scholarly journals A regulatory network of a piRNA and lncRNA initiates responder and trailer piRNA formation during embryonic development of Aedes mosquitoes

2020 ◽  
Author(s):  
Valerie Betting ◽  
Joep Joosten ◽  
Rebecca Halbach ◽  
Melissa Thaler ◽  
Pascal Miesen ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Regulatory Network ◽  
Target Display ◽  
Seed Region ◽  
Base Pairing ◽  
Aedes Mosquitoes ◽  
Single Target ◽  
Somatic Tissues ◽  
Pirna Pathway ◽  
High Degree

ABSTRACTPIWI-interacting (pi)RNAs are small silencing RNAs that are crucial for the defense against transposable elements in germline tissues of animals. In the mosquito Aedes aegypti, the piRNA pathway also contributes to gene regulation in somatic tissues, illustrating additional roles for piRNAs and PIWI proteins besides transposon repression. Here, we identify a highly abundant, endogenous piRNA (propiR1) that associates with both Piwi4 and Piwi5. PropiR1-mediated target silencing requires base pairing in the seed region with supplemental base pairing at the piRNA 3’ end. Yet, propiR1 strongly represses a single target, the lncRNA AAEL027353 (lnc027353). Slicing of this target initiates the production of responder and trailer piRNAs from the 3’ cleavage fragment. Expression of propiR1 commences early during embryonic development and mediates degradation of maternally provided lnc027353. Both propiR1 and its lncRNA target display a high degree of sequence conservation in the closely related Aedes albopictus, underscoring the importance of this regulatory network for mosquito development.

scholarly journals SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jurre A. Steens ◽  
Yifan Zhu ◽  
David W. Taylor ◽  
Jack P. K. Bravo ◽  
Stijn H. P. Prinsen ◽  
...  
Keyword(s):  
Immune Response ◽  
Diagnostic Tool ◽  
Nasal Swab ◽  
Rna Binding ◽  
Seed Region ◽  
Base Pairing ◽  
Specific Detection ◽  
Type Iii ◽  
Single Host ◽  
Target Rna

AbstractCharacteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.

scholarly journals DUX4 Role in Normal Physiology and in FSHD Muscular Dystrophy

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3322
Author(s):  
Emanuele Mocciaro ◽  
Valeria Runfola ◽  
Paola Ghezzi ◽  
Maria Pannese ◽  
Davide Gabellini
Keyword(s):  
Muscular Dystrophy ◽  
Embryonic Development ◽  
Transcriptional Activation ◽  
Current Knowledge ◽  
Relevant Information ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Healthy Humans ◽  
Somatic Tissues ◽  
Key Factor ◽  
Development Regulation

In the last decade, the sequence-specific transcription factor double homeobox 4 (DUX4) has gone from being an obscure entity to being a key factor in important physiological and pathological processes. We now know that expression of DUX4 is highly regulated and restricted to the early steps of embryonic development, where DUX4 is involved in transcriptional activation of the zygotic genome. While DUX4 is epigenetically silenced in most somatic tissues of healthy humans, its aberrant reactivation is associated with several diseases, including cancer, viral infection and facioscapulohumeral muscular dystrophy (FSHD). DUX4 is also translocated, giving rise to chimeric oncogenic proteins at the basis of sarcoma and leukemia forms. Hence, understanding how DUX4 is regulated and performs its activity could provide relevant information, not only to further our knowledge of human embryonic development regulation, but also to develop therapeutic approaches for the diseases associated with DUX4. Here, we summarize current knowledge on the cellular and molecular processes regulated by DUX4 with a special emphasis on FSHD muscular dystrophy.

scholarly journals Golden hamster piRNAs are necessary for early embryonic development and establishment of spermatogonia

2021 ◽  
Author(s):  
Zuzana Loubalova ◽  
Helena Fulka ◽  
Filip Horvat ◽  
Josef Pasulka ◽  
Radek Malik ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Golden Hamster ◽  
Developmental Competence ◽  
Early Embryonic Development ◽  
Spermatogenic Cells ◽  
Adaptive Nature ◽  
Pirna Pathway

ABSTRACTPIWI-associated RNAs (piRNAs) support the germline by suppressing retrotransposons and genes. In mice, piRNAs are essential for spermatogenesis but not oogenesis. To test how this applies to other mammals, we deleted Mov10l1 helicase in golden hamster, whose piRNA pathway is configured more similarly to that of other mammals. Mov10l1−/− male hamsters showed impaired establishment of spermatogonia accompanied by transcriptome dysregulation and a surge in MYSERV retrotransposon expression. The rare viable spermatogenic cells showed a meiotic failure phenotype like Mov10l1−/− mice. Female Mov10l1−/− hamsters were sterile due to post-meiotic loss of developmental competence in zygotes. Unique phenotypes of Mov10l1−/− hamsters demonstrate the adaptive nature of piRNA-mediated control of genes and retrotransposons in order to confront emerging genomic threats or acquire new physiological roles.

scholarly journals Chemical Modification of the siRNA Seed Region Suppresses Off-Target Effects by Steric Hindrance to Base-Pairing with Targets

ACS Omega ◽  
2017 ◽  
Vol 2 (5) ◽  
pp. 2055-2064 ◽  
Author(s):  
Hanna Iribe ◽  
Kengo Miyamoto ◽  
Tomoko Takahashi ◽  
Yoshiaki Kobayashi ◽  
Jastina Leo ◽  
...  
Keyword(s):  
Chemical Modification ◽  
Steric Hindrance ◽  
Seed Region ◽  
Base Pairing ◽  
Target Effects

Alterations in Ecdysone Content during the Post-Embryonic Development of Chironomus thummi: Correlations with Chromosomal Puffing

1978 ◽  
Vol 33 (7-8) ◽  
pp. 557-560 ◽  
Author(s):  
M. Valentin ◽  
W. E. Bollenbacher ◽  
L. I. Gilbert ◽  
H. Kroeger
Keyword(s):  
High Pressure ◽  
Liquid Chromatography ◽  
Embryonic Development ◽  
Fresh Weight ◽  
Pupal Development ◽  
Radioimmune Assay ◽  
Chromosomal Site ◽  
Titer Curve ◽  
High Degree ◽  
Chironomus Thummi

Abstract The ecdysone titer of larvae and pupae of Chironomus thummi was determined by radioimmune assay (RIA) and revealed a concentration of about 150 ng/g fresh weigth in late third instar larvae and a peak of more than 450 ng/g fresh weight just preceding pupation. The ecdysone titer curve shows a high degree of correlation with previously observed puffing activity at the ecdysone sensitive chromosomal site IIIdl. Further, β-ecdysone is the only endogenous ecdysone detected by high pressure liquid chromatography during larval-pupal development. It was also observed that developmentally arrested Chironomus contain less ecdysone than “normal” larvae.

scholarly journals Somatic piRNAs and Transposons are Differentially Expressed Coincident with Skeletal Muscle Atrophy and Programmed Cell Death

2021 ◽  
Vol 12 ◽  
Author(s):  
Junko Tsuji ◽  
Travis Thomson ◽  
Christine Brown ◽  
Subhanita Ghosh ◽  
William E. Theurkauf ◽  
...  
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Skeletal Muscle Atrophy ◽  
Rna Seq ◽  
Developmentally Regulated ◽  
Transposon Silencing ◽  
Ping Pong ◽  
Somatic Tissues ◽  
Oxidation Resistant ◽  
Pirna Pathway

PIWI-interacting RNAs (piRNAs) are small single-stranded RNAs that can repress transposon expression via epigenetic silencing and transcript degradation. They have been identified predominantly in the ovary and testis, where they serve essential roles in transposon silencing in order to protect the integrity of the genome in the germline. The potential expression of piRNAs in somatic cells has been controversial. In the present study we demonstrate the expression of piRNAs derived from both genic and transposon RNAs in the intersegmental muscles (ISMs) from the tobacco hawkmoth Manduca sexta. These piRNAs are abundantly expressed, ∼27 nt long, map antisense to transposons, are oxidation resistant, exhibit a 5’ uridine bias, and amplify via the canonical ping-pong pathway. An RNA-seq analysis demonstrated that 19 piRNA pathway genes are expressed in the ISMs and are developmentally regulated. The abundance of piRNAs does not change when the muscles initiate developmentally-regulated atrophy, but are repressed coincident with the commitment of the muscles undergo programmed cell death at the end of metamorphosis. This change in piRNA expression is correlated with the repression of several retrotransposons and the induction of specific DNA transposons. The developmentally-regulated changes in the expression of piRNAs, piRNA pathway genes, and transposons are all regulated by 20-hydroxyecdysone, the steroid hormone that controls the timing of ISM death. Taken together, these data provide compelling evidence for the existence of piRNA in somatic tissues and suggest that they may play roles in developmental processes such as programmed cell death.

scholarly journals Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Martin H Fabry ◽  
Federica A Falconio ◽  
Fadwa Joud ◽  
Emily K Lythgoe ◽  
Benjamin Czech ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Germ Cells ◽  
Genome Stability ◽  
Mobile Element ◽  
Piwi Protein ◽  
Heterochromatin Formation ◽  
Zygotic Transcription ◽  
Time Required ◽  
Pirna Pathway ◽  
Genome Activation

The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal lineage, and this has demonstrated importance in the specification of piRNA source loci and in silencing of I- and P-elements in the germ cells of daughters. Maternally inherited Piwi protein enters somatic nuclei in early embryos prior to zygotic genome activation and persists therein for roughly half of the time required to complete embryonic development. To investigate the role of the piRNA pathway in the embryonic soma, we created a conditionally unstable Piwi protein. This enabled maternally deposited Piwi to be cleared from newly laid embryos within 30 minutes and well ahead of the activation of zygotic transcription. Examination of RNA and protein profiles over time, and correlation with patterns of H3K9me3 deposition, suggests a role for maternally deposited Piwi in attenuating zygotic transposon expression in somatic cells of the developing embryo. In particular, robust deposition of piRNAs targeting roo, an element whose expression is mainly restricted to embryonic development, results in the deposition of transient heterochromatic marks at active roo insertions. We hypothesize that roo, an extremely successful mobile element, may have adopted a lifestyle of expression in the embryonic soma to evade silencing in germ cells.

scholarly journals Bovine piRNA-like RNAs are associated with both transposable elements and mRNAs

Reproduction ◽  
2017 ◽  
Vol 153 (3) ◽  
pp. 305-318 ◽  
Author(s):  
Stewart Russell ◽  
Mehool Patel ◽  
Graham Gilchrist ◽  
Leanne Stalker ◽  
Daniel Gillis ◽  
...  
Keyword(s):  
Large Population ◽  
Early Embryo ◽  
Fold Change ◽  
The Novel ◽  
The Past ◽  
Ping Pong ◽  
Somatic Tissues ◽  
Pirna Pathway ◽  
Generation Sequencing ◽  
Specific Mrna

PIWI proteins and their associated piRNAs have been the focus of intensive research in the past decade; therefore, their participation in the maintenance of genomic integrity during spermatogenesis has been well established. Recent studies have suggested important roles for the PIWI/piRNA system outside of gametogenesis, based on the presence of piRNAs and PIWI proteins in several somatic tissues, cancers, and the early embryo. Here, we investigated the small RNA complement present in bovine gonads, gametes, and embryos through next-generation sequencing. A distinct piRNA population was present in the testis as expected. However, we also found a large population of slightly shorter, 24–27 nt piRNA-like RNA (pilRNAs) in pools of oocytes and zygotes. These oocyte and embryo pilRNAs exhibited many of the canonical characteristics of piRNAs including a 1U bias, the presence of a ‘ping-pong’ signature, genomic clustering, and transposable element targeting. Some of the major transposons targeted by oocyte and zygote pilRNA were from the LINE RTE and ERV1 classes. We also identified pools of pilRNA potentially derived from, or targeted at, specific mRNA sequences. We compared the frequency of these gene-associated pilRNAs to the fold change in the expression of respective mRNAs from two previously reported transcriptome datasets. We observed significant negative correlations between the number of pilRNAs targeting mRNAs, and their fold change in expression between the 4–8 cell and 8–16 cell stages. Together, these results represent one of the first characterizations of the PIWI/piRNA pathway in the translational bovine model, and in the novel context of embryogenesis.

scholarly journals Cyclic peptides can engage a single binding pocket through highly divergent modes

2020 ◽  
Vol 117 (43) ◽  
pp. 26728-26738
Author(s):  
Karishma Patel ◽  
Louise J. Walport ◽  
James L. Walshe ◽  
Paul D. Solomon ◽  
Jason K. K. Low ◽  
...  
Keyword(s):  
Cyclic Peptides ◽  
Cyclic Peptide ◽  
Binding Pocket ◽  
Binding Mode ◽  
Structural Features ◽  
Binding Modes ◽  
Single Target ◽  
Bromodomain Proteins ◽  
High Degree ◽  
Drug Leads

Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 106-fold. Crystal structures of 13 peptide–bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.

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