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Li Y, Baptista RP, Mei X, Kissinger JC. Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics. Microb Genom 2022; 8. [PMID: 35536609 PMCID: PMC9465071 DOI: 10.1099/mgen.0.000821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Small and intermediate-size noncoding RNAs (sRNAs and is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Cryptosporidium parvum, an obligate zoonotic protist parasite responsible for the diarrhoeal disease cryptosporidiosis. Using Illumina sequencing of a small RNA library, a systematic identification of novel small and is-ncRNAs was performed in C. parvum excysted sporozoites. A total of 79 novel is-ncRNA candidates, including antisense, intergenic and intronic is-ncRNAs, were identified, including 7 new small nucleolar RNAs (snoRNAs). Expression of select novel is-ncRNAs was confirmed by RT-PCR. Phylogenetic conservation was analysed using covariance models (CMs) in related Cryptosporidium and apicomplexan parasite genome sequences. A potential new type of small ncRNA derived from tRNA fragments was observed. Overall, a deep profiling analysis of novel is-ncRNAs in C. parvum and related species revealed structural features and conservation of these novel is-ncRNAs. Covariance models can be used to detect is-ncRNA genes in other closely related parasites. These findings provide important new sequences for additional functional characterization of novel is-ncRNAs in the protist pathogen C. parvum.
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Affiliation(s)
- Yiran Li
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.,Present address: Houston Methodist Research Institute, Houston, TX, USA
| | - Xiaohan Mei
- Department of Physiology and Pharmacology, University of Georgia, Athens, GA, USA
| | - Jessica C Kissinger
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA.,Department of Genetics, University of Georgia, Athens, GA, USA
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LRIK interacts with the Ku70-Ku80 heterodimer enhancing the efficiency of NHEJ repair. Cell Death Differ 2020; 27:3337-3353. [PMID: 32587379 DOI: 10.1038/s41418-020-0581-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
Despite recent advances in our understanding of the function of long noncoding RNAs (lncRNAs), their roles and functions in DNA repair pathways remain poorly understood. By screening a panel of uncharacterized lncRNAs to identify those whose transcription is induced by double-strand breaks (DSBs), we identified a novel lncRNA referred to as LRIK that interacts with Ku, which enhances the ability of the Ku heterodimer to detect the presence of DSBs. Here, we show that depletion of LRIK generates significantly enhanced sensitivity to DSB-inducing agents and reduced DSB repair efficiency. In response to DSBs, LRIK enhances the recruitment of repair factors at DSB sites and facilitates γH2AX signaling. Our results demonstrate that LRIK is necessary for efficient repairing DSBs via nonhomologous end-joining pathway.
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Imsnc761 and DDX6 synergistically suppress cell proliferation and promote apoptosis via p53 in testicular embryonal carcinoma cells. Biosci Rep 2018; 38:BSR20180271. [PMID: 29769412 PMCID: PMC6028756 DOI: 10.1042/bsr20180271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 12/25/2022] Open
Abstract
Intermediate-sized non-coding RNAs (imsncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. In the present research, we selected imsncRNA 761 (imsnc761) as a research target. Expression analyses in a previous study showed that imsnc761 was down-regulated in maturation-arrested testis tissues as compared with the level in normal controls. In the present study, we found that imsnc761 could interact with DEAD-box helicase 6 (DDX6) to induce NTERA-2 (NT2 (testicular embryonal carcinoma cell)) cell apoptosis and proliferation inhibition via the p53 pathway. This interaction between imsnc761 and DDX6 also inhibited mitochondrial function and specific gene transcription and translation. To facilitate further research, we used label-free quantitation method to analyze the associated differences in Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways and biological processes. This confirmed the changes in several specific pathways, which matched our molecular experimental results.
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Identification and analysis of intermediate-size noncoding RNAs in the rhesus macaque fetal brain. J Genet Genomics 2017; 44:171-174. [PMID: 28302421 DOI: 10.1016/j.jgg.2017.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 01/01/2017] [Accepted: 01/06/2017] [Indexed: 11/19/2022]
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Ayana R, Singh S, Pati S. Decoding Crucial LncRNAs Implicated in Neurogenesis and Neurological Disorders. Stem Cells Dev 2017; 26:541-553. [PMID: 28095733 DOI: 10.1089/scd.2016.0290] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Unraveling transcriptional heterogeneity and the labyrinthine nature of neurodevelopment can probe insights into neuropsychiatric disorders. It is noteworthy that adult neurogenesis is restricted to the subventricular and subgranular zones of the brain. Recent studies suggest long non-coding RNAs (lncRNAs) as an avant-garde class of regulators implicated in neurodevelopment. But, paucity exists in the knowledge regarding lncRNAs in neurogenesis and their associations with neurodevelopmental defects. To address this, we extensively reviewed the existing literature databases as well as performed relevant in-silico analysis. We utilized Allen Brain Atlas (ABA) differential search module and generated a catalogue of ∼30,000 transcripts specific to the neurogenic zones, including coding and non-coding transcripts. To explore the existing lncRNAs reported in neurogenesis, we performed extensive literature mining and identified 392 lncRNAs. These degenerate lncRNAs were mapped onto the ABA transcript list leading to detection of 20 lncRNAs specific to neurogenic zones (Dentate gyrus/Lateral ventricle), among which 10 showed associations to several neurodevelopmental disorders following in-silico mapping onto brain disease databases like Simons Foundation Autism Research Initiative, AutDB, and lncRNADisease. Notably, using ABA correlation module, we could establish lncRNA-to-mRNA coexpression networks for the above 10 candidate lncRNAs. Finally, pathway prediction revealed physical, biochemical, or regulatory interactions for nine lncRNAs. In addition, ABA differential search also revealed 54 novel significant lncRNAs from the null set (∼30,000). Conclusively, this review represents an updated catalogue of lncRNAs in neurogenesis and neurological diseases, and overviews the field of OMICs-based data analysis for understanding lncRNome-based regulation in neurodevelopment.
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Affiliation(s)
- R Ayana
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India
| | - Shailja Singh
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India .,2 Special Center for Molecular Medicine, Jawaharlal Nehru University , Delhi, India
| | - Soumya Pati
- 1 Department of Life Sciences, School of Natural Sciences, Shiv Nadar University , Greater Noida, Uttar Pradesh, India
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Kiyosawa H, Okumura A, Okui S, Ushida C, Kawai G. Secondary structure-based analysis of mouse brain small RNA sequences obtained by using next-generation sequencing. Genomics 2015; 106:122-8. [DOI: 10.1016/j.ygeno.2015.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/05/2015] [Accepted: 05/13/2015] [Indexed: 01/21/2023]
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Deep profiling of the novel intermediate-size noncoding RNAs in intraerythrocytic Plasmodium falciparum. PLoS One 2014; 9:e92946. [PMID: 24713982 PMCID: PMC3979661 DOI: 10.1371/journal.pone.0092946] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 02/27/2014] [Indexed: 11/23/2022] Open
Abstract
Intermediate-size noncoding RNAs (is-ncRNAs) have been shown to play important regulatory roles in the development of several eukaryotic organisms. However, they have not been thoroughly explored in Plasmodium falciparum, which is the most virulent malaria parasite infecting human being. By using Illumina/Solexa paired-end sequencing of an is-ncRNA-specific library, we performed a systematic identification of novel is-ncRNAs in intraerythrocytic P. falciparum, strain 3D7. A total of 1,198 novel is-ncRNA candidates, including antisense, intergenic, and intronic is-ncRNAs, were identified. Bioinformatics analyses showed that the intergenic is-ncRNAs were the least conserved among different Plasmodium species, and antisense is-ncRNAs were more conserved than their sense counterparts. Twenty-two novel snoRNAs were identified, and eight potential novel classes of P. falciparum is-ncRNAs were revealed by clustering analysis. The expression of randomly selected novel is-ncRNAs was confirmed by RT-PCR and northern blotting assays. An obvious different expressional profile of the novel is-ncRNA between the early and late intraerythrocytic developmental stages of the parasite was observed. The expression levels of the antisense RNAs correlated with those of their cis-encoded sense RNA counterparts, suggesting that these is-ncRNAs are involved in the regulation of gene expression of the parasite. In conclusion, we accomplished a deep profiling analysis of novel is-ncRNAs in P. falciparum, analysed the conservation and structural features of these novel is-ncRNAs, and revealed their differential expression patterns during the development of the parasite. These findings provide important information for further functional characterisation of novel is-ncRNAs during the development of P. falciparum.
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Fan Z, Chen X, Chen R. Transcriptome-wide analysis of TDP-43 binding small RNAs identifies miR-NID1 (miR-8485), a novel miRNA that represses NRXN1 expression. Genomics 2013; 103:76-82. [PMID: 23827811 DOI: 10.1016/j.ygeno.2013.06.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/13/2013] [Accepted: 06/21/2013] [Indexed: 12/14/2022]
Abstract
The Tar DNA-binding protein 43 (TARDBP, TDP-43) regulates RNA processing and miRNA biogenesis and is known to be involved in neurodegeneration. Messenger RNA (mRNA) targets of TDP-43 have recently been systematically identified, but small RNAs (sRNAs) bound by TDP-43 have not been studied in details. Here, we reexamine cross-linking, immunoprecipitation and sequencing (CLIP-seq) data, and identify pre-miRNAs, miRNAs and piRNAs bound by TDP-43 in human and mouse brains. Subsequent analysis of TDP-43 binding miRNAs suggests that target genes are enriched in functions involving synaptic activities. We further identify a novel miRNA (miR-NID1) processed from the intron 5 of human neurexin 1, NRXN1, and show that miR-NID1 represses NRXN1 expression by binding to TDP-43. Our results are in accordance with previously published data indicating TDP-43 through binding of specific miRNAs to play roles in neurodevelopmental activities and neurological disorders and further our understanding of TDP-43 function.
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Affiliation(s)
- Zhen Fan
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaowei Chen
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runsheng Chen
- Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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Makarova JA, Ivanova SM, Tonevitsky AG, Grigoriev AI. New functions of small nucleolar RNAs. BIOCHEMISTRY (MOSCOW) 2013; 78:638-50. [DOI: 10.1134/s0006297913060096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M. Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. Genome Biol 2013; 14:R45. [PMID: 23706177 PMCID: PMC4053766 DOI: 10.1186/gb-2013-14-5-r45] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/15/2013] [Accepted: 05/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins. RESULTS Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein. CONCLUSIONS We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
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Affiliation(s)
- Shivendra Kishore
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Dominik J Jedlinski
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Afzal P Syed
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Hadi Jorjani
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
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Li A, Wei G, Wang Y, Zhou Y, Zhang XE, Bi L, Chen R. Identification of intermediate-size non-coding RNAs involved in the UV-induced DNA damage response in C. elegans. PLoS One 2012; 7:e48066. [PMID: 23144846 PMCID: PMC3492359 DOI: 10.1371/journal.pone.0048066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 09/19/2012] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND A network of DNA damage response (DDR) mechanisms functions coordinately to maintain genome integrity and prevent disease. The Nucleotide Excision Repair (NER) pathway is known to function in the response to UV-induced DNA damage. Although numbers of coding genes and miRNAs have been identified and reported to participate in UV-induced DNA damage response (UV-DDR), the precise role of non-coding RNAs (ncRNAs) in UV-DDR remains largely unknown. METHODOLOGY/PRINCIPAL FINDINGS We used high-throughput RNA-sequencing (RNA-Seq) to discover intermediate-size (70-500 nt) ncRNAs (is-ncRNAs) in C. elegans, using the strains of L4 larvae of wild-type (N2), UV-irradiated (N2/UV100) and NER-deficient mutant (xpa-1), and 450 novel non-coding transcripts were initially identified. A customized microarray assay was then applied to examine the expression profiles of both novel transcripts and known is-ncRNAs, and 57 UV-DDR-related is-ncRNA candidates showed expression variations at different levels between UV irradiated strains and non- irradiated strains. The top ranked is-ncRNA candidates with expression differences were further validated by qRT-PCR analysis, of them, 8 novel is-ncRNAs were significantly up-regulated after UV irradiation. Knockdown of two novel is-ncRNAs, ncRNA317 and ncRNA415, by RNA interference, resulted in higher UV sensitivity and significantly decreased expression of NER-related genes in C. elegans. CONCLUSIONS/SIGNIFICANCE The discovery of above two novel is-ncRNAs in this study indicated the functional roles of is-ncRNAs in the regulation of UV-DDR network, and aided our understanding of the significance of ncRNA involvement in the UV-induced DNA damage response.
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Affiliation(s)
- Aqian Li
- Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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Characterization of multiple exon 1 variants in mammalian HuD mRNA and neuron-specific transcriptional control via neurogenin 2. J Neurosci 2012; 32:11164-75. [PMID: 22895702 DOI: 10.1523/jneurosci.2247-12.2012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The RBP (RNA-binding protein) and Hu/ELAV family member HuD regulates mRNA metabolism of genes directly or indirectly involved in neuronal differentiation, learning and memory, and several neurological diseases. Given the important functions of HuD in a variety of processes, we set out to determine the mechanisms that promote HuD mRNA expression in neurons using a mouse model. Through several complementary approaches, we determined that the abundance of HuD mRNA is predominantly under transcriptional control in developing neurons. Bioinformatic and 5'RACE (rapid amplification of cDNA ends) analyses of the 5' genomic flanking region identified eight conserved HuD leader exons (E1s), two of which are novel. Expression of all E1 variants was determined in mouse embryonic (E14.5) and adult brains. Sequential deletion of the 5' regulatory region upstream of the predominantly expressed E1c variant revealed a well conserved 400 bp DNA region that contains five E-boxes and is capable of directing HuD expression specifically in neurons. Using EMSA (electrophoretic mobility shift assay), ChIP (chromatin immunoprecipitation), and 5' regulatory region deletion and mutation analysis, we found that two of these E-boxes are targets of Neurogenin 2 (Ngn2) and that this mechanism is important for HuD mRNA induction. Together, our findings reveal that transcriptional regulation of HuD involves the use of alternate leader exons and Ngn2 mediates neuron-specific mRNA expression. To our knowledge, this is the first study to identify molecular events that positively regulate HuD mRNA expression.
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