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Article ; Online: Caenorhabditis elegans

Erdmann, Emily A / Abraham, Olivia / Hundley, Heather A

microPublication biology

2022 Volume 2022

Abstract: Vitellogenin::GFP fusion proteins have been used in several studies of the synthesis, endocytosis, and function of yolk ... ...

Abstract	Vitellogenin::GFP fusion proteins have been used in several studies of the synthesis, endocytosis, and function of yolk in
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2578-9430
ISSN (online)	2578-9430
DOI	10.17912/micropub.biology.000532
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Article ; Online: ADARs regulate cuticle collagen expression and promote survival to pathogen infection.

Dhakal, Alfa / Salim, Chinnu / Skelly, Mary / Amichan, Yarden / Lamm, Ayelet T / Hundley, Heather A

BMC biology

2024 Volume 22, Issue 1, Page(s) 37

Abstract: Background: In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that ... ...

Abstract	Background: In all organisms, the innate immune system defends against pathogens through basal expression of molecules that provide critical barriers to invasion and inducible expression of effectors that combat infection. The adenosine deaminase that act on RNA (ADAR) family of RNA-binding proteins has been reported to influence innate immunity in metazoans. However, studies on the susceptibility of ADAR mutant animals to infection are largely lacking. Results: Here, by analyzing adr-1 and adr-2 null mutants in well-established slow-killing assays, we find that both Caenorhabditis elegans ADARs are important for organismal survival to gram-negative and gram-positive bacteria, all of which are pathogenic to humans. Furthermore, our high-throughput sequencing and genetic analysis reveal that ADR-1 and ADR-2 function in the same pathway to regulate collagen expression. Consistent with this finding, our scanning electron microscopy studies indicate adr-1;adr-2 mutant animals also have altered cuticle morphology prior to pathogen exposure. Conclusions: Our data uncover a critical role of the C. elegans ADAR family of RNA-binding proteins in promoting cuticular collagen expression, which represents a new post-transcriptional regulatory node that influences the extracellular matrix. In addition, we provide the first evidence that ADAR mutant animals have altered susceptibility to infection with several opportunistic human pathogens, suggesting a broader role of ADARs in altering physical barriers to infection to influence innate immunity.
MeSH term(s)	Animals ; Humans ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; RNA Editing ; Adenosine Deaminase/genetics ; Adenosine Deaminase/metabolism ; Collagen/genetics ; Collagen/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; Adenosine Deaminase (EC 3.5.4.4) ; Collagen (9007-34-5) ; RNA-Binding Proteins
Language	English
Publishing date	2024-02-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2133020-7
ISSN	1741-7007 ; 1741-7007
ISSN (online)	1741-7007
ISSN	1741-7007
DOI	10.1186/s12915-024-01840-1
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Article ; Online: Involvement of the SAGA and TFIID coactivator complexes in transcriptional dysregulation caused by the separation of core and tail Mediator modules.

Saleh, Moustafa M / Hundley, Heather A / Zentner, Gabriel E

G3 (Bethesda, Md.)

2022 Volume 12, Issue 12

Abstract: Regulation of RNA polymerase II transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNA polymerase II preinitiation complex to stimulate transcription. We previously showed that separation ... ...

Abstract	Regulation of RNA polymerase II transcription requires the concerted efforts of several multisubunit coactivator complexes, which interact with the RNA polymerase II preinitiation complex to stimulate transcription. We previously showed that separation of the Mediator core from Mediator's tail module results in modest overactivation of genes annotated as highly dependent on TFIID for expression. However, it is unclear if other coactivators are involved in this phenomenon. Here, we show that the overactivation of certain genes by Mediator core/tail separation is blunted by disruption of the Spt-Ada-Gcn5-Acetyl transferase complex through the removal of its structural Spt20 subunit, though this downregulation does not appear to completely depend on reduced Spt-Ada-Gcn5-Acetyl transferase association with the genome. Consistent with the enrichment of TFIID-dependent genes among genes overactivated by Mediator core/tail separation, depletion of the essential TFIID subunit Taf13 suppressed the overactivation of these genes when Med16 was simultaneously removed. As with Spt-Ada-Gcn5-Acetyl transferase, this effect did not appear to be fully dependent on the reduced genomic association of TFIID. Given that the observed changes in gene expression could not be clearly linked to alterations in Spt-Ada-Gcn5-Acetyl transferase or TFIID occupancy, our data may suggest that the Mediator core/tail connection is important for the modulation of Spt-Ada-Gcn5-Acetyl transferase and/or TFIID conformation and/or function at target genes.
MeSH term(s)	Saccharomyces cerevisiae Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Gene Expression Regulation, Fungal ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Trans-Activators/metabolism ; Transcription Factor TFIID/genetics ; Transcription Factor TFIID/metabolism ; Transcription, Genetic
Chemical Substances	Saccharomyces cerevisiae Proteins ; RNA Polymerase II (EC 2.7.7.-) ; Trans-Activators ; Transcription Factor TFIID
Language	English
Publishing date	2022-09-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2629978-1
ISSN	2160-1836 ; 2160-1836
ISSN (online)	2160-1836
ISSN	2160-1836
DOI	10.1093/g3journal/jkac290
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Article: A high-throughput screen identifies RNA binding proteins that affect fertility in

Erdmann, Emily A / Forbes, Melanie / Becker, Margaret / Perez, Sarina / Skelly, Mary / Hundley, Heather A

bioRxiv : the preprint server for biology

2023

Abstract: RNA binding proteins play essential roles in coordinating germline gene expression and development in all organisms. Characterization of gross fertility defects, such as sterility, has identified RNA binding proteins that are critical regulators of ... ...

Abstract	RNA binding proteins play essential roles in coordinating germline gene expression and development in all organisms. Characterization of gross fertility defects, such as sterility, has identified RNA binding proteins that are critical regulators of germline gene expression; however, broader screens for RNA binding proteins involved in specific reproductive processes are lacking. Here, a reverse genetic screen was performed to identify RNA binding proteins that impact yolk and embryo production in
Language	English
Publishing date	2023-11-02
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.01.565157
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Article: ADARs employ a neural-specific mechanism to regulate PQM-1 expression and survival from hypoxia.

Mahapatra, Ananya / Dhakal, Alfa / Noguchi, Aika / Vadlamani, Pranathi / Hundley, Heather A

bioRxiv : the preprint server for biology

2023

Abstract: The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about ... ...

Abstract	The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA binding protein, ADR-1, binds to
Language	English
Publishing date	2023-05-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.05.539519
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Article ; Online: ADAR-mediated regulation of PQM-1 expression in neurons impacts gene expression throughout C. elegans and regulates survival from hypoxia.

Mahapatra, Ananya / Dhakal, Alfa / Noguchi, Aika / Vadlamani, Pranathi / Hundley, Heather A

PLoS biology

2023 Volume 21, Issue 9, Page(s) e3002150

Abstract	The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA-binding protein (RBP), ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RBP, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia, phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important posttranscriptional gene regulatory mechanism in Caenorhabditis elegans that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
MeSH term(s)	Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/genetics ; Caenorhabditis elegans Proteins/metabolism ; Hypoxia/genetics ; Hypoxia/metabolism ; Neurons/metabolism ; Gene Expression ; Longevity/genetics ; Gene Expression Regulation ; Trans-Activators/metabolism
Chemical Substances	Caenorhabditis elegans Proteins ; PQM-1 protein, C elegans ; Trans-Activators
Language	English
Publishing date	2023-09-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3002150
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Article ; Online: MicroRNA mediated regulation of the onset of enteroblast differentiation in the Drosophila adult intestine.

Mukherjee, Sromana / Calvi, Brian R / Hundley, Heather A / Sokol, Nicholas S

Cell reports

2022 Volume 41, Issue 3, Page(s) 111495

Abstract: Somatic adult stem cell lineages in high-turnover tissues are under tight gene regulatory control. Like its mammalian counterpart, the Drosophila intestine precisely adjusts the rate of stem cell division with the onset of differentiation based on ... ...

Abstract	Somatic adult stem cell lineages in high-turnover tissues are under tight gene regulatory control. Like its mammalian counterpart, the Drosophila intestine precisely adjusts the rate of stem cell division with the onset of differentiation based on physiological demand. Although Notch signaling is indispensable for these decisions, the regulation of Notch activity that drives the differentiation of stem cell progenies into functional, mature cells is not well understood. Here, we report that commitment to the terminally differentiated enterocyte (EC) cell fate is under microRNA control. We show that an intestinally enriched microRNA, miR-956, fine-tunes Notch signaling activity specifically in intermediate, enteroblast (EB) progenitor cells to control EC differentiation. We further identify insensitive mRNA as a target of miR-956 that regulates EB/EC ratios by repressing Notch activity in EBs. In summary, our study highlights a post-transcriptional gene-regulatory mechanism for controlling differentiation in an adult intestinal stem cell lineage.
MeSH term(s)	Animals ; Drosophila/genetics ; Drosophila Proteins/genetics ; Receptors, Notch/genetics ; Drosophila melanogaster/physiology ; MicroRNAs/genetics ; Intestines ; RNA, Messenger ; Mammals/genetics
Chemical Substances	Drosophila Proteins ; Receptors, Notch ; MicroRNAs ; RNA, Messenger
Language	English
Publishing date	2022-10-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111495
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Article ; Online: RNA immunoprecipitation to identify in vivo targets of RNA editing and modifying enzymes.

Mukherjee, Priyanka / Raghava Kurup, Reshma / Hundley, Heather A

Methods in enzymology

2021 Volume 658, Page(s) 137–160

Abstract: The past decade has seen an exponential increase in the identification of individual nucleobases that undergo base conversion and/or modification in transcriptomes. While the enzymes that catalyze these types of changes have been identified, the global ... ...

Abstract	The past decade has seen an exponential increase in the identification of individual nucleobases that undergo base conversion and/or modification in transcriptomes. While the enzymes that catalyze these types of changes have been identified, the global interactome of these modifiers is still largely unknown. Furthermore, in some instances, redundancy among a family of enzymes leads to an inability to pinpoint the protein responsible for modifying a given transcript merely from high-throughput sequencing data. This chapter focuses on a method for global identification of transcripts recognized by an RNA modification/editing enzyme via capture of the RNAs that are bound in vivo, a method referred as RNA immunoprecipitation (RIP). We provide a guide of the major issues to consider when designing a RIP experiment, a detailed experimental protocol as well as troubleshooting advice. The RIP protocol presented here can be readily applied to any organism or cell line of interest as well as both RNA modification enzymes and RNA-binding proteins (RBPs) that regulate RNA modification levels. As mentioned at the end of the protocol, the RIP assay can be coupled to high-throughput sequencing to globally identify bound targets. For more quantitative investigations, such as how binding of an RNA modification enzyme/regulator to a given target changes during development/in specific tissues or assessing how the presence or absence of RNA modification affects transcript recognition by a particular RBP (irrespective of a role for the RBP in modulating modification levels); the RIP assay should be coupled to quantitative real-time PCR (qRT-PCR).
MeSH term(s)	High-Throughput Nucleotide Sequencing ; Immunoprecipitation ; RNA/genetics ; RNA/metabolism ; RNA Editing ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
Chemical Substances	RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2021-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1557-7988
ISSN (online)	1557-7988
DOI	10.1016/bs.mie.2021.06.005
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Article ; Online: mRNA Editing, Processing and Quality Control in

Arribere, Joshua A / Kuroyanagi, Hidehito / Hundley, Heather A

Genetics

2020 Volume 215, Issue 3, Page(s) 531–568

Abstract: While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated ... ...

Abstract	While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in
MeSH term(s)	Animals ; Caenorhabditis elegans/genetics ; Nonsense Mediated mRNA Decay ; RNA Editing ; RNA Splicing ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2020-07-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.119.301807
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Article ; Online: ADAR-mediated regulation of PQM-1 expression in neurons impacts gene expression throughout C. elegans and regulates survival from hypoxia.

Ananya Mahapatra / Alfa Dhakal / Aika Noguchi / Pranathi Vadlamani / Heather A Hundley

PLoS Biology, Vol 21, Iss 9, p e

2023 Volume 3002150

Abstract	The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA-binding protein (RBP), ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RBP, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia, phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important posttranscriptional gene regulatory mechanism in Caenorhabditis elegans that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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