1
|
Larsen GA, Laporta J. Carry-over effects of maternal late-gestation heat stress on granddaughter's growth and mammary gland development. J Dairy Sci 2024:S0022-0302(24)00764-1. [PMID: 38642652 DOI: 10.3168/jds.2024-24678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/16/2024] [Indexed: 04/22/2024]
Abstract
Maternal (F0) exposure to late-gestation heat stress reduces their daughter's (F1) mammary gland fat pad mass (FP), parenchyma (PAR) mass, and epithelial cell proliferation when evaluated at birth and weaning, and go on to produce less milk in their first lactation. Herein, we investigated the effect of maternal late-gestation heat stress on whole-body growth and mammary development of their granddaughters (F2). Multiparous F0 cows had access to heat abatement (n = 41, shade, and active cooling via fans and water soakers) or not (n = 41, shade only) for the last 56 d of gestation during a subtropical summer. Consequently, the F1 daughters, born to F0 cows, were heat-stressed (HTF1, n = 36) or cooled (CLF1, n = 37) in utero during the last 2 mo of gestation. All F1 heifers were raised as an identically managed cohort until first calving. The F2 granddaughters, born to HTF1 (HTF2, n = 12) or CLF1 (CLF2, n = 17), were raised as an identically managed cohort until 70 d of age. Dry matter intake (DMI), body weight, hip height, wither height, chest girth, head circumference, mammary gland teat length, and left-right and front-rear teat distances were measured. Average daily gain (ADG) was calculated for the pre-weaned period (0-49 d). Mammary ultrasounds were performed on d 21, 49, and 70 (n = 9/group) on the rear left and right quarters to quantify PAR and FP areas. Mammary biopsies were collected for histological evaluation of epithelial structures (H&E staining), and to quantify cells positive for ERα (estrogen receptor, α subunit), cell proliferation (Ki67), and apoptosis (TUNEL). Heifer growth from birth to d 49 was similar between CLF2 and HTF2 for all parameters evaluated. Distances between teats and teat length were not different between groups. On d 70, CLF2 tended to have a greater average PAR (right and left quarters) relative to HTF2. Although the left FP was smaller in HTF2 relative to CLF2, the average FP was not different. The lumenal and non-lumenal epithelial structures in the PAR of HTF2 were significantly smaller than those of CLF2. In addition, HTF2 had a reduced percentage of proliferating cells in the epithelial and stromal compartments and a greater percentage of apoptotic cells, particularly in the stroma. The percentage of ERα positive cells was significantly reduced in HTF2. In summary, although HTF2 heifer's DMI was similar and they grew at the same rate as CLF2 heifers throughout the pre-weaning phase, their mammary glands had smaller PAR areas with fewer epithelial structures characterized by reduced cell turnover and lower ERα expression. These early changes in the microstructure and cellular turnover of the mammary gland may partly explain the reduction in lactation performance relative to CLF2 counterparts at maturity.
Collapse
Affiliation(s)
- Grace A Larsen
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, WI, USA, 53706
| | - Jimena Laporta
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, WI, USA, 53706.
| |
Collapse
|
2
|
Brown HE, Varderesian HV, Keane SA, Ryder SP. The mex-3 3' untranslated region is essential for reproduction during temperature stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587367. [PMID: 38798418 PMCID: PMC11123400 DOI: 10.1101/2024.04.01.587367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Organisms must sense temperature and modify their physiology to ensure survival during environmental stress. Elevated temperature leads to reduced fertility in most sexually reproducing organisms. Maternally supplied mRNAs are required for embryogenesis. They encode proteins that govern early events in embryonic patterning. RNA-binding proteins (RBPs) are major effectors of maternal mRNA regulation. MEX-3 is a conserved RBP essential for anterior patterning of Caenorhabditis elegans embryos. We previously demonstrated that the mex-3 3' untranslated region (3'UTR) represses MEX-3 abundance in the germline yet is dispensable for fertility. Here, we show that the 3'UTR becomes essential during thermal stress. Deletion of the 3'UTR causes a highly penetrant temperature sensitive embryonic lethality phenotype distinct from a mex-3 null. Loss of the 3'UTR decreases MEX-3 abundance specifically in maturing oocytes and early embryos experiencing temperature stress, suggesting a mechanism that regulates MEX-3 abundance at the oocyte-to-embryo transition is sensitive to temperature. We propose that a primary role of the mex-3 3'UTR is to buffer MEX-3 expression to ensure viability during fluctuating temperature. We hypothesize that a major role of maternally supplied mRNAs is to ensure robust expression of key cell fate determinants in uncertain conditions.
Collapse
|
3
|
Taylor M, Marx O, Norris A. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation. Nucleic Acids Res 2023; 51:9610-9628. [PMID: 37587694 PMCID: PMC10570059 DOI: 10.1093/nar/gkad665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/20/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
Gene expression is a multistep process and crosstalk among regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant gene expression coordination, we performed a systematic reverse-genetic interaction screen in C. elegans, combining RNA binding protein (RBP) and transcription factor (TF) mutants to generate over 100 RBP;TF double mutants. We identified many unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no effect on the health of the organism. However, fust-1;ceh-14 and tdp-1;ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-Seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. A skipped exon in the polyglutamine-repeat protein pqn-41 is aberrantly included in tdp-1 mutants, and genetically forcing this exon to be skipped in tdp-1;ceh-14 double mutants rescues their fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility and a shared molecular role in exon inhibition.
Collapse
Affiliation(s)
- Morgan Taylor
- Southern Methodist University, Dallas, TX 75205, USA
| | - Olivia Marx
- Southern Methodist University, Dallas, TX 75205, USA
| | - Adam Norris
- Southern Methodist University, Dallas, TX 75205, USA
| |
Collapse
|
4
|
Abay-Nørgaard S, Tapia MC, Zeijdner M, Kim JH, Won KJ, Porse B, Salcini AE. Inter and transgenerational impact of H3K4 methylation in neuronal homeostasis. Life Sci Alliance 2023; 6:e202301970. [PMID: 37225426 PMCID: PMC10209521 DOI: 10.26508/lsa.202301970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/26/2023] Open
Abstract
Epigenetic marks and associated traits can be transmitted for one or more generations, phenomena known respectively as inter- or transgenerational epigenetic inheritance. It remains unknown if genetically and conditionally induced aberrant epigenetic states can influence the development of the nervous system across generations. Here, we show, using Caenorhabditis elegans as a model system, that alteration of H3K4me3 levels in the parental generation, caused by genetic manipulation or changes in parental conditions, has, respectively, trans- and intergenerational effects on H3K4 methylome, transcriptome, and nervous system development. Thus, our study reveals the relevance of H3K4me3 transmission and maintenance in preventing long-lasting deleterious effects in nervous system homeostasis.
Collapse
Affiliation(s)
- Steffen Abay-Nørgaard
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marta Cecylia Tapia
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Mandoh Zeijdner
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeonghwan Henry Kim
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kyoung Jae Won
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Porse
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
5
|
Taylor M, Marx O, Norris A. TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.18.537345. [PMID: 37131843 PMCID: PMC10153140 DOI: 10.1101/2023.04.18.537345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Gene expression is a multistep, carefully controlled process, and crosstalk between regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant coordination between transcriptional and post-transcriptional gene regulation, we performed a systematic reverse-genetic interaction screen in C. elegans . We combined RNA binding protein (RBP) and transcription factor (TF) mutants, creating over 100 RBP; TF double mutants. This screen identified a variety of unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs, fust-1 and tdp-1 , and the homeodomain TF ceh-14 . Losing any one of these genes alone has no significant effect on the health of the organism. However, fust-1; ceh-14 and tdp-1; ceh-14 double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-seq analysis of double mutants identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. We identify a cassette exon in the polyglutamine-repeat protein pqn-41 which tdp-1 inhibits. Loss of tdp-1 causes the pqn-41 exon to be aberrantly included, and forced skipping of this exon in tdp-1; ceh-14 double mutants rescues fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility in a ceh-14 mutant background and reveal a shared molecular function of fust-1 and tdp-1 in exon inhibition.
Collapse
|
6
|
Phillips CM, Updike DL. Germ granules and gene regulation in the Caenorhabditis elegans germline. Genetics 2022; 220:6541922. [PMID: 35239965 PMCID: PMC8893257 DOI: 10.1093/genetics/iyab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/10/2021] [Indexed: 01/27/2023] Open
Abstract
The transparency of Caenorhabditis elegans provides a unique window to observe and study the function of germ granules. Germ granules are specialized ribonucleoprotein (RNP) assemblies specific to the germline cytoplasm, and they are largely conserved across Metazoa. Within the germline cytoplasm, they are positioned to regulate mRNA abundance, translation, small RNA production, and cytoplasmic inheritance to help specify and maintain germline identity across generations. Here we provide an overview of germ granules and focus on the significance of more recent observations that describe how they further demix into sub-granules, each with unique compositions and functions.
Collapse
Affiliation(s)
- Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Corresponding author: (C.M.P.); (D.L.U.)
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA,Corresponding author: (C.M.P.); (D.L.U.)
| |
Collapse
|
7
|
Almarghalani DA, Boddu SHS, Ali M, Kondaka A, Ta D, Shah RA, Shah ZA. Small interfering RNAs based therapies for intracerebral hemorrhage: challenges and progress in drug delivery systems. Neural Regen Res 2022; 17:1717-1725. [PMID: 35017419 PMCID: PMC8820693 DOI: 10.4103/1673-5374.332129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Intracerebral hemorrhage (ICH) is a subtype of stroke associated with higher rates of mortality. Currently, no effective drug treatment is available for ICH. The molecular pathways following ICH are complicated and diverse. Nucleic acid therapeutics such as gene knockdown by small interfering RNAs (siRNAs) have been developed in recent years to modulate ICH’s destructive pathways and mitigate its outcomes. However, siRNAs delivery to the central nervous system is challenging and faces many roadblocks. Existing barriers to systemic delivery of siRNA limit the use of naked siRNA; therefore, siRNA-vectors developed to protect and deliver these therapies into the specific-target areas of the brain, or cell types seem quite promising. Efficient delivery of siRNA via nanoparticles emerged as a viable and effective alternative therapeutic tool for central nervous system-related diseases. This review discusses the obstacles to siRNA delivery, including the advantages and disadvantages of viral and nonviral vectors. Additionally, we provide a comprehensive overview of recent progress in nanotherapeutics areas, primarily focusing on the delivery system of siRNA for ICH treatment.
Collapse
Affiliation(s)
- Daniyah A Almarghalani
- Department of Pharmacology and Experimental Therapeutics; Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | - Sai H S Boddu
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates
| | - Mohammad Ali
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | - Akhila Kondaka
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | - Devin Ta
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | - Rayyan A Shah
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| | - Zahoor A Shah
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, USA
| |
Collapse
|
8
|
Seroussi U, Li C, Sundby AE, Lee TL, Claycomb JM, Saltzman AL. Mechanisms of epigenetic regulation by C. elegans nuclear RNA interference pathways. Semin Cell Dev Biol 2021; 127:142-154. [PMID: 34876343 DOI: 10.1016/j.semcdb.2021.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/06/2023]
Abstract
RNA interference (RNAi) is a highly conserved gene regulatory phenomenon whereby Argonaute/small RNA (AGO/sRNA) complexes target transcripts by antisense complementarity to modulate gene expression. While initially appreciated as a cytoplasmic process, RNAi can also occur in the nucleus where AGO/sRNA complexes are recruited to nascent transcripts. Nuclear AGO/sRNA complexes recruit co-factors that regulate transcription by inhibiting RNA Polymerase II, modifying histones, compacting chromatin and, in some organisms, methylating DNA. C. elegans has a longstanding history in unveiling the mechanisms of RNAi and has become an outstanding model to delineate the mechanisms underlying nuclear RNAi. In this review we highlight recent discoveries in the field of nuclear RNAi in C. elegans and the roles of nuclear RNAi in the regulation of gene expression, chromatin organization, genome stability, and transgenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chengyin Li
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Adam E Sundby
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tammy L Lee
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Arneet L Saltzman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
9
|
Zaghet N, Madsen K, Rossi F, Perez DF, Amendola PG, Demharter S, Pfisterer U, Khodosevich K, Pasini D, Salcini AE. Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality. Cell Rep 2021; 37:110050. [PMID: 34818537 PMCID: PMC8640224 DOI: 10.1016/j.celrep.2021.110050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/18/2021] [Accepted: 11/02/2021] [Indexed: 12/01/2022] Open
Abstract
Germ cells have evolved unique mechanisms to ensure the transmission of genetically and nongenetically encoded information, whose alteration compromises germ cell immortality. Chromatin factors play fundamental roles in these mechanisms. H3K36 and H3K27 methyltransferases shape and propagate a pattern of histone methylation essential for C. elegans germ cell maintenance, but the role of respective histone demethylases remains unexplored. Here, we show that jmjd-5 regulates H3K36me2 and H3K27me3 levels, preserves germline immortality, and protects germ cell identity by controlling gene expression. The transcriptional and biological effects of jmjd-5 loss can be hindered by the removal of H3K27demethylases, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the balance between H3K36 and H3K27 methylation required for germ cell immortality. Furthermore, we find that in wild-type, but not in jmjd-5 mutants, alterations of H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes. jmjd-5 is required for germ cell immortality at high temperature jmjd-5 sustains the expression of germline genes and represses somatic fate Mutations in jmjd-5 result in a global increase of H3K36me2 and H3K27me3 Ablation of H3K27 demethylases counteracts the effects of jmjd-5 mutations
Collapse
Affiliation(s)
- Nico Zaghet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Katrine Madsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Federico Rossi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernandez Perez
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Pier Giorgio Amendola
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Samuel Demharter
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Diego Pasini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark.
| |
Collapse
|
10
|
Spichal M, Heestand B, Billmyre KK, Frenk S, Mello CC, Ahmed S. Germ granule dysfunction is a hallmark and mirror of Piwi mutant sterility. Nat Commun 2021; 12:1420. [PMID: 33658512 PMCID: PMC7930041 DOI: 10.1038/s41467-021-21635-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023] Open
Abstract
In several species, Piwi/piRNA genome silencing defects cause immediate sterility that correlates with transposon expression and transposon-induced genomic instability. In C. elegans, mutations in the Piwi-related gene (prg-1) and other piRNA deficient mutants cause a transgenerational decline in fertility over a period of several generations. Here we show that the sterility of late generation piRNA mutants correlates poorly with increases in DNA damage signaling. Instead, sterile individuals consistently exhibit altered perinuclear germ granules. We show that disruption of germ granules does not activate transposon expression but induces multiple phenotypes found in sterile prg-1 pathway mutants. Furthermore, loss of the germ granule component pgl-1 enhances prg-1 mutant infertility. Environmental restoration of germ granule function for sterile pgl-1 mutants restores their fertility. We propose that Piwi mutant sterility is a reproductive arrest phenotype that is characterized by perturbed germ granule structure and is phenocopied by germ granule dysfunction, independent of genomic instability.
Collapse
Affiliation(s)
- Maya Spichal
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA
| | - Bree Heestand
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA
| | - Katherine Kretovich Billmyre
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.250820.d0000 0000 9420 1591Present Address: Stowers Institute for Medical Research, Kansas City, MO USA
| | - Stephen Frenk
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,Present Address: Achilles Therapeutics Limited, London, UK
| | - Craig C. Mello
- grid.168645.80000 0001 0742 0364RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA ,grid.413575.10000 0001 2167 1581Howard Hughes Medical Institute, Worcester, MA USA
| | - Shawn Ahmed
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Biology, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC USA
| |
Collapse
|
11
|
Sundby AE, Molnar RI, Claycomb JM. Connecting the Dots: Linking Caenorhabditis elegans Small RNA Pathways and Germ Granules. Trends Cell Biol 2021; 31:387-401. [PMID: 33526340 DOI: 10.1016/j.tcb.2020.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Abstract
Germ granules are non-membrane bound, phase-separated organelles, composed of RNAs and proteins. Germ granules are present only within the germ cells of animals, including model systems such as Caenorhabditis elegans, Drosophila, mice, and zebrafish, where they play critical roles in specifying the germ lineage, the inheritance of epigenetic information, and post-transcriptional gene regulation. Across species, conserved germ granule proteins reflect these essential functions. A significant proportion of proteins that localize to germ granules are components of RNA metabolism and small RNA (sRNA) gene regulatory pathways. Here we synthesize our current knowledge of the roles that germ granules and their components play in sRNA pathway functions, transgenerational inheritance, and fertility in the C. elegans germline.
Collapse
Affiliation(s)
- Adam E Sundby
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ruxandra I Molnar
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| |
Collapse
|
12
|
Lev I, Rechavi O. Germ Granules Allow Transmission of Small RNA-Based Parental Responses in the "Germ Plasm". iScience 2020; 23:101831. [PMID: 33305186 PMCID: PMC7718480 DOI: 10.1016/j.isci.2020.101831] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the recent decade small RNA-based inheritance has been implicated in a variety of transmitted physiological responses to the environment. In Caenorhabditis elegans, heritable small RNAs rely on RNA-dependent RNA polymerases, RNA-processing machinery, chromatin modifiers, and argonauts for their biogenesis and gene-regulatory effects. Importantly, many of these factors reside in evolutionary conserved germ granules that are required for maintaining germ cell identity and gene expression. Recent literature demonstrated that transient disturbance to the stability of the germ granules leads to changes in the pools of heritable small RNAs and the physiology of the progeny. In this piece, we discuss the heritable consequences of transient destabilization of germ granules and elaborate on the various small RNA-related processes that act in the germ granules. We further propose that germ granules may serve as environment sensors that translate environmental changes to inheritable small RNA-based responses.
Collapse
Affiliation(s)
- Itamar Lev
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
13
|
Vishnupriya R, Thomas L, Wahba L, Fire A, Subramaniam K. PLP-1 is essential for germ cell development and germline gene silencing in Caenorhabditis elegans. Development 2020; 147:dev.195578. [PMID: 33051256 DOI: 10.1242/dev.195578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
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 Caenorhabditis elegans protein related to the human single-stranded nucleic acid-binding protein Pur-alpha, as a component of germ granules in C. elegans We show that PLP-1 is essential for silencing different types of transgenes in the germ line and for suppressing the expression of several endogenous genes controlled by the germline gene-silencing pathways. Our results reveal that PLP-1 functions downstream of small RNA biogenesis during initiation of gene silencing. Based on these results and the earlier findings that Pur-alpha proteins interact with both RNA and protein, we propose that PLP-1 couples certain RNAs with their protein partners in the silencing complex. PLP-1 orthologs localized on RNA granules may similarly contribute to germline gene silencing in other organisms.
Collapse
Affiliation(s)
- Rajaram Vishnupriya
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
| | - Linitha Thomas
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kuppuswamy Subramaniam
- Department of Biotechnology, Indian Institute of Technology-Madras, Chennai 600036, India
| |
Collapse
|
14
|
Robert VJ, Knutson AK, Rechtsteiner A, Garvis S, Yvert G, Strome S, Palladino F. Caenorhabditis elegans SET1/COMPASS Maintains Germline Identity by Preventing Transcriptional Deregulation Across Generations. Front Cell Dev Biol 2020; 8:561791. [PMID: 33072747 PMCID: PMC7536326 DOI: 10.3389/fcell.2020.561791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin regulators contribute to the maintenance of the germline transcriptional program. In the absence of SET-2, the Caenorhabditis elegans homolog of the SET1/COMPASS H3 Lys4 (H3K4) methyltransferase, animals show transgenerational loss of germline identity, leading to sterility. To identify transcriptional signatures associated with progressive loss of fertility, we performed expression profiling of set-2 mutant germlines across generations. We identify a subset of genes whose misexpression is first observed in early generations, a step we refer to as priming; their misexpression then further progresses in late generations, as animals reach sterility. Analysis of misregulated genes shows that down-regulation of germline genes, expression of somatic transcriptional programs, and desilencing of the X-chromosome are concurrent events leading to loss of germline identity in both early and late generations. Upregulation of transcription factor LIN-15B, the C/EBP homolog CEBP-1, and TGF-β pathway components strongly contribute to loss of fertility, and RNAi inactivation of cebp-1 and TGF-β/Smad signaling delays the onset of sterility, showing they individually contribute to maintenance of germ cell identity. Our approach therefore identifies genes and pathways whose misexpression actively contributes to the loss of germ cell fate. More generally, our data shows how loss of a chromatin regulator in one generation leads to transcriptional changes that are amplified over subsequent generations, ultimately leading to loss of appropriate cell fate.
Collapse
Affiliation(s)
- Valérie J Robert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Andrew K Knutson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Andreas Rechtsteiner
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Steven Garvis
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| |
Collapse
|
15
|
Abstract
A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.
Collapse
Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| |
Collapse
|
16
|
Rogers AK, Phillips CM. A Small-RNA-Mediated Feedback Loop Maintains Proper Levels of 22G-RNAs in C. elegans. Cell Rep 2020; 33:108279. [PMID: 33086057 PMCID: PMC7603289 DOI: 10.1016/j.celrep.2020.108279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/27/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
RNA interference (RNAi) is an essential regulatory mechanism in all animals. In Caenorhabditis elegans, several classes of small RNAs act to silence or license expression of mRNA targets. ERI-6/7 is required for the production of some endogenous small interfering RNAs (siRNAs) and acts as a negative regulator of the exogenous RNAi pathway. We find that the genomic locus encoding eri-6/7 contains two distinct regions that are targeted by endogenous siRNAs. Loss of these siRNAs disrupts eri-6/7 mRNA expression, resulting in increased production of siRNAs from other small RNA pathways because these pathways compete with eri-6/7-dependent transcripts for access to the downstream siRNA amplification machinery. Thus, the pathway acts like a small-RNA-mediated feedback loop to ensure homeostasis of gene expression by small RNA pathways. Similar feedback loops that maintain chromatin homeostasis have been identified in yeast and Drosophila melanogaster, suggesting an evolutionary conservation of feedback mechanisms in gene regulatory pathways.
Collapse
Affiliation(s)
- Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
17
|
Manage KI, Rogers AK, Wallis DC, Uebel CJ, Anderson DC, Nguyen DAH, Arca K, Brown KC, Cordeiro Rodrigues RJ, de Albuquerque BF, Ketting RF, Montgomery TA, Phillips CM. A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans. eLife 2020; 9:56731. [PMID: 32338603 PMCID: PMC7255803 DOI: 10.7554/elife.56731] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the mutator complex are unknown. Here, we identify the Tudor domain protein, SIMR-1, as acting downstream of piRNA production and upstream of mutator complex-dependent siRNA biogenesis. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting mRNA regulation by the mutator complex. In the biological world, a process known as RNA interference helps cells to switch genes on and off and to defend themselves against harmful genetic material. This mechanism works by deactivating RNA sequences, the molecular templates cells can use to create proteins. Overall, RNA interference relies on the cell creating small RNA molecules that can target and inhibit the harmful RNA sequences that need to be silenced. More precisely, in round worms such as Caenorhabditis elegans, RNA interference happens in two steps. First, primary small RNAs identify the target sequences, which are then combatted by newly synthetised, secondary small RNAs. A number of proteins are also involved in both steps of the process. RNA interference is particularly important to preserve fertility, guarding sex cells against ‘rogue’ segments of genetic information that could be passed on to the next generation. In future sex cells, the proteins involved in RNA interference cluster together, forming a structure called a germ granule. Yet, little is known about the roles and identity of these proteins. To fill this knowledge gap, Manage et al. focused on the second stage of the RNA interference pathway in the germ granules of C. elegans, examining the molecules that physically interact with a key protein. This work revealed a new protein called SIMR-1. Looking into the role of SIMR-1 showed that the protein is required to amplify secondary small RNAs, but not to identify target sequences. However, it only promotes the creation of secondary small RNAs if a specific subtype of primary small RNAs have recognized the target RNAs for silencing. Further experiments also showed that within the germ granule, SIMR-1 is present in a separate substructure different from any compartment previously identified. This suggests that each substep of the RNA interference process takes place at a different location in the granule. In both C. elegans and humans, disruptions in the RNA interference pathway can lead to conditions such as cancer or infertility. Dissecting the roles of the proteins involved in this process in roundworms may help to better grasp how this process unfolds in mammals, and how it could be corrected in the case of disease.
Collapse
Affiliation(s)
- Kevin I Manage
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dylan C Wallis
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Celja J Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dorian C Anderson
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dieu An H Nguyen
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Katerina Arca
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Kristen C Brown
- Department of Biology, Colorado State University, Fort Collins, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, United States
| | - Ricardo J Cordeiro Rodrigues
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany.,International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, Mainz, Germany
| | | | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Carolyn Marie Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| |
Collapse
|
18
|
Rogers AK, Phillips CM. Disruption of the mutator complex triggers a low penetrance larval arrest phenotype. MICROPUBLICATION BIOLOGY 2020; 2020:252. [PMID: 32542232 PMCID: PMC7295153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Alicia Kathryn Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Carolyn Marie Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America,To whom correspondence should be addressed:
| |
Collapse
|