andrew Z / Morishita, Shinichi / Schwarz, Erich M

    Genome research

    2019  Volume 29, Issue 6, Page(s) 1009–1022

    Abstract: Caenorhabditis ... ...

    Abstract Caenorhabditis elegans
    MeSH term(s) Animals ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans Proteins/genetics ; Computational Biology/methods ; Genome, Helminth ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Reproducibility of Results
    Chemical Substances Caenorhabditis elegans Proteins
    Language English
    Publishing date 2019-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.244830.118
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  8. Article ; Online: The homologous recombination machinery modulates the formation of RNA–DNA hybrids and associated chromosome instability

    Lamia Wahba / Steven K Gore / Douglas Koshland

    eLife, Vol

    2013  Volume 2

    Abstract: Genome instability in yeast and mammals is caused by RNA–DNA hybrids that form as a result of defects in different aspects of RNA biogenesis. We report that in yeast mutants defective for transcription repression and RNA degradation, hybrid formation ... ...

    Abstract Genome instability in yeast and mammals is caused by RNA–DNA hybrids that form as a result of defects in different aspects of RNA biogenesis. We report that in yeast mutants defective for transcription repression and RNA degradation, hybrid formation requires Rad51p and Rad52p. These proteins normally promote DNA–DNA strand exchange in homologous recombination. We suggest they also directly promote the DNA–RNA strand exchange necessary for hybrid formation since we observed accumulation of Rad51p at a model hybrid-forming locus. Furthermore, we provide evidence that Rad51p mediates hybridization of transcripts to homologous chromosomal loci distinct from their site of synthesis. This hybrid formation in trans amplifies the genome-destabilizing potential of RNA and broadens the exclusive co-transcriptional models that pervade the field. The deleterious hybrid-forming activity of Rad51p is counteracted by Srs2p, a known Rad51p antagonist. Thus Srs2p serves as a novel anti-hybrid mechanism in vivo.
    Keywords R loop ; RNA-DNA hybrid ; Rad51 ; genome instability ; DNA repair ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2013-06-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
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  9. Article ; Online: Identification of a pangolin niche for a 2019-nCoV-like coronavirus through an extensive meta-metagenomic search

    Wahba, Lamia / Jain, Nimit / Fire, Andrew Z. / Artiles, Karen L. / McCoy, Matthew J. / Jeong, Dae-Eun

    bioRxiv

    Abstract: In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which that sequence is present. Many metagenomic datasets are now available, with deep ... ...

    Abstract In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which that sequence is present. Many metagenomic datasets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic dataset can be readily queried using web-based tools, meta-searches through all such datasets are less accessible. In this brief communication, we demonstrate such a meta-meta-genomic approach, examining close matches to the Wuhan coronavirus 2019-nCoV in all high-throughput sequencing datasets in the NCBI Sequence Read Archive accessible with the keyword “virome”. In addition to the homology to bat coronaviruses observed in descriptions of the 2019-nCoV sequence [1,2], we note a strong homology to numerous sequence reads in a metavirome dataset generated from the lungs of deceased Pangolins reported by Liu et al. [3]. Our observations are relevant to discussions of the derivation of 2019-nCoV, and illustrate the utility of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.
    Keywords covid19
    Publisher BioRxiv; MedRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.02.08.939660
    Database COVID19

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  10. Article ; Online: S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation.

    Wahba, Lamia / Costantino, Lorenzo / Tan, Frederick J / Zimmer, Anjali / Koshland, Douglas

    Genes & development

    2016  Volume 30, Issue 11, Page(s) 1327–1338

    Abstract: R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. ... ...

    Abstract R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA:RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae Using this methodology, we identified ∼800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast.
    MeSH term(s) Chromosome Mapping ; DNA, Fungal/metabolism ; Gene Expression ; Genome, Fungal/genetics ; Genomics ; Histones/metabolism ; Poly A/chemistry ; Poly A/genetics ; Poly A/metabolism ; Protein Conformation ; RNA, Fungal/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Single-Strand Specific DNA and RNA Endonucleases/metabolism
    Chemical Substances DNA, Fungal ; Histones ; RNA, Fungal ; Poly A (24937-83-5) ; Single-Strand Specific DNA and RNA Endonucleases (EC 3.1.30.1)
    Language English
    Publishing date 2016-06-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.280834.116
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