1
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Ng AQE, Chan SN, Pek JW. Nutrient-dependent regulation of a stable intron modulates germline mitochondrial quality control. Nat Commun 2024; 15:1252. [PMID: 38341415 PMCID: PMC10858910 DOI: 10.1038/s41467-024-45651-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Mitochondria are inherited exclusively from the mothers and are required for the proper development of embryos. Hence, germline mitochondrial quality is highly regulated during oogenesis to ensure oocyte viability. How nutrient availability influences germline mitochondrial quality control is unclear. Here we find that fasting leads to the accumulation of mitochondrial clumps and oogenesis arrest in Drosophila. Fasting induces the downregulation of the DIP1-Clueless pathway, leading to an increase in the expression of a stable intronic sequence RNA called sisR-1. Mechanistically, sisR-1 localizes to the mitochondrial clumps to inhibit the poly-ubiquitination of the outer mitochondrial protein Porin/VDAC1, thereby suppressing p62-mediated mitophagy. Alleviation of the fasting-induced high sisR-1 levels by either sisR-1 RNAi or refeeding leads to mitophagy, the resumption of oogenesis and an improvement in oocyte quality. Thus, our study provides a possible mechanism by which fasting can improve oocyte quality by modulating the mitochondrial quality control pathway. Of note, we uncover that the sisR-1 response also regulates mitochondrial clumping and oogenesis during protein deprivation, heat shock and aging, suggesting a broader role for this mechanism in germline mitochondrial quality control.
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Affiliation(s)
- Annabel Qi En Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Seow Neng Chan
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore.
- Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore, 117543, Singapore.
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2
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Wang W, Hu J, Li H, Yan J, Sun X. PlantIntronDB: a database for plant introns that host functional elements. Database (Oxford) 2023; 2023:baad082. [PMID: 37951713 PMCID: PMC10640381 DOI: 10.1093/database/baad082] [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: 05/26/2023] [Revised: 10/03/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
Although more and more attention has been focused on introns and the important role of plant introns in plant growth and development has been discovered, there is still a lack of an open and comprehensive database on plant introns with functional elements in current research. In order to make full use of large-scale sequencing data and help researchers in related fields to achieve high-throughput functional verification of identified plant introns with functional elements, we designed a database containing five plant species, PlantIntronDB and systematically analyzed 358, 59, 185, 210 and 141 RNA-seq samples from Arabidopsis thaliana (Arabidopsis), Gossypium raimondii (cotton), Zea mays (maize), Brassica napus (oilseed rape) and Oryza sativa Japonica Group (rice). In total, we found 100 126 introns that host functional elements in these five species. Specifically, we found that among all species, the number of introns with functional elements on the positive and negative strands is similar, with a length mostly smaller than 1500 bp, and the Adenine/Thymine (A/T) content is much higher than that of Guanine/Cytosine (G/C). In addition, the distribution of functional elements in introns varies among different species. All the above data can be downloaded for free in this database. This database provides a concise, comprehensive and user-friendly web interface, allowing users to easily retrieve target data based on their needs, using relevant organizational options. The database operation is simple and convenient, aiming to provide strong data support for researchers in related fields to study plant introns that host functional elements, including circular RNAs, lncRNAs, etc. Database URL: http://deepbiology.cn/PlantIntronDB/.
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Affiliation(s)
| | - Jiming Hu
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Han Li
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jun Yan
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiaoyong Sun
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, Shandong 271018, China
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3
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Li H, Zhang Y, Bing J, Han J, Hu J, Zhao H, Sun X. Intron-capture RNA-seq reveals the landscape of intronic RNAs in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:75-88. [PMID: 36701993 DOI: 10.1016/j.plaphy.2023.01.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Intronic RNAs have been overlooked for a long time: They are functional, but treated as "junk." In this work, we designed a new sequencing strategy to investigate intronic RNAs. By using intron-capture RNA-seq, we systematically analyzed the intronic RNAs in Arabidopsis by zooming into the intronic regions an order of magnitude deeper than in previous work. Our key findings include: (1) Intron-capture RNA-seq is a much more efficient approach to analyze intronic RNAs than total RNA-seq and mRNA-seq. (2) We identified three types of intronic RNAs, and found that the GC pattern differs significantly between the introns with and without intronic RNAs. (3) We detected many hidden elements in introns, including circular RNAs, splice junctions, and transcripts that have previously been overlooked. (4) The expression of these intronic RNAs varies during the time course of pathogen infection, which indicates that an unknown mechanism may exist for these RNAs. (5) We also demonstrated that most of intronic RNAs are detectable in both Arabidopsis and rice, suggesting that these non-coding molecules are conserved. Taken together, this work proposes an efficient strategy to analyze intronic RNAs, and provides an unprecedented view of this essential component in biological pathways.
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Affiliation(s)
- Han Li
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Yimai Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jianhao Bing
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Jinyu Han
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Jiming Hu
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Hongwei Zhao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
| | - Xiaoyong Sun
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China.
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4
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Chan SN, Pek JW. Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA. EMBO Rep 2023; 24:e54350. [PMID: 36533631 PMCID: PMC9900350 DOI: 10.15252/embr.202154350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are stable, long noncoding RNAs containing intronic sequences. While sisRNAs have been found across diverse species, their level of conservation remains poorly understood. Here we report that the biogenesis and functions of a sisRNA transcribed from the highly conserved Arglu1 locus are distinct in human and Drosophila melanogaster. The Arglu1 genes in both species show similar exon-intron structures where the intron 2 is orthologous and positionally conserved. In humans, Arglu1 sisRNA retains the entire intron 2 and promotes host gene splicing. Mechanistically, Arglu1 sisRNA represses the splicing-inhibitory activity of ARGLU1 protein by binding to ARGLU1 protein and promoting its localization to nuclear speckles, away from the Arglu1 gene locus. In contrast, Drosophila dArglu1 sisRNA forms via premature cleavage of intron 2 and represses host gene splicing. This repression occurs through a local accumulation of dARGLU1 protein and inhibition of telescripting by U1 snRNPs at the dArglu1 locus. We propose that distinct biogenesis of positionally conserved Arglu1 sisRNAs in both species may have led to functional divergence.
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Affiliation(s)
- Seow Neng Chan
- Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
| | - Jun Wei Pek
- Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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5
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Robic A, Cerutti C, Demars J, Kühn C. From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194815. [PMID: 35513260 DOI: 10.1016/j.bbagrm.2022.194815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Circular intronic RNAs (ciRNAs) are still unexplored regarding mechanisms for their emergence. We considered the ATXN2L intron lariat-derived circular RNA (ciRNA-ATXN2L) as an opportunity to conduct a cross-species examination of ciRNA genesis. To this end, we investigated 207 datasets from 4 tissues and from 13 mammalian species. While in eight species, ciRNA-ATXN2L was never detected, in pigs and rabbits, ciRNA-ATXN2L was expressed in all tissues and sometimes at very high levels. Bovine tissues were an intermediate case and in macaques and cats, only ciRNA-ATXN2L traces were detected. The pattern of ciRNA-ATXN2L restricted to only five species is not related to a particular evolution of intronic sequences. To empower our analysis, we considered 221 additional introns including 80 introns where a lariat-derived ciRNA was previously described. The primary driver of micro-ciRNA genesis (< 155 nt as ciRNA-ATXN2L) appears to be the absence of a canonical "A" (i.e. a "tnA" located in the usual branching region) to build the lariat around this adenosine. The balance between available "non canonical-A" (no ciRNA genesis) and "non-A" (ciRNA genesis) for use as a branch point to build the lariat could modify the expression level of ciRNA-ATXN2L. In addition, the rare localization of the 2'-5' bond in an open RNA secondary structure could also negatively affect the lifetime of ciRNAs (macaque ciRNA-ATXN2L). Our analyses suggest that ciRNA-ATXN2L is likely a functionless splice remnant. This study provides a better understanding of the ciRNAs origin, especially drivers for micro ciRNA genesis.
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Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Chloé Cerutti
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany.
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6
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Maternal starvation primes progeny response to nutritional stress. PLoS Genet 2021; 17:e1009932. [PMID: 34843464 PMCID: PMC8659306 DOI: 10.1371/journal.pgen.1009932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 12/09/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022] Open
Abstract
Organisms adapt to environmental changes in order to survive. Mothers exposed to nutritional stresses can induce an adaptive response in their offspring. However, the molecular mechanisms behind such inheritable links are not clear. Here we report that in Drosophila, starvation of mothers primes the progeny against subsequent nutritional stress. We found that RpL10Ab represses TOR pathway activity by genetically interacting with TOR pathway components TSC2 and Rheb. In addition, starved mothers produce offspring with lower levels of RpL10Ab in the germline, which results in higher TOR pathway activity, conferring greater resistance to starvation-induced oocyte loss. The RpL10Ab locus encodes for the RpL10Ab mRNA and a stable intronic sequence RNA (sisR-8), which collectively repress RpL10Ab pre-mRNA splicing in a negative feedback mechanism. During starvation, an increase in maternally deposited RpL10Ab and sisR-8 transcripts leads to the reduction of RpL10Ab expression in the offspring. Our study suggests that the maternally deposited RpL10Ab and sisR-8 transcripts trigger a negative feedback loop that mediates intergenerational adaptation to nutritional stress as a starvation response. In the wild, animals need to adapt to frequent changes in the environment. Mothers who are exposed to nutritional stresses are known to produce offspring which are preconditioned to adapt to the mothers’ environment. However, it is unclear how such maternal “memory” is being passed on to the offspring. Here we show that Drosophila mothers exposed to starvation produce offspring which are more resistant to starvation during oogenesis. This process is mediated by maternally inherited RpL10Ab mRNA and a stable intronic sequence RNA (sisR-8), which collectively repress the splicing of RpL10Ab pre-mRNA, leading to lower RpL10Ab expression in the offspring ovaries. As a consequence, lower RpL10Ab expression results in higher TOR pathway activity, conferring greater resistance to starvation during oogenesis. Hence, maternally inherited transcripts may play a role as mediators in conferring intergenerational adaption to starvation.
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7
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Maternally inherited intron coordinates primordial germ cell homeostasis during Drosophila embryogenesis. Cell Death Differ 2020; 28:1208-1221. [PMID: 33093656 DOI: 10.1038/s41418-020-00642-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Primordial germ cells (PGCs) give rise to the germline stem cells (GSCs) in the adult Drosophila gonads. Both PGCs and GSCs need to be tightly regulated to safeguard the survival of the entire species. During larval development, a non-cell autonomous homeostatic mechanism is in place to maintain PGC number in the gonads. Whether such germline homeostasis occurs during early embryogenesis before PGCs reach the gonads remains unclear. We have previously shown that the maternally deposited sisRNA sisR-2 can influence GSC number in the female progeny. Here we uncover the presence of a homeostatic mechanism regulating PGCs during embryogenesis. sisR-2 represses PGC number by promoting PGC death. Surprisingly, increasing maternal sisR-2 leads to an increase in PGC death, but no drop in PGC number was observed. This is due to ectopic division of PGCs via the de-repression of Cyclin B, which is governed by a genetic pathway involving sisR-2, bantam and brat. We propose a cell autonomous model whereby germline homeostasis is achieved by preserving PGC number during embryogenesis.
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8
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Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs. Genes (Basel) 2020; 11:genes11091111. [PMID: 32972011 PMCID: PMC7565381 DOI: 10.3390/genes11091111] [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: 08/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2′–5′ bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.
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9
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Robic A, Demars J, Kühn C. In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences. Cells 2020; 9:cells9081806. [PMID: 32751504 PMCID: PMC7464727 DOI: 10.3390/cells9081806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/05/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced by RNase_MRP (ribozyme RNA). We specifically investigated the intronic circRNA of ATXN2L, which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.
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Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France;
- Correspondence:
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France;
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
- Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany
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10
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Finkel Y, Schmiedel D, Tai-Schmiedel J, Nachshon A, Winkler R, Dobesova M, Schwartz M, Mandelboim O, Stern-Ginossar N. Comprehensive annotations of human herpesvirus 6A and 6B genomes reveal novel and conserved genomic features. eLife 2020; 9:e50960. [PMID: 31944176 PMCID: PMC6964970 DOI: 10.7554/elife.50960] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/27/2019] [Indexed: 12/14/2022] Open
Abstract
Human herpesvirus-6 (HHV-6) A and B are ubiquitous betaherpesviruses, infecting the majority of the human population. They encompass large genomes and our understanding of their protein coding potential is far from complete. Here, we employ ribosome-profiling and systematic transcript-analysis to experimentally define HHV-6 translation products. We identify hundreds of new open reading frames (ORFs), including upstream ORFs (uORFs) and internal ORFs (iORFs), generating a complete unbiased atlas of HHV-6 proteome. By integrating systematic data from the prototypic betaherpesvirus, human cytomegalovirus, we uncover numerous uORFs and iORFs conserved across betaherpesviruses and we show uORFs are enriched in late viral genes. We identified three highly abundant HHV-6 encoded long non-coding RNAs, one of which generates a non-polyadenylated stable intron appearing to be a conserved feature of betaherpesviruses. Overall, our work reveals the complexity of HHV-6 genomes and highlights novel features conserved between betaherpesviruses, providing a rich resource for future functional studies.
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Affiliation(s)
- Yaara Finkel
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Dominik Schmiedel
- The Lautenberg Center for General and Tumor ImmunologyInstitute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical SchoolJerusalemIsrael
| | | | - Aharon Nachshon
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Roni Winkler
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Martina Dobesova
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Michal Schwartz
- Department of Molecular GeneticsWeizmann Institute of ScienceRehovotIsrael
| | - Ofer Mandelboim
- The Lautenberg Center for General and Tumor ImmunologyInstitute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical SchoolJerusalemIsrael
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11
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Tay MLI, Pek JW. SON protects nascent transcripts from unproductive degradation by counteracting DIP1. PLoS Genet 2019; 15:e1008498. [PMID: 31730657 PMCID: PMC6881055 DOI: 10.1371/journal.pgen.1008498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/27/2019] [Accepted: 10/28/2019] [Indexed: 11/18/2022] Open
Abstract
Gene expression involves the transcription and splicing of nascent transcripts through the removal of introns. In Drosophila, a double-stranded RNA binding protein Disco-interacting protein 1 (DIP1) targets INE-1 stable intronic sequence RNAs (sisRNAs) for degradation after splicing. How nascent transcripts that also contain INE-1 sequences escape degradation remains unknown. Here we observe that these nascent transcripts can also be bound by DIP1 but the Drosophila homolog of SON (Dsn) protects them from unproductive degradation in ovaries. Dsn localizes to the satellite body where active decay of INE-1 sisRNAs by DIP1 occurs. Dsn is a repressor of DIP1 posttranslational modifications (primarily sumoylation) that are assumed to be required for efficient DIP1 activity. Moreover, the pre-mRNA destabilization caused by Dsn depletion is rescued in DIP1 or Sumo heterozygous mutants, suggesting that Dsn is a negative regulator of DIP1. Our results reveal that under normal circumstances nascent transcripts are susceptible to DIP1-mediated degradation, however intronic sequences are protected by Dsn until intron excision has taken place.
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Affiliation(s)
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail:
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12
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Parenteau J, Abou Elela S. Introns: Good Day Junk Is Bad Day Treasure. Trends Genet 2019; 35:923-934. [PMID: 31668856 DOI: 10.1016/j.tig.2019.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 02/01/2023]
Abstract
Introns are ubiquitous in eukaryotic transcripts. They are often viewed as junk RNA but the huge energetic burden of transcribing, removing, and degrading them suggests a significant evolutionary advantage. Ostensibly, an intron functions within the host pre-mRNA to regulate its splicing, transport, and degradation. However, recent studies have revealed an entirely new class of trans-acting functions where the presence of intronic RNA in the cell impacts the expression of other genes in trans. Here, we review possible new mechanisms of intron functions, with a focus on the role of yeast introns in regulating the cell growth response to starvation.
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Affiliation(s)
- Julie Parenteau
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada.
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13
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Postnikova O, Poliakov E, Golestaneh N, Rogozin IB, Redmond TM. Stable Intronic Sequences and Exon Skipping Events in the Human RPE65 Gene: Analysis of Expression in Retinal Pigment Epithelium Cells and Cell Culture Models. Front Genet 2019; 10:634. [PMID: 31379919 PMCID: PMC6658614 DOI: 10.3389/fgene.2019.00634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/17/2019] [Indexed: 12/04/2022] Open
Abstract
Currently, there is much interest in intronic sequence-containing long non-coding RNAs and the role of intronic transcription in regulation of cellular metabolism and fate. Several stable intronic sequence RNAs (sisRNAs) were recently implicated in regulation of parental genes. To investigate transcription from introns of the RPE65 gene, we analyzed RNA-seq and Nanopore sequencing data from different cell models of human retinal pigment epithelium (RPE) and native bovine RPE. We discovered putative stable poly-adenylated transcripts with sequences corresponding to intronic regions of the RPE65 gene in the cytoplasm of RPE cells. These stable intronic sequences could be important for RPE65 transcription, splicing or translation. We also analyzed alternative splicing events in RPE65. Frequent exon skipping events involving exons 2, 3, and 7 were detected. The rate of these events was much higher in human RPE cell cultures compared with native RPE , consistent with lack of translation of RPE65 mRNA in cell cultures.
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Affiliation(s)
- Olga Postnikova
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH, Bethesda, MD, United States
| | - Eugenia Poliakov
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH, Bethesda, MD, United States
| | - Nady Golestaneh
- Departments of Ophthalmology, Neurology, Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, United States
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, United States
| | - T Michael Redmond
- Laboratory of Retinal Cell & Molecular Biology, National Eye Institute, NIH, Bethesda, MD, United States
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14
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Robic A, Faraut T, Djebali S, Weikard R, Feve K, Maman S, Kuehn C. Analysis of pig transcriptomes suggests a global regulation mechanism enabling temporary bursts of circular RNAs. RNA Biol 2019; 16:1190-1204. [PMID: 31120323 DOI: 10.1080/15476286.2019.1621621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
To investigate the dynamics of circRNA expression in pig testes, we designed specific strategies to individually study circRNA production from intron lariats and circRNAs originating from back-splicing of two exons. By applying these methods on seven Total-RNA-seq datasets sampled during the testicular puberty, we detected 126 introns in 114 genes able to produce circRNAs and 5,236 exonic circRNAs produced by 2,516 genes. Comparing our RNA-seq datasets to datasets from the literature (embryonic cortex and postnatal muscle stages) revealed highly abundant intronic and exonic circRNAs in one sample each in pubertal testis and embryonic cortex, respectively. This abundance was due to higher production of circRNA by the same genes in comparison to other testis samples, rather than to the recruitment of new genes. No global relationship between circRNA and mRNA production was found. We propose ExoCirc-9244 (SMARCA5) as a marker of a particular stage in testis, which is characterized by a very low plasma estradiol level and a high abundance of circRNA in testis. We hypothesize that the abundance of testicular circRNA is associated with an abrupt switch of the cellular process to overcome a particular challenge that may have arisen in the early stages of steroid production. We also hypothesize that, in certain circumstances, isoforms and circular transcripts from different genes share functions and that a global regulation of circRNA production is established. Our data indicate that this massive production of circRNAs is much more related to the structure of the genes generating circRNAs than to their function. Abbreviations: PE: Paired Ends; CR: chimeric Read; SR: Split Read; circRNA: circular RNA; NC: non conventional; ExoCirc-RNA: exonic circular RNA; IntroLCirc-: name of a porcine intronic lariat circRNA; ExoCirc-: name of a porcine exonic circRNA; IntronCircle-: name of a porcine intron circle; sisRNA: stable intronic sequence RNA; P: porcine breed Pietrain; LW: porcine breed Large White; RT: reverse transcription/reverse transcriptase; Total-RNA-seq: RNA-seq obtained from total RNA after ribosomal depletion; mRNA-seq: RNA-seq of poly(A) transcripts; TPM: transcripts per million; CR-PM: chimeric reads per million; RBP: RNA binding protein; miRNA: micro RNA; E2: estradiol; DHT: dihydrotestesterone.
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Affiliation(s)
- Annie Robic
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Thomas Faraut
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Sarah Djebali
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Rosemarie Weikard
- b Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany
| | - Katia Feve
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France
| | - Sarah Maman
- a GenPhySE, Université de Toulouse, INRA, ENVT , Castanet-Tolosan , France.,c Sigenae group, GenPhySE, INRA Auzeville , Castanet Tolosan , France
| | - Christa Kuehn
- b Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN) , Dummerstorf , Germany.,d Faculty of Agricultural and Environmental Sciences, University of Rostock , Rostock , Germany
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15
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Montes M, Sanford BL, Comiskey DF, Chandler DS. RNA Splicing and Disease: Animal Models to Therapies. Trends Genet 2019; 35:68-87. [PMID: 30466729 PMCID: PMC6339821 DOI: 10.1016/j.tig.2018.10.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023]
Abstract
Alternative splicing of pre-mRNA increases genetic diversity, and recent studies estimate that most human multiexon genes are alternatively spliced. If this process is not highly regulated and accurate, it leads to mis-splicing events, which may result in proteins with altered function. A growing body of work has implicated mis-splicing events in a range of diseases, including cancer, neurodegenerative diseases, and muscular dystrophies. Understanding the mechanisms that cause aberrant splicing events and how this leads to disease is vital for designing effective therapeutic strategies. In this review, we focus on advances in therapies targeting splicing, and highlight the animal models developed to recapitulate disease phenotypes as a model for testing these therapies.
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Affiliation(s)
- Matías Montes
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Brianne L Sanford
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel F Comiskey
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Dawn S Chandler
- Molecular, Cellular, and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA; Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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16
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Stable Intronic Sequence RNAs (sisRNAs): An Expanding Universe. Trends Biochem Sci 2018; 44:258-272. [PMID: 30391089 DOI: 10.1016/j.tibs.2018.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/11/2018] [Accepted: 09/21/2018] [Indexed: 12/26/2022]
Abstract
Intronic sequences are often regarded as 'nonsense' transcripts that are rapidly degraded. We highlight here recent studies on intronic sequences that play regulatory roles as long noncoding RNAs (lncRNAs) which are classified as sisRNAs. Interestingly, sisRNAs come in different forms and are produced via a variety of ways. They regulate genes at the DNA, RNA, and protein levels, and frequently engage in autoregulatory feedback loops to ensure cellular homeostasis under normal and stress conditions. Future directions, evolutionary insights, and potential implications of dysregulated sisRNAs are also discussed, especially in relation to human pathogenesis.
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17
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Osman I, Pek JW. A sisRNA/miRNA Axis Prevents Loss of Germline Stem Cells during Starvation in Drosophila. Stem Cell Reports 2018; 11:4-12. [PMID: 30008327 PMCID: PMC6067505 DOI: 10.1016/j.stemcr.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
Animal reproduction responds to nutritional status. During starvation, Drosophila and Caenorhabditis elegans enter a period of reproductive diapause with increase apoptosis, while maintaining a stable pool of germline stem cells (GSCs). How GSCs are protected is not understood. Here, we show that a sisRNA/miRNA axis maintains ovarian GSCs during starvation in Drosophila. Starvation induces the expression of an ovary-enriched sisRNA sisR-2, which negatively regulates GSC maintenance via a fatty acid metabolism gene dFAR1. sisR-2 promotes the expression of bantam, which in turn inhibits the activity of sisR-2, forming a negative feedback loop. Therefore, bantam acts as a buffer to counteract sisR-2 activity to prevent GSC loss during starvation. We propose that the sisR-2/bantam axis confers robustness to GSCs in Drosophila. sisR-2 regulates the number of GSCs sisR-2 regulates GSC maintenance by repressing dFAR1 bantam regulates GSC maintenance by repressing sisR-2 activity sisR-2/bantam axis protects GSCs from starvation
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Affiliation(s)
- Ismail Osman
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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18
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Ng AYE, Peralta KRG, Pek JW. Germline Stem Cell Heterogeneity Supports Homeostasis in Drosophila. Stem Cell Reports 2018; 11:13-21. [PMID: 29887366 PMCID: PMC6066994 DOI: 10.1016/j.stemcr.2018.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/07/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023] Open
Abstract
Adult and embryonic stem cells exhibit fluctuating gene expression; however, the biological significance of stem cell heterogeneity is not well understood. We show that, in Drosophila, female germline stem cells (GSCs) exhibit heterogeneous expression of a GSC differentiation-promoting factor Regena (Rga). The Drosophila homolog of human SON, dsn, is required to maintain GSC heterogeneity by suppressing sustained high levels of Rga. Reducing the expression of Rga in dsn mutants restores GSC heterogeneity and self-renewal. Thus, GSC heterogeneity is linked to GSC homeostasis. Female germline stem cells have heterogeneous Rga expression dsn suppresses rga transcription and maintains heterogeneity dsn maintains germline stem cells Lowering rga restores heterogeneity and suppresses dsn phenotypes
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Affiliation(s)
- Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | | | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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19
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Jia Ng SS, Zheng RT, Osman I, Pek JW. Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns. iScience 2018; 4:68-75. [PMID: 30240754 PMCID: PMC6146417 DOI: 10.1016/j.isci.2018.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/25/2018] [Accepted: 05/14/2018] [Indexed: 01/26/2023] Open
Abstract
Although stable intronic sequence RNAs (sisRNAs) are conserved in plants and animals, their functional significance is still unclear. We identify a pool of polyadenylated maternally deposited sisRNAs in Drosophila melanogaster. These sisRNAs can be generated by independent transcription from the cognate introns. The ovary-specific poly(A) polymerase Wispy mediates the polyadenylation of maternal sisRNAs and confers their stability as maternal transcripts. A developmentally regulated sisRNA sisR-3 represses the expression of a long noncoding RNA CR44148 and is required during development. Our results expand the pool of sisRNAs and suggest that sisRNAs perform regulatory functions during development in Drosophila. Identification of polyadenylated sisRNAs sisRNAs can be produced from independent transcription sisR-3 regulates a long noncoding RNA sisR-3 is required during development
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Affiliation(s)
- Sharon Si Jia Ng
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore 529757, Singapore
| | - Ruther Teo Zheng
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore 599489, Singapore
| | - Ismail Osman
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore 117543, Singapore, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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20
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Pek JW. Stable Intronic Sequence RNAs Engage in Feedback Loops. Trends Genet 2018; 34:330-332. [DOI: 10.1016/j.tig.2018.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/10/2018] [Indexed: 01/27/2023]
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21
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Irimie AI, Zimta AA, Ciocan C, Mehterov N, Dudea D, Braicu C, Berindan-Neagoe I. The Unforeseen Non-Coding RNAs in Head and Neck Cancer. Genes (Basel) 2018; 9:genes9030134. [PMID: 29494516 PMCID: PMC5867855 DOI: 10.3390/genes9030134] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/18/2022] Open
Abstract
Previously ignored non-coding RNAs (ncRNAs) have become the subject of many studies. However, there is an imbalance in the amount of consideration that ncRNAs are receiving. Some transcripts such as microRNAs (miRNAs) or small interfering RNAs (siRNAs) have gained much attention, but it is necessary to investigate other “pieces of the RNA puzzle”. These can offer a more complete view over normal and pathological cell behavior. The other ncRNA species are less studied, either due to their recent discovery, such as stable intronic sequence RNA (sisRNA), YRNA, miRNA-offset RNAs (moRNA), telomerase RNA component (TERC), natural antisense transcript (NAT), transcribed ultraconserved regions (T-UCR), and pseudogene transcript, or because they are still largely seen as non-coding transcripts with no relevance to pathogenesis. Moreover, some are still considered housekeeping RNAs, for instance small nucleolar RNAs (snoRNAs) and TERC. Our review summarizes the biogenesis, mechanism of action and potential role of less known ncRNAs in head and neck cancer, with a particular focus on the installment and progress for this particular cancer type.
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Affiliation(s)
- Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Alina-Andreea Zimta
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cristina Ciocan
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University Plovdiv, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
- Technological Center for Emergency Medicine, BulVasilAprilov 15-А, Plovdiv 4002, Bulgaria.
| | - Diana Dudea
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutic, Aesthetic, "IuliuHatieganu" University of Medicine and Pharmacy, Cluj-Napoca, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu-Hatieganu, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Research Center for Functional Genomics and Translational Medicine, "IuliuHatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Republicii 34 Street, 400015 Cluj-Napoca, Romania.
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22
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Tompkins VS, Valverde DP, Moss WN. Human regulatory proteins associate with non-coding RNAs from the EBV IR1 region. BMC Res Notes 2018; 11:139. [PMID: 29458410 PMCID: PMC5819218 DOI: 10.1186/s13104-018-3250-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/12/2018] [Indexed: 12/11/2022] Open
Abstract
Objective The function of Epstein–Barr virus (EBV) stable intronic sequence (sis)RNAs, non-coding RNAs transcribed from a region required for EBV-mediated cellular transformation, remain unknown. To better understand the function of ebv-sisRNA-1 and ebv-sisRNA-2 from the internal repeat (IR)1 region of EBV, we used a combination of bioinformatics and biochemistry to identify associated RNA binding proteins. The findings reported here are part of ongoing studies to determine the functions of non-coding RNAs from the IR1 region of EBV. Results Human regulatory proteins HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPC, HNRNPL, HuR (human antigen R), and protein LIN28A (lin-28 homolog A) were predicted to bind ebv-sisRNA-1 and/or ebv-sisRNA-2; FUS (fused in sarcoma) was predicted to associate with ebv-sisRNA-2. Protein interactions were validated using a combination of RNA immunoprecipitation and biotin pulldown assays. Both sisRNAs also precipitated with HNRNPD and NONO (non-POU domain-containing octamer-binding protein). Interestingly, each of these interacting proteins also precipitated non-spliced non-coding RNA sequences transcribed from the IR1 region. Our findings suggest interesting roles for sisRNAs (through their interactions with regulatory proteins) and provide further evidence for the existence of non-spliced stable non-coding RNAs. Electronic supplementary material The online version of this article (10.1186/s13104-018-3250-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- V S Tompkins
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - D P Valverde
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - W N Moss
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA.
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23
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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24
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Wong JT, Akhbar F, Ng AYE, Tay MLI, Loi GJE, Pek JW. DIP1 modulates stem cell homeostasis in Drosophila through regulation of sisR-1. Nat Commun 2017; 8:759. [PMID: 28970471 PMCID: PMC5624886 DOI: 10.1038/s41467-017-00684-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/19/2017] [Indexed: 01/09/2023] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are by-products of splicing and regulate gene expression. How sisRNAs are regulated is unclear. Here we report that a double-stranded RNA binding protein, Disco-interacting protein 1 (DIP1) regulates sisRNAs in Drosophila. DIP1 negatively regulates the abundance of sisR-1 and INE-1 sisRNAs. Fine-tuning of sisR-1 by DIP1 is important to maintain female germline stem cell homeostasis by modulating germline stem cell differentiation and niche adhesion. Drosophila DIP1 localizes to a nuclear body (satellite body) and associates with the fourth chromosome, which contains a very high density of INE-1 transposable element sequences that are processed into sisRNAs. DIP1 presumably acts outside the satellite bodies to regulate sisR-1, which is not on the fourth chromosome. Thus, our study identifies DIP1 as a sisRNA regulatory protein that controls germline stem cell self-renewal in Drosophila. Stable intronic sequence RNAs (sisRNAs) are by-products of splicing from introns with roles in embryonic development in Drosophila. Here, the authors show that the RNA binding protein DIP1 regulates sisRNAs in Drosophila, which is necessary for germline stem cell homeostasis.
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Affiliation(s)
- Jing Ting Wong
- Ngee Ann Polytechnic, 535 Clementi Road, Singapore, 599489, Singapore
| | - Farzanah Akhbar
- Temasek Polytechnic, 21 Tampines Avenue 1, Singapore, 529757, Singapore
| | - Amanda Yunn Ee Ng
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Mandy Li-Ian Tay
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore
| | - Gladys Jing En Loi
- National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, 1 Research Link National University of Singapore, Singapore, 117604, Singapore.
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25
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Tay MLI, Pek JW. Maternally Inherited Stable Intronic Sequence RNA Triggers a Self-Reinforcing Feedback Loop during Development. Curr Biol 2017; 27:1062-1067. [DOI: 10.1016/j.cub.2017.02.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/15/2017] [Accepted: 02/16/2017] [Indexed: 12/01/2022]
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