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  1. AU="Antonio J Giraldez"
  2. AU="Krutenkova A.P."
  3. AU="Hotaling, Jim"
  4. AU="Saywell, Alex"
  5. AU="Ahmad, Nadia N"
  6. AU=Gonzalez-Periz Ana
  7. AU="Gardner, Colin J"
  8. AU="James, Timothy Y"
  9. AU="Giorgadze, Tamar A"
  10. AU="Laudicina, Vito Armando"
  11. AU="M.Cho, "
  12. AU="Balkan, Ayhan"
  13. AU="Akiyoshi Nakakura"
  14. AU="Yusuf, Amman"
  15. AU="Shastri, Jayanthi S."
  16. AU=McMaster Mary L
  17. AU="Ren, Xiaojie"
  18. AU="Grubbs, Griffin L"
  19. AU="Shen, Jianping"
  20. AU="Thuss-Patience, Peter"
  21. AU="Feng, Qingguo"
  22. AU="Mikayla Schowalter"
  23. AU=Milman Evgenia

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  1. Artikel ; Online: Stage Specific Transcriptomic Analysis and Database for Zebrafish Oogenesis

    Yoel Bogoch / Allison Jamieson-Lucy / Charles E. Vejnar / Karine Levy / Antonio J. Giraldez / Mary C. Mullins / Yaniv M. Elkouby

    Frontiers in Cell and Developmental Biology, Vol

    2022  Band 10

    Abstract: Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte ... ...

    Abstract Oogenesis produces functional eggs and is essential for fertility, embryonic development, and reproduction. The zebrafish ovary is an excellent model to study oogenesis in vertebrates, and recent studies have identified multiple regulators in oocyte development through forward genetic screens, as well as reverse genetics by CRISPR mutagenesis. However, many developmental steps in oogenesis, in zebrafish and other species, remain poorly understood, and their underlying mechanisms are unknown. Here, we take a genomic approach to systematically uncover biological activities throughout oogenesis. We performed transcriptomic analysis on five stages of oogenesis, from the onset of oocyte differentiation through Stage III, which precedes oocyte maturation. These transcriptomes revealed thousands of differentially expressed genes across stages of oogenesis. We analyzed trends of gene expression dynamics along oogenesis, as well as their expression in pair-wise comparisons between stages. We determined their functionally enriched terms, identifying uniquely characteristic biological activities in each stage. These data identified two prominent developmental phases in oocyte differentiation and traced the accumulation of maternally deposited embryonic regulator transcripts in the developing oocyte. Our analysis provides the first molecular description for oogenesis in zebrafish, which we deposit online as a resource for the community. Further, the presence of multiple gene paralogs in zebrafish, and the exclusive curation by many bioinformatic tools of the single paralogs present in humans, challenge zebrafish genomic analyses. We offer an approach for converting zebrafish gene name nomenclature to the human nomenclature for supporting genomic analyses generally in zebrafish. Altogether, our work provides a valuable resource as a first step to uncover oogenesis mechanisms and candidate regulators and track accumulating transcripts of maternal regulators of embryonic development.
    Schlagwörter zebrafish (brachydanio rerio) ; oogenesis ; transcriptomic (RNA-seq) ; oocyte development ; meiosis ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2022-06-01T00:00:00Z
    Verlag Frontiers Media S.A.
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

    Valerie A Tornini / Liyun Miao / Ho-Joon Lee / Timothy Gerson / Sarah E Dube / Valeria Schmidt / François Kroll / Yin Tang / Katherine Du / Manik Kuchroo / Charles E Vejnar / Ariel Alejandro Bazzini / Smita Krishnaswamy / Jason Rihel / Antonio J Giraldez

    eLife, Vol

    2023  Band 12

    Abstract: Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode ... ...

    Abstract Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode micropeptides. However, systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here, we show that two putative lincRNAs (linc-mipep, also called lnc-rps25, and linc-wrb) encode micropeptides with homology to the vertebrate-specific chromatin architectural protein, Hmgn1, and demonstrate that they are required for development of vertebrate-specific brain cell types. Specifically, we show that NMDA receptor-mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes – evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions, with implications for neurodevelopmental disorders and disease.
    Schlagwörter micropeptides ; neurodevelopment ; behavior ; single cell analyses ; cell identity ; gene regulation ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2023-05-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel: miR-430 regulates oriented cell division during neural tube development in zebrafish

    Takacs, Carter M / Antonio J. Giraldez

    Developmental biology. 2016 Jan. 15, v. 409

    2016  

    Abstract: MicroRNAs have emerged as critical regulators of gene expression. Originally shown to regulate developmental timing, microRNAs have since been implicated in a wide range of cellular functions including cell identity, migration and signaling. miRNA-430, ... ...

    Abstract MicroRNAs have emerged as critical regulators of gene expression. Originally shown to regulate developmental timing, microRNAs have since been implicated in a wide range of cellular functions including cell identity, migration and signaling. miRNA-430, the earliest expressed microRNA during zebrafish embryogenesis, is required to undergo morphogenesis and has previously been shown to regulate maternal mRNA clearance, Nodal signaling, and germ cell migration. The functions of miR-430 in brain morphogenesis, however, remain unclear. Herein we find that miR-430 instructs oriented cell divisons in the neural rod required for neural midline formation. Loss of miR-430 function results in mitotic spindle misorientation in the neural rod, failed neuroepithelial integration after cell division, and ectopic cell accumulation in the dorsal neural tube. We propose that miR-430, independently of canonical apicobasal and planar cell polarity (PCP) pathways, coordinates the stereotypical cell divisons that instruct neural tube morphogenesis.
    Schlagwörter Danio rerio ; brain ; cell division ; cell movement ; cell polarity ; embryogenesis ; gene expression ; germ cells ; messenger RNA ; microRNA ; mitotic spindle apparatus ; morphogenesis ; regulator genes
    Sprache Englisch
    Erscheinungsverlauf 2016-0115
    Umfang p. 442-450.
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    ZDB-ID 1114-9
    ISSN 1095-564X ; 0012-1606
    ISSN (online) 1095-564X
    ISSN 0012-1606
    DOI 10.1016/j.ydbio.2015.11.016
    Datenquelle NAL Katalog (AGRICOLA)

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  4. Artikel ; Online: Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis

    Saurabh J. Pradhan / Puli Chandramouli Reddy / Michael Smutny / Ankita Sharma / Keisuke Sako / Meghana S. Oak / Rini Shah / Mrinmoy Pal / Ojas Deshpande / Greg Dsilva / Yin Tang / Rakesh Mishra / Girish Deshpande / Antonio J. Giraldez / Mahendra Sonawane / Carl-Philipp Heisenberg / Sanjeev Galande

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 19

    Abstract: Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, ... ...

    Abstract Activation of the zygotic genome is a critical transition during development, though the link to tissue-specific gene regulation remains unclear. Here the authors demonstrate distinct functions for Satb2 before and after zygotic genome activation, highlighting the temporal coordination of these roles.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-10-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Genome editing in animals with minimal PAM CRISPR-Cas9 enzymes

    Jeremy Vicencio / Carlos Sánchez-Bolaños / Ismael Moreno-Sánchez / David Brena / Charles E. Vejnar / Dmytro Kukhtar / Miguel Ruiz-López / Mariona Cots-Ponjoan / Alejandro Rubio / Natalia Rodrigo Melero / Jesús Crespo-Cuadrado / Carlo Carolis / Antonio J. Pérez-Pulido / Antonio J. Giráldez / Benjamin P. Kleinstiver / Julián Cerón / Miguel A. Moreno-Mateos

    Nature Communications, Vol 13, Iss 1, Pp 1-

    2022  Band 13

    Abstract: PAM requirement is a constraint for genome editing but this has been circumvented by engineered Cas9 nucleases as SpG and SpRY recognizing minimal PAM sequences. Here, the authors validate and optimize SpG and SpRY in vivo expanding the targeting ... ...

    Abstract PAM requirement is a constraint for genome editing but this has been circumvented by engineered Cas9 nucleases as SpG and SpRY recognizing minimal PAM sequences. Here, the authors validate and optimize SpG and SpRY in vivo expanding the targeting landscape in animals.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2022-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Bicc1 and Dicer regulate left-right patterning through post-transcriptional control of the Nodal inhibitor Dand5

    Markus Maerker / Maike Getwan / Megan E. Dowdle / Jason C. McSheene / Vanessa Gonzalez / José L. Pelliccia / Danielle S. Hamilton / Valeria Yartseva / Charles Vejnar / Melanie Tingler / Katsura Minegishi / Philipp Vick / Antonio J. Giraldez / Hiroshi Hamada / Rebecca D. Burdine / Michael D. Sheets / Martin Blum / Axel Schweickert

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 15

    Abstract: The authors show that post-transcriptional regulation of the cilia-driven leftward flow target dand5 is central to symmetry breakage in frog, fish and mouse and is mediated by a 139 nt Bicc1 responsive element in the dand5 3′UTR, and they present ... ...

    Abstract The authors show that post-transcriptional regulation of the cilia-driven leftward flow target dand5 is central to symmetry breakage in frog, fish and mouse and is mediated by a 139 nt Bicc1 responsive element in the dand5 3′UTR, and they present evidence that Pkd2 regulates this Bicc1/dand5 module.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-09-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing

    Miguel A. Moreno-Mateos / Juan P. Fernandez / Romain Rouet / Charles E. Vejnar / Maura A. Lane / Emily Mis / Mustafa K. Khokha / Jennifer A. Doudna / Antonio J. Giraldez

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Band 9

    Abstract: Cpf1 is a promising addition to the CRISPR toolkit but displays wide variability of activity in different eurkaryotes. Here the authors identify temperature as a modulator of activity and use this to efficiently edit ectothermic vertebrate species. ...

    Abstract Cpf1 is a promising addition to the CRISPR toolkit but displays wide variability of activity in different eurkaryotes. Here the authors identify temperature as a modulator of activity and use this to efficiently edit ectothermic vertebrate species.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2017-12-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: CRISPR-Cpf1 mediates efficient homology-directed repair and temperature-controlled genome editing

    Miguel A. Moreno-Mateos / Juan P. Fernandez / Romain Rouet / Charles E. Vejnar / Maura A. Lane / Emily Mis / Mustafa K. Khokha / Jennifer A. Doudna / Antonio J. Giraldez

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Band 9

    Abstract: Cpf1 is a promising addition to the CRISPR toolkit but displays wide variability of activity in different eurkaryotes. Here the authors identify temperature as a modulator of activity and use this to efficiently edit ectothermic vertebrate species. ...

    Abstract Cpf1 is a promising addition to the CRISPR toolkit but displays wide variability of activity in different eurkaryotes. Here the authors identify temperature as a modulator of activity and use this to efficiently edit ectothermic vertebrate species.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2017-12-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel: Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish

    Bazzini, Ariel A / Antonio J. Giraldez / Miler T. Lee

    Science. 2012 Apr. 13, v. 336, no. 6078

    2012  

    Abstract: MicroRNAs regulate gene expression through deadenylation, repression, and messenger RNA (mRNA) decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of ... ...

    Abstract MicroRNAs regulate gene expression through deadenylation, repression, and messenger RNA (mRNA) decay. However, the contribution of each mechanism in non-steady-state situations remains unclear. We monitored the impact of miR-430 on ribosome occupancy of endogenous mRNAs in wild-type and dicer mutant zebrafish embryos and found that miR-430 reduces the number of ribosomes on target mRNAs before causing mRNA decay. Translational repression occurs before complete deadenylation, and disrupting deadenylation with use of an internal polyadenylate tail did not block target repression. Lastly, we observed that ribosome density along the length of the message remains constant, suggesting that translational repression occurs by reducing the rate of initiation rather than affecting elongation or causing ribosomal drop-off. These results show that miR-430 regulates translation initiation before inducing mRNA decay during zebrafish development.
    Schlagwörter Danio rerio ; gene expression ; messenger RNA ; microRNA ; mutants ; ribosomes ; translation (genetics)
    Sprache Englisch
    Erscheinungsverlauf 2012-0413
    Umfang p. 233-237.
    Erscheinungsort American Association for the Advancement of Science
    Dokumenttyp Artikel
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.1215704
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  10. Artikel ; Online: Poly(A)-Specific Ribonuclease Mediates 3′-End Trimming of Argonaute2-Cleaved Precursor MicroRNAs

    Mayuko Yoda / Daniel Cifuentes / Natsuko Izumi / Yuriko Sakaguchi / Tsutomu Suzuki / Antonio J. Giraldez / Yukihide Tomari

    Cell Reports, Vol 5, Iss 3, Pp 715-

    2013  Band 726

    Abstract: MicroRNAs (miRNAs) are typically generated as ∼22-nucleotide double-stranded RNAs via the processing of precursor hairpins by the ribonuclease III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form an RNA-induced silencing ... ...

    Abstract MicroRNAs (miRNAs) are typically generated as ∼22-nucleotide double-stranded RNAs via the processing of precursor hairpins by the ribonuclease III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form an RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythropoietic miRNA conserved in vertebrates, occurs independently of Dicer and instead requires cleavage of the 3′ arm of the pre-miR-451 precursor hairpin by Ago2. The 3′ end of the Ago2-cleaved pre-miR-451 intermediate is then trimmed to the mature length by an unknown nuclease. Here, using a classical chromatographic approach, we identified poly(A)-specific ribonuclease (PARN) as the enzyme responsible for the 3′–5′ exonucleolytic trimming of Ago2-cleaved pre-miR-451. Surprisingly, our data show that trimming of Ago2-cleaved precursor miRNAs is not essential for target silencing, indicating that RISC is functional with miRNAs longer than the mature length. Our findings define the maturation step in the miRNA biogenesis pathway that depends on Ago2-mediated cleavage.
    Schlagwörter Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2013-11-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
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