scholarly journals Mediator Is Essential for Small Nuclear and Nucleolar RNA Transcription in Yeast

2018 ◽  
Vol 38 (24) ◽  
Author(s):  
Jason P. Tourigny ◽  
Moustafa M. Saleh ◽  
Kenny Schumacher ◽  
Didier Devys ◽  
Gabriel E. Zentner
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Snorna Gene ◽  
Protein Coding ◽  
Structural Subunit ◽  
Mrna Gene ◽  
Gene Regulatory ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

ABSTRACT Eukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes and non-protein-coding RNA (ncRNA) genes, including those encoding small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has been proposed that yeast sn/snoRNA and mRNA expression relies on a set of common factors, but the extent to which regulators of mRNA genes function at yeast sn/snoRNA genes is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in sn/snoRNA gene transcription. We found that Mediator maps to sn/snoRNA gene regulatory regions and that rapid depletion of the essential structural subunit Med14 strongly reduces RNAPII and TFIIB occupancy as well as nascent transcription of sn/snoRNA genes. Deletion of Med3 and Med15, subunits of the activator-interacting Mediator tail module, does not affect Mediator recruitment to or RNAPII and TFIIB occupancy of sn/snoRNA genes. Our analyses suggest that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.

scholarly journals Mediator is essential for small nuclear and nucleolar RNA transcription in yeast

2018 ◽  
Author(s):  
Jason P. Tourigny ◽  
Moustafa M. Saleh ◽  
Gabriel E. Zentner
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Mediator Complex ◽  
Snorna Gene ◽  
Protein Coding ◽  
Mrna Gene ◽  
Gene Regulatory ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

AbstractEukaryotic RNA polymerase II (RNAPII) transcribes mRNA genes as well as non-protein coding RNAs (ncRNAs) including small nuclear and nucleolar RNAs (sn/snoRNAs). In metazoans, RNAPII transcription of sn/snoRNAs is facilitated by a number of specialized complexes, but no such complexes have been discovered in yeast. It has thus been proposed that yeast sn/snoRNA promoters use the same complement of factors as mRNA promoters, but the extent to which key regulators of mRNA genes act at sn/snoRNA genes in yeast is unclear. Here, we investigated a potential role for the Mediator complex, essential for mRNA gene transcription, in the transcription of sn/snoRNA genes. We found that the complete Mediator complex maps to most sn/snoRNA gene regulatory regions and that loss of Mediator function results in a robust reduction in RNAPII and TFIIB occupancy at sn/snoRNA genes. Furthermore, deletion of subunits of the activator-interacting Mediator tail module does not affect Mediator recruitment to, or transcription of, sn/snoRNAs. Taken together, our analyses indicate that Mediator promotes PIC formation and transcription at sn/snoRNA genes, expanding the role of this critical regulator beyond its known functions in mRNA gene transcription and demonstrating further mechanistic similarity between the transcription of mRNA and sn/snoRNA genes.

scholarly journals The emerging role of microRNAs and long noncoding RNAs in drug resistance of hepatocellular carcinoma

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Ling Wei ◽  
Xingwu Wang ◽  
Liyan Lv ◽  
Jibing Liu ◽  
Huaixin Xing ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Drug Resistance ◽  
Human Cancer ◽  
Noncoding Rnas ◽  
Circular Rna ◽  
Long Noncoding Rnas ◽  
Protein Coding ◽  
Multiple Tumor ◽  
Nucleolar Rnas

Abstract Hepatocellular carcinoma (HCC) is the fifth most common malignancy worldwide and the second most lethal human cancer. A portion of patients with advanced HCC can significantly benefit from treatments with sorafenib, adriamycin, 5-fluorouracil and platinum drugs. However, most HCC patients eventually develop drug resistance, resulting in a poor prognosis. The mechanisms involved in HCC drug resistance are complex and inconclusive. Human transcripts without protein-coding potential are known as noncoding RNAs (ncRNAs), including microRNAs (miRNAs), small nucleolar RNAs (snoRNAs), long noncoding RNAs (lncRNAs) and circular RNA (circRNA). Accumulated evidences demonstrate that several deregulated miRNAs and lncRNAs are important regulators in the development of HCC drug resistance which elucidates their potential clinical implications. In this review, we summarized the detailed mechanisms by which miRNAs and lncRNAs affect HCC drug resistance. Multiple tumor-specific miRNAs and lncRNAs may serve as novel therapeutic targets and prognostic biomarkers for HCC.

Small nucleolar RNA

1995 ◽  
Vol 73 (11-12) ◽  
pp. 845-858 ◽  
Author(s):  
Susan A. Gerbi
Keyword(s):  
Rna Polymerase Ii ◽  
Binding Sites ◽  
Ribosome Biogenesis ◽  
Internal Transcribed Spacers ◽  
28S Rrna ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
Conserved Sequence ◽  
Nucleolar Rna ◽  
Nucleolar Rnas

A growing list of small nucleolar RNAs (snoRNAs) has been characterized in eukaryotes. They are transcribed by RNA polymerase II or III; some snoRNAs are encoded in the introns of other genes. The nonintronic polymerase II transcribed snoRNAs receive a trimethylguanosine cap, probably in the nucleus, and move to the nucleolus. snoRNAs are complexed with proteins, sometimes including fibrillarin. Localization and maintenance in the nucleolus of some snoRNAs requires the presence of initial precursor rRNA (pre-rRNA). Many snoRNAs have conserved sequence boxes C and D and a 3′ terminal stem; the roles of these features are discussed. Functional assays done for a few snoRNAs indicate their roles in rRNA processing for cleavage of the external and internal transcribed spacers (ETS and ITS). U3 is the most abundant snoRNA and is needed for cleavage of ETS1 and ITS1; experimental results on U3 binding sites in pre-rRNA are reviewed. 18S rRNA production also needs U14, U22, and snR30 snoRNAs, whereas U8 snoRNA is needed for 5.8S and 28S rRNA production. Other snoRNAs that are complementary to 18S or 28S rRNA might act as chaperones to mediate RNA folding. Whether snoRNAs join together in a large rRNA processing complex (the "processome") is not yet clear. It has been hypothesized that such complexes could anchor the ends of loops in pre-rRNA containing 18S or 28S rRNA, thereby replacing base-paired stems found in pre-rRNA of prokaryotes.Key words: RNA processing, small nucleolar RNAs, nucleolus, ribosome biogenesis, rRNA processing complex.

scholarly journals An important role of the interplay between Bdnf transcription and histone acetylation in epileptogenesis

2020 ◽  
Author(s):  
Agnieszka Walczak ◽  
Iwona Czaban ◽  
Anna Skupien ◽  
Katarzyna K. Pels ◽  
Andrzej A. Szczepankiewicz ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Histone Deacetylases ◽  
Mossy Fiber ◽  
Trichostatin A ◽  
Nuclear Periphery ◽  
Neuronal Activation ◽  
Neuronal Excitation

AbstractBrain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation of Bdnf gene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning of Bdnf alleles from the nuclear periphery towards the nuclear center. This change of Bdnf intranuclear position was associated with transcriptional gene activity.In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of the Bdnf allele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of the Bdnf allele at the nuclear periphery correlates with stronger mossy fiber sprouting - an aberrant form of excitatory circuits formation. Moreover, using in vitro hippocampal cultures we showed that Bdnf repositioning is a consequence of the transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning observed after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase of Bdnf gene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.

Genome Wide Location Analysis Reveals Deregulated MicroRNA Genes In MLL Rearragned Leukemic Genome

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2507-2507
Author(s):  
Shuangli Mi ◽  
Fuhong He ◽  
Jun Wu ◽  
Jing Zhou ◽  
George Wu ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Fusion Proteins ◽  
Target Genes ◽  
Wild Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Mrna Gene

Abstract Abstract 2507 The MLL (mixed-lineage leukemia) gene encodes a histone methyltransferase that is critical in maintaining gene expression during hematopoiesis. Chromosomal translocations disrupting MLL often leads to the creation of MLL fusion genes that act as potent drivers of acute leukemia. MLL fusion proteins are oncogenic transcription factors that activate the expression of downstream target genes. Expression profiling on patient primary samples and established mouse models has revealed hundreds of protein coding genes which are either up-regulated or down-regulated in MLL associated leukemias. Persistent coexpression of two of those genes, HoxA9 and Meis1, is essential for the initiation and maintenance of MLL leukemia. Our studies have also shown strong association of a microRNA (miRNA) expression signature with MLL- rearranged leukemia, and the expression of several miRNAs were under the control of MLL wild type and fusion proteins. Although profiling of miRNA expression has been reported, the mechanisms underlying deregulated miRNA expression in MLL associated leukemia are poorly understood. Given the role of miRNA as a global suppressor of mRNA gene expression, we hypothesized that the expression of miRNAs could be directly activated by MLL fusion and/or wild type proteins upon MLL gene rearrangement and subsequently down-regulate pertinent target mRNAs to contribute to leukemogenesis. To test our hypothesis in a systematic way, we examined an inducible MLL-ENL-ER transformed mouse cell line, which grow as myeloblastic cells in the presence of MLL-ENL, and differentiate into neutrophils upon inactivation of the fusion protein. Using chromatin immunoprecipitation assay followed by next generation sequencing (ChIP-Seq), we determined whole genome MLL binding pattern in this cellular model. Upon activation of MLL-ENL, 24 miRNAs showed a significant increase in the level of MLL binding (FDR<0.25), suggesting that those genes are directly bound by the MLL-ENL fusion protein. To explore the impact of MLL fusion protein on miRNA and mRNA gene regulation, we performed whole genome expression analysis using Affymetrix mouse microarray in the presence or absence of MLL-ENL. Upon induction of MLL-ENL, the expression levels of 38 miRNAs (out of 609 tiled on the array) were increased, and 57 of 7858 expressed protein-coding genes were down-regulated. An integrative analysis of MLL binding and mRNA/miRNA expression profiling data showed that transcription of three miRNAs were activated upon binding of MLL-ENL, and ten protein coding genes are potential targets of these miRNAs. We are currently exploring the role of these three miRNAs and their respective mRNA target genes in leukemogenesis using in vitro and in vivo models. Taken together, our data suggest that MLL fusion protein may play an important role in leukemogenesis by promoting miRNA transcription, which subsequently inhibit the expression of critical mRNA target genes. Our study provides a basis to further explore the regulatory network involving MLL fusion protein and its key miRNA target genes in the leukemic genome. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner

2017 ◽  
Vol 114 (20) ◽  
pp. E3944-E3953 ◽  
Author(s):  
Corey M. Nemec ◽  
Fan Yang ◽  
Joshua M. Gilmore ◽  
Corinna Hintermair ◽  
Yi-Hsuan Ho ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Protein Complexes ◽  
Transcription Termination ◽  
Structural Data ◽  
Side Chain ◽  
Protein Coding ◽  
Pol Ii ◽  
Carboxyl Terminal ◽  
Nucleolar Rna

The carboxyl-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) orchestrates dynamic recruitment of specific cellular machines during different stages of transcription. Signature phosphorylation patterns of Y1S2P3T4S5P6S7 heptapeptide repeats of the CTD engage specific “readers.” Whereas phospho-Ser5 and phospho-Ser2 marks are ubiquitous, phospho-Thr4 is reported to only impact specific genes. Here, we identify a role for phospho-Thr4 in transcription termination at noncoding small nucleolar RNA (snoRNA) genes. Quantitative proteomics reveals an interactome of known readers as well as protein complexes that were not known to rely on Thr4 for association with Pol II. The data indicate a key role for Thr4 in engaging the machinery used for transcription elongation and termination. We focus on Rtt103, a protein that binds phospho-Ser2 and phospho-Thr4 marks and facilitates transcription termination at protein-coding genes. To elucidate how Rtt103 engages two distinct CTD modifications that are differentially enriched at noncoding genes, we relied on NMR analysis of Rtt103 in complex with phospho-Thr4– or phospho-Ser2–bearing CTD peptides. The structural data reveal that Rtt103 interacts with phospho-Thr4 in a manner analogous to its interaction with phospho-Ser2–modified CTD. The same set of hydrogen bonds involving either the oxygen on phospho-Thr4 and the hydroxyl on Ser2, or the phosphate on Ser2 and the Thr4 hydroxyl, can be formed by rotation of an arginine side chain, leaving the intermolecular interface otherwise unperturbed. This economy of design enables Rtt103 to engage Pol II at distinct sets of genes with differentially enriched CTD marks.

scholarly journals Deep sequencing of small RNA facilitates tissue and sex specific microRNA discovery in zebrafish

2015 ◽  
Author(s):  
Candida Vaz ◽  
Choon Wei Wee ◽  
Serene Gek Ping Lee ◽  
Philip W Ingham ◽  
Vivek Tanavde ◽  
...  
Keyword(s):  
The Novel ◽  
Sequencing Technology ◽  
Next Generation Sequencing Technology ◽  
Mirna Expression Data ◽  
Mrna Gene ◽  
Gene Regulatory ◽  
Genomic Resource ◽  
The Brain ◽  
Generation Sequencing

Role of microRNAs in gene regulation has been well established. Though the number of genes appear to be equal between human and zebrafish, miRNAs detected in zebrafish (~247) is significantly low compared to human (~2000; miRBase Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. Using next generation sequencing technology, we sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In few tissues (brain, gut, liver) sequencing was done sex specifically. About 16-62% of the sequenced reads mapped to known miRNAs of zebrafish, with the exceptions of ovary (5.7%) and testis (7.8%). We used miRDeep2, the miRNA predication tool, to discover the novel miRNAs using the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%) that had the largest pool of un-annotated reads. The prediction tool identified a total of 459 novel pre-miRNAs. Comparison of miRNA expression data of the tissues showed the presence of tissue and sex specific miRNAs that could serve as biomarkers. The brain and liver had highest number of tissue specific (36) and sex specific (34) miRNAs, respectively. Taken together, we have made a comprehensive approach to identify tissue and sex specific miRNAs from zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30% homology to human miRNA) as additional genomic resource for zebrafish. This resource can facilitate further investigations to understand miRNA-mRNA gene regulatory network in zebrafish which will have implications to understand human miRNA function.

scholarly journals The interplay of seizures-induced axonal sprouting and transcription-dependent Bdnf repositioning in the model of temporal lobe epilepsy

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0239111
Author(s):  
Anna Skupien-Jaroszek ◽  
Agnieszka Walczak ◽  
Iwona Czaban ◽  
Katarzyna Karolina Pels ◽  
Andrzej Antoni Szczepankiewicz ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Mossy Fiber ◽  
Trichostatin A ◽  
Nuclear Periphery ◽  
Neuronal Activation ◽  
Neuronal Excitation ◽  
The Brain

The Brain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation of Bdnf gene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning of Bdnf alleles from the nuclear periphery towards the nuclear center. This change of Bdnf intranuclear position was associated with transcriptional gene activity. In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of the Bdnf allele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of the Bdnf allele at the nuclear periphery correlates with stronger mossy fiber sprouting—an aberrant form of excitatory circuits formation. Moreover, using in vitro hippocampal cultures we showed that Bdnf repositioning is a consequence of transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning occurring after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase of Bdnf gene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.

scholarly journals Elucidating the Role of C/D snoRNA in rRNA Processing and Modification in Trypanosoma brucei

2007 ◽  
Vol 7 (1) ◽  
pp. 86-101 ◽  
Author(s):  
Sarit Barth ◽  
Boaz Shalem ◽  
Avraham Hury ◽  
Itai Dov Tkacz ◽  
Xue-hai Liang ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Gene Clusters ◽  
Snorna Gene ◽  
Small Nucleolar Rnas ◽  
Rrna Processing ◽  
Temperature Changes ◽  
Core Proteins ◽  
Processing Defects ◽  
Nucleolar Rnas

ABSTRACT Most eukaryotic C/D small nucleolar RNAs (snoRNAs) guide 2′-O methylation (Nm) on rRNA and are also involved in rRNA processing. The four core proteins that bind C/D snoRNA in Trypanosoma brucei are fibrillarin (NOP1), NOP56, NOP58, and SNU13. Silencing of NOP1 by RNA interference identified rRNA-processing and modification defects that caused lethality. Systematic mapping of 2′-O-methyls on rRNA revealed the existence of hypermethylation at certain positions of the rRNA in the bloodstream form of the parasites, suggesting that this modification may assist the parasites in coping with the major temperature changes during cycling between their insect and mammalian hosts. The rRNA-processing defects of NOP1-depleted cells suggest the involvement of C/D snoRNA in trypanosome-specific rRNA-processing events to generate the small rRNA fragments. MRP RNA, which is involved in rRNA processing, was identified in this study in one of the snoRNA gene clusters, suggesting that trypanosomes utilize a combination of unique C/D snoRNAs and conserved snoRNAs for rRNA processing.

scholarly journals ATM and ATR Pathways Signal Alternative Splicing of Drosophila TAF1 Pre-mRNA in Response to DNA Damage

2006 ◽  
Vol 26 (24) ◽  
pp. 9256-9267 ◽  
Author(s):  
Rebeccah J. Katzenberger ◽  
Matthew S. Marengo ◽  
David A. Wassarman
Keyword(s):  
Dna Damage ◽  
Alternative Splicing ◽  
Ionizing Radiation ◽  
Rna Polymerase Ii ◽  
Protein Coding ◽  
Major Mechanism ◽  
Radiation Induced ◽  
A Subunit ◽  
Eukaryotic Organisms

ABSTRACT Alternative pre-mRNA splicing is a major mechanism utilized by eukaryotic organisms to expand their protein-coding capacity. To examine the role of cell signaling in regulating alternative splicing, we analyzed the splicing of the Drosophila melanogaster TAF1 pre-mRNA. TAF1 encodes a subunit of TFIID, which is broadly required for RNA polymerase II transcription. We demonstrate that TAF1 alternative splicing generates four mRNAs, TAF1-1, TAF1-2, TAF1-3, and TAF1-4, of which TAF1-2 and TAF1-4 encode proteins that directly bind DNA through AT hooks. TAF1 alternative splicing was regulated in a tissue-specific manner and in response to DNA damage induced by ionizing radiation or camptothecin. Pharmacological inhibitors and RNA interference were used to demonstrate that ionizing-radiation-induced upregulation of TAF1-3 and TAF1-4 splicing in S2 cells was mediated by the ATM (ataxia-telangiectasia mutated) DNA damage response kinase and checkpoint kinase 2 (CHK2), a known ATM substrate. Similarly, camptothecin-induced upregulation of TAF1-3 and TAF1-4 splicing was mediated by ATR (ATM-RAD3 related) and CHK1. These findings suggest that inducible TAF1 alternative splicing is a mechanism to regulate transcription in response to developmental or DNA damage signals and provide the first evidence that the ATM/CHK2 and ATR/CHK1 signaling pathways control gene expression by regulating alternative splicing.

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