ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation

Abstract Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However, how ZFC3H1 retains RNAs and how its roles in RNA retention and degradation are related remain largely unclear. Here, we found that upon degradation inhibition, ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles (NSs) where many RNAs gain export competence. Systematic mapping of ZFC3H1 revealed that it utilizes distinct domains for condensation and RNA degradation. Interestingly, ZFC3H1 condensation activity is required for preventing RNA trafficking to NSs, but not for RNA degradation. Considering that no apparent ZFC3H1 condensates are formed in normal cells, our study suggests that nuclear RNA degradation and retention are two independent mechanisms with different preference for controlling proper export RNA pool—degradation is preferred in normal cells, and condensation retention is activated upon degradation inhibition.

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Gene expression amplification by nuclear speckle association

The Journal of Cell Biology ◽

10.1083/jcb.201904046 ◽

2019 ◽

pp. jcb.201904046 ◽

Cited By ~ 7

Author(s):

Jiah Kim ◽

Neha Chivukula Venkata ◽

Gabriela Andrea Hernandez Gonzalez ◽

Nimish Khanna ◽

Andrew S. Belmont

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Liquid Droplet ◽

Transcript Level ◽

Rna Degradation ◽

Nuclear Speckles ◽

Nascent Transcript ◽

Nuclear Compartment ◽

Transcript Levels ◽

Endogenous Genes

Many active genes reproducibly position near nuclear speckles, but the functional significance of this positioning is unknown. Here we show that HSPA1B BAC transgenes and endogenous Hsp70 genes turn on 2–4 min after heat shock (HS), irrespective of their distance to speckles. However, both total HSPA1B mRNA counts and nascent transcript levels measured adjacent to the transgene are approximately twofold higher for speckle-associated alleles 15 min after HS. Nascent transcript level fold-increases for speckle-associated alleles are 12–56-fold and 3–7-fold higher 1–2 h after HS for HSPA1B transgenes and endogenous genes, respectively. Severalfold higher nascent transcript levels for several Hsp70 flanking genes also correlate with speckle association at 37°C. Live-cell imaging reveals that HSPA1B nascent transcript levels increase/decrease with speckle association/disassociation. Initial investigation reveals that increased nascent transcript levels accompanying speckle association correlate with reduced exosome RNA degradation and larger Ser2p CTD-modified RNA polymerase II foci. Our results demonstrate stochastic gene expression dependent on positioning relative to a liquid-droplet nuclear compartment through “gene expression amplification.”

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CDK13 Mutations Drive Melanoma via Accumulation of Prematurely Terminated Transcripts

10.1101/824193 ◽

2019 ◽

Author(s):

Megan L. Insco ◽

Brian J. Abraham ◽

Sara J. Dubbury ◽

Sofia Dust ◽

Constance Wu ◽

...

Keyword(s):

Gene Expression ◽

Overall Survival ◽

Rna Polymerase Ii ◽

Kinase Activity ◽

Prognostic Significance ◽

Rna Degradation ◽

Poor Overall Survival ◽

Cyclin Dependent Kinases ◽

Nuclear Rna ◽

Melanoma Patients

AbstractTranscriptional Cyclin Dependent Kinases modulate RNA Polymerase II function to impact gene expression. Here, we show that CDK13 is mutated in 4% of patient melanomas and mutation or downregulation is associated with poor overall survival. Mutant CDK13 lacks kinase activity and overexpression in zebrafish leads to accelerated melanoma. CDK13 mutant fish and human melanomas accumulate prematurely terminated RNAs that are translated into truncated proteins. CDK13 binds to and regulates the phosphorylation of ZC3H14, a member of the PolyA eXosome Targeting (PAXT) RNA degradation complex. ZC3H14 phosphorylation recruits the PAXT complex to degrade prematurely terminated polyadenylated transcripts in the nucleus. In the presence of mutant CDK13, ZC3H14 phosphorylation is compromised and consequently fails to recruit the PAXT complex, leading to truncated transcript stabilization. This work establishes a role for CDK13 and the PAXT nuclear RNA degradation complex in cancer and has prognostic significance for melanoma patients with mutated or downregulated CDK13.

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The multitasking polyA tail: nuclear RNA maturation, degradation and export

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2018.0169 ◽

2018 ◽

Vol 373 (1762) ◽

pp. 20180169 ◽

Cited By ~ 12

Author(s):

Agnieszka Tudek ◽

Marta Lloret-Llinares ◽

Torben Heick Jensen

Keyword(s):

Saccharomyces Cerevisiae ◽

Nuclear Export ◽

Rna Degradation ◽

Human Cells ◽

Theme Issue ◽

Polya Tail ◽

Wide Range ◽

Nuclear Rna ◽

Non Coding Rnas ◽

Rna Maturation

A polyA (pA) tail is an essential modification added to the 3′ ends of a wide range of RNAs at different stages of their metabolism. Here, we describe the main sources of polyadenylation and outline their underlying biochemical interactions within the nuclei of budding yeast Saccharomyces cerevisiae , human cells and, when relevant, the fission yeast Schizosaccharomyces pombe . Polyadenylation mediated by the S. cerevisiae Trf4/5 enzymes, and their human homologues PAPD5/7, typically leads to the 3′-end trimming or complete decay of non-coding RNAs. By contrast, the primary function of canonical pA polymerases (PAPs) is to produce stable and nuclear export-competent mRNAs. However, this dichotomy is becoming increasingly blurred, at least in S. pombe and human cells, where polyadenylation mediated by canonical PAPs may also result in transcript decay. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

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Promoter-dependent nuclear RNA degradation ensures cell cycle-specific gene expression

Communications Biology ◽

10.1038/s42003-019-0441-3 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 2

Author(s):

Mathieu Catala ◽

Sherif Abou Elela

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Rna Degradation ◽

Specific Gene ◽

Specific Gene Expression ◽

Nuclear Rna

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Global Role for Polyadenylation-Assisted Nuclear RNA Degradation in Posttranscriptional Gene Silencing

Molecular and Cellular Biology ◽

10.1128/mcb.01531-07 ◽

2007 ◽

Vol 28 (2) ◽

pp. 656-665 ◽

Cited By ~ 69

Author(s):

Shao-Win Wang ◽

Abigail L. Stevenson ◽

Stephen E. Kearsey ◽

Stephen Watt ◽

Jürg Bähler

Keyword(s):

Gene Expression ◽

Gene Silencing ◽

Global Gene Expression ◽

Rna Degradation ◽

Genomic Integrity ◽

Repeat Elements ◽

Posttranscriptional Gene Silencing ◽

Rna Targets ◽

Nuclear Rna ◽

Rna Quality Control

ABSTRACT Fission yeast Cid14, a component of the TRAMP (Cid14/Trf4-Air1-Mtr4 polyadenylation) complex, polyadenylates nuclear RNA and stimulates degradation by the exosome for RNA quality control. Here, we analyze patterns of global gene expression in cells lacking the Cid14 or the Dis3/Rpr44 subunit of the nuclear exosome. We found that transcripts from many genes induced during meiosis, including key regulators, accumulated in the absence of Cid14 or Dis3. Moreover, our data suggest that additional substrates include transcripts involved in heterochromatin assembly. Mutant cells lacking Cid14 and/or Dis3 accumulate transcripts corresponding to naturally silenced repeat elements within heterochromatic domains, reflecting defects in centromeric gene silencing and derepression of subtelomeric gene expression. We also uncover roles for Cid14 and Dis3 in maintaining the genomic integrity of ribosomal DNA. Our data indicate that polyadenylation-assisted nuclear RNA turnover functions in eliminating a variety of RNA targets to control diverse processes, such as heterochromatic gene silencing, meiotic differentiation, and maintenance of genomic integrity.

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Reverse Screening Bioinformatics Approach to Identify Potential Anti Breast Cancer Targets Using Thymoquinone from Neutraceuticals Black Cumin Oil

Anti-Cancer Agents in Medicinal Chemistry ◽

10.2174/1871520619666190124155359 ◽

2019 ◽

Vol 19 (5) ◽

pp. 599-609 ◽

Cited By ~ 1

Author(s):

Sumathi Sundaravadivelu ◽

Sonia K. Raj ◽

Banupriya S. Kumar ◽

Poornima Arumugamand ◽

Padma P. Ragunathan

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Cell Cycle ◽

Cell Death ◽

In Silico ◽

Chemotherapeutic Agents ◽

Normal Cells ◽

Black Cumin ◽

In Silico Docking ◽

Wide Range

Background: Functional foods, neutraceuticals and natural antioxidants have established their potential roles in the protection of human health and diseases. Thymoquinone (TQ), the main bioactive component of Nigella sativa seeds (black cumin seeds), a plant derived neutraceutical was used by ancient Egyptians because of their ability to cure a variety of health conditions and used as a dietary food supplement. Owing to its multi targeting nature, TQ interferes with a wide range of tumorigenic processes and counteracts carcinogenesis, malignant growth, invasion, migration, and angiogenesis. Additionally, TQ can specifically sensitize tumor cells towards conventional cancer treatments (e.g., radiotherapy, chemotherapy, and immunotherapy) and simultaneously minimize therapy-associated toxic effects in normal cells besides being cost effective and safe. TQ was found to play a protective role when given along with chemotherapeutic agents to normal cells. Methods: In the present study, reverse in silico docking approach was used to search for potential molecular targets for cancer therapy. Various metastatic and apoptotic targets were docked with the target ligand. TQ was also tested for its anticancer activities for its ability to cause cell death, arrest cell cycle and ability to inhibit PARP gene expression. Results: In silico docking studies showed that TQ effectively docked metastatic targets MMPs and other apoptotic and cell proliferation targets EGFR. They were able to bring about cell death mediated by apoptosis, cell cycle arrest in the late apoptotic stage and induce DNA damage too. TQ effectively down regulated PARP gene expression which can lead to enhanced cancer cell death. Conclusion: Thymoquinone a neutraceutical can be employed as a new therapeutic agent to target triple negative breast cancer which is otherwise difficult to treat as there are no receptors on them. Can be employed along with standard chemotherapeutic drugs to treat breast cancer as a combinatorial therapy.

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Nuclear speckles: dynamic hubs of gene expression regulation

FEBS Journal ◽

10.1111/febs.16117 ◽

2021 ◽

Author(s):

İbrahim Avşar Ilık ◽

Tuğçe Aktaş

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Expression Regulation ◽

Nuclear Speckles

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The crucial roles of N6-methyladenosine (m6A) modification in the carcinogenesis and progression of colorectal cancer

Cell & Bioscience ◽

10.1186/s13578-021-00583-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhihao Fang ◽

Yiqiu Hu ◽

Jinhui Hu ◽

Yanqin Huang ◽

Shu Zheng ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Nuclear Export ◽

Messenger Rna ◽

Regulatory Proteins ◽

Biological Processes ◽

The Past ◽

Common Cancer ◽

Potential Applications ◽

Regulated Gene Expression

AbstractAs the predominant modification in RNA, N6-methyladenosine (m6A) has attracted increasing attention in the past few years since it plays vital roles in many biological processes. This chemical modification is dynamic, reversible and regulated by several methyltransferases, demethylases and proteins that recognize m6A modification. M6A modification exists in messenger RNA and affects their splicing, nuclear export, stability, decay, and translation, thereby modulating gene expression. Besides, the existence of m6A in noncoding RNAs (ncRNAs) could also directly or indirectly regulated gene expression. Colorectal cancer (CRC) is a common cancer around the world and of high mortality. Increasing evidence have shown that the changes of m6A level and the dysregulation of m6A regulatory proteins have been implicated in CRC carcinogenesis and progression. However, the underlying regulation laws of m6A modification to CRC remain elusive and better understanding of these mechanisms will benefit the diagnosis and therapy. In the present review, the latest studies about the dysregulation of m6A and its regulators in CRC have been summarized. We will focus on the crucial roles of m6A modification in the carcinogenesis and development of CRC. Moreover, we will also discuss the potential applications of m6A modification in CRC diagnosis and therapeutics.

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RNA polyadenylation and its consequences in prokaryotes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2018.0166 ◽

2018 ◽

Vol 373 (1762) ◽

pp. 20180166 ◽

Cited By ~ 7

Author(s):

Eliane Hajnsdorf ◽

Vladimir R. Kaberdin

Keyword(s):

Gene Expression ◽

State Level ◽

Rna Degradation ◽

Plasmid Copy Number ◽

Plasmid Copy ◽

Protein Coding ◽

Mrna Metabolism ◽

Isolation And Characterization ◽

Polymerase I ◽

The Impact

Post-transcriptional addition of poly(A) tails to the 3′ end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin–antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

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