151
|
Fujita KI, Ishizuka T, Mitsukawa M, Kurata M, Masuda S. Regulating Divergent Transcriptomes through mRNA Splicing and Its Modulation Using Various Small Compounds. Int J Mol Sci 2020; 21:ijms21062026. [PMID: 32188117 PMCID: PMC7139312 DOI: 10.3390/ijms21062026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Human transcriptomes are more divergent than genes and contribute to the sophistication of life. This divergence is derived from various isoforms arising from alternative splicing. In addition, alternative splicing regulated by spliceosomal factors and RNA structures, such as the RNA G-quadruplex, is important not only for isoform diversity but also for regulating gene expression. Therefore, abnormal splicing leads to serious diseases such as cancer and neurodegenerative disorders. In the first part of this review, we describe the regulation of divergent transcriptomes using alternative mRNA splicing. In the second part, we present the relationship between the disruption of splicing and diseases. Recently, various compounds with splicing inhibitor activity were established. These splicing inhibitors are recognized as a biological tool to investigate the molecular mechanism of splicing and as a potential therapeutic agent for cancer treatment. Food-derived compounds with similar functions were found and are expected to exhibit anticancer effects. In the final part, we describe the compounds that modulate the messenger RNA (mRNA) splicing process and their availability for basic research and future clinical potential.
Collapse
|
152
|
SRSF7 maintains its homeostasis through the expression of Split-ORFs and nuclear body assembly. Nat Struct Mol Biol 2020; 27:260-273. [PMID: 32123389 PMCID: PMC7096898 DOI: 10.1038/s41594-020-0385-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/23/2020] [Indexed: 02/08/2023]
Abstract
SRSF7 is an essential RNA-binding protein whose misexpression promotes cancer. Here, we describe how SRSF7 maintains its protein homeostasis in murine P19 cells using an intricate negative feedback mechanism. SRSF7 binding to its premessenger RNA promotes inclusion of a poison cassette exon and transcript degradation via nonsense-mediated decay (NMD). However, elevated SRSF7 levels inhibit NMD and promote translation of two protein halves, termed Split-ORFs, from the bicistronic SRSF7-PCE transcript. The first half acts as dominant-negative isoform suppressing poison cassette exon inclusion and instead promoting the retention of flanking introns containing repeated SRSF7 binding sites. Massive SRSF7 binding to these sites and its oligomerization promote the assembly of large nuclear bodies, which sequester SRSF7 transcripts at their transcription site, preventing their export and restoring normal SRSF7 protein levels. We further show that hundreds of human and mouse NMD targets, especially RNA-binding proteins, encode potential Split-ORFs, some of which are expressed under specific cellular conditions.
Collapse
|
153
|
Elton TS, Ozer HG, Yalowich JC. Effects of DNA topoisomerase IIα splice variants on acquired drug resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:161-170. [PMID: 32566920 PMCID: PMC7304410 DOI: 10.20517/cdr.2019.117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DNA topoisomerase IIα (170 kDa, TOP2α/170) induces transient DNA double-strand breaks in proliferating cells to resolve DNA topological entanglements during chromosome condensation, replication, and segregation. Therefore, TOP2α/170 is a prominent target for anticancer drugs whose clinical efficacy is often compromised due to chemoresistance. Although many resistance mechanisms have been defined, acquired resistance of human cancer cell lines to TOP2α interfacial inhibitors/poisons is frequently associated with a reduction of Top2α/170 expression levels. Recent studies by our laboratory, in conjunction with earlier findings by other investigators, support the hypothesis that a major mechanism of acquired resistance to TOP2α-targeted drugs is due to alternative RNA processing/splicing. Specifically, several TOP2α mRNA splice variants have been reported which retain introns and are translated into truncated TOP2α isoforms lacking nuclear localization sequences and subsequent dysregulated nuclear-cytoplasmic disposition. In addition, intron retention can lead to truncated isoforms that lack both nuclear localization sequences and the active site tyrosine (Tyr805) necessary for forming enzyme-DNA covalent complexes and inducing DNA damage in the presence of TOP2α-targeted drugs. Ultimately, these truncated TOP2α isoforms result in decreased drug activity against TOP2α in the nucleus and manifest drug resistance. Therefore, the complete characterization of the mechanism(s) regulating the alternative RNA processing of TOP2α pre-mRNA may result in new strategies to circumvent acquired drug resistance. Additionally, novel TOP2α splice variants and truncated TOP2α isoforms may be useful as biomarkers for drug resistance, prognosis, and/or direct future TOP2α-targeted therapies.
Collapse
Affiliation(s)
- Terry S Elton
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| | - Hatice Gulcin Ozer
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Jack C Yalowich
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
154
|
Broseus L, Ritchie W. Challenges in detecting and quantifying intron retention from next generation sequencing data. Comput Struct Biotechnol J 2020; 18:501-508. [PMID: 32206209 PMCID: PMC7078297 DOI: 10.1016/j.csbj.2020.02.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/29/2019] [Accepted: 02/15/2020] [Indexed: 12/17/2022] Open
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computational assumptions that may lead to dramatically different results. We describe the various approaches for mitigating errors in detecting intron retention and for discovering IR signatures between different conditions.
Collapse
|
155
|
Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
Collapse
|
156
|
Li HD, Funk CC, Price ND. iREAD: a tool for intron retention detection from RNA-seq data. BMC Genomics 2020; 21:128. [PMID: 32028886 PMCID: PMC7006120 DOI: 10.1186/s12864-020-6541-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating transcriptomes because it has been recognized to carry out important biological functions such as gene expression regulation and it has been found to be associated with complex diseases such as cancers. However, methods for detecting IR today are limited. Thus, there is a need to develop novel methods to improve IR detection. RESULTS Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events genome-wide from high-throughput RNA-seq data. The command line interface for iREAD is implemented in Python. iREAD takes as input a BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. It then 1) counts all reads that overlap intron regions, 2) detects IR events by analyzing the features of reads such as depth and distribution patterns, and 3) outputs a list of retained introns into a tab-delimited text file. iREAD provides significant added value in detecting IR compared with output from IRFinder with a higher AUC on all datasets tested. Both methods showed low false positive rates and high false negative rates in different regimes, indicating that use together is generally beneficial. The output from iREAD can be directly used for further exploratory analysis such as differential intron expression and functional enrichment. The software is freely available at https://github.com/genemine/iread. CONCLUSION Being complementary to existing tools, iREAD provides a new and generic tool to interrogate poly-A enriched transcriptomic data of intron regions. Intron retention analysis provides a complementary approach for understanding transcriptome.
Collapse
Affiliation(s)
- Hong-Dong Li
- Center for Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, Hunan Province, 410083, People's Republic of China
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | |
Collapse
|
157
|
Ninomiya K, Adachi S, Natsume T, Iwakiri J, Terai G, Asai K, Hirose T. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. EMBO J 2020; 39:e102729. [PMID: 31782550 PMCID: PMC6996502 DOI: 10.15252/embj.2019102729] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/17/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
A number of long noncoding RNAs (lncRNAs) are induced in response to specific stresses to construct membrane-less nuclear bodies; however, their function remains poorly understood. Here, we report the role of nuclear stress bodies (nSBs) formed on highly repetitive satellite III (HSATIII) lncRNAs derived from primate-specific satellite III repeats upon thermal stress exposure. A transcriptomic analysis revealed that depletion of HSATIII lncRNAs, resulting in elimination of nSBs, promoted splicing of 533 retained introns during thermal stress recovery. A HSATIII-Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) analysis identified multiple splicing factors in nSBs, including serine and arginine-rich pre-mRNA splicing factors (SRSFs), the phosphorylation states of which affect splicing patterns. SRSFs are rapidly de-phosphorylated upon thermal stress exposure. During stress recovery, CDC like kinase 1 (CLK1) was recruited to nSBs and accelerated the re-phosphorylation of SRSF9, thereby promoting target intron retention. Our findings suggest that HSATIII-dependent nSBs serve as a conditional platform for phosphorylation of SRSFs by CLK1 to promote the rapid adaptation of gene expression through intron retention following thermal stress exposure.
Collapse
Grants
- JP26113002 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06279 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17H03630 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP17K19335 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP19K06478 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
- Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- Tokyo Biochemical Research Foundation (TBRF)
Collapse
Affiliation(s)
| | - Shungo Adachi
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Tohru Natsume
- Molecular Profiling Research CenterNational Institute for Advanced Industrial Science and Technology (AIST)TokyoJapan
| | - Junichi Iwakiri
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Goro Terai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Kiyoshi Asai
- Graduate School of Frontier SciencesUniversity of TokyoKashiwaJapan
| | - Tetsuro Hirose
- Institute for Genetic MedicineHokkaido UniversitySapporoJapan
| |
Collapse
|
158
|
Yin Y, Shen X. Identification of cis-Elements for RNA Subcellular Localization Through REL-seq. Methods Mol Biol 2020; 2161:143-160. [PMID: 32681511 DOI: 10.1007/978-1-0716-0680-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The subcellular localization of RNAs is regulated by cis-regulatory elements together with interacting trans factors. Here we describe a high-throughput sequencing-based method named REL-seq (RNA elements for subcellular localization by sequencing) to identify the cis-elements that contribute to RNA subcellular localization. By coupling REL-seq with random mutagenesis (mutREL-seq), we can further narrow down the cis-elements to key motifs at single-nucleotide resolution.
Collapse
Affiliation(s)
- Yafei Yin
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohua Shen
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| |
Collapse
|
159
|
Nimeth BA, Riegler S, Kalyna M. Alternative Splicing and DNA Damage Response in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:91. [PMID: 32140165 PMCID: PMC7042379 DOI: 10.3389/fpls.2020.00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.
Collapse
|
160
|
Fang J, Ma Q, Chu C, Huang B, Li L, Cai P, Batista PJ, Tolentino KEM, Xu J, Li R, Du P, Qu K, Chang HY. PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications. Genome Biol 2019; 20:292. [PMID: 31862000 PMCID: PMC6924075 DOI: 10.1186/s13059-019-1880-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/05/2019] [Indexed: 01/10/2023] Open
Abstract
We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromatin and are classified into functional groups based on the patterns of their association with specific histone modifications. We find single-stranded RNA bases are more chromatin-associated, and we discover hundreds of allele-specific RNA-chromatin interactions. These results provide a unique resource to globally study the functions of chromatin-associated lncRNAs and elucidate the basic mechanisms of chromatin-RNA interactions.
Collapse
Affiliation(s)
- Jingwen Fang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qing Ma
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Ci Chu
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
| | - Beibei Huang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Lingjie Li
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
| | - Pengfei Cai
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Pedro J Batista
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
- Present Address: Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Karen Erisse Martin Tolentino
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA
| | - Pengcheng Du
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Kun Qu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Sciences, Department of Oncology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2155c, 269 Campus Drive, Stanford, CA, 94305-5168, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
161
|
Price AJ, Hwang T, Tao R, Burke EE, Rajpurohit A, Shin JH, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR. Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation. Genome Res 2019; 30:1-11. [PMID: 31852722 PMCID: PMC6961577 DOI: 10.1101/gr.250217.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022]
Abstract
Transcriptome compartmentalization by the nuclear membrane provides both stochastic and functional buffering of transcript activity in the cytoplasm, and has recently been implicated in neurodegenerative disease processes. Although many mechanisms regulating transcript compartmentalization are also prevalent in brain development, the extent to which subcellular localization differs as the brain matures has yet to be addressed. To characterize the nuclear and cytoplasmic transcriptomes during brain development, we sequenced both RNA fractions from homogenate prenatal and adult human postmortem cortex using poly(A)+ and Ribo-Zero library preparation methods. We find that while many genes are differentially expressed by fraction and developmental expression changes are similarly detectable in nuclear and cytoplasmic RNA, the compartmented transcriptomes become more distinct as the brain matures, perhaps reflecting increased utilization of nuclear retention as a regulatory strategy in adult brain. We examined potential mechanisms of this developmental divergence including alternative splicing, RNA editing, nuclear pore composition, RNA-binding protein motif enrichment, and RNA secondary structure. Intron retention is associated with greater nuclear abundance in a subset of transcripts, as is enrichment for several splicing factor binding motifs. Finally, we examined disease association with fraction-regulated gene sets and found nuclear-enriched genes were also preferentially enriched in gene sets associated with neurodevelopmental psychiatric disorders. These results suggest that although gene-level expression is globally comparable between fractions, nuclear retention of transcripts may play an underappreciated role in developmental regulation of gene expression in brain, particularly in genes whose dysregulation is related to neuropsychiatric disorders.
Collapse
Affiliation(s)
- Amanda J Price
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA.,McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Taeyoung Hwang
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA
| | - Ran Tao
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA
| | - Emily E Burke
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA
| | | | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA.,McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, Maryland 21205, USA.,McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| |
Collapse
|
162
|
Saini H, Bicknell AA, Eddy SR, Moore MJ. Free circular introns with an unusual branchpoint in neuronal projections. eLife 2019; 8:e47809. [PMID: 31697236 PMCID: PMC6879206 DOI: 10.7554/elife.47809] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.
Collapse
Affiliation(s)
- Harleen Saini
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
| | - Alicia A Bicknell
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Sean R Eddy
- Department of Molecular and Cellular BiologyHoward Hughes Medical Institute, Harvard UniversityCambridgeUnited States
- John A Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeUnited States
| | - Melissa J Moore
- RNA Therapeutics InstituteUniversity of Massachusetts Medical SchoolWorcesterUnited States
| |
Collapse
|
163
|
Maita H, Nakagawa S. What is the switch for coupling transcription and splicing? RNA Polymerase II C‐terminal domain phosphorylation, phase separation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1574. [DOI: 10.1002/wrna.1574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Hiroshi Maita
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan
| |
Collapse
|
164
|
Obeng EA, Stewart C, Abdel-Wahab O. Altered RNA Processing in Cancer Pathogenesis and Therapy. Cancer Discov 2019; 9:1493-1510. [PMID: 31611195 PMCID: PMC6825565 DOI: 10.1158/2159-8290.cd-19-0399] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/21/2019] [Accepted: 08/08/2019] [Indexed: 12/17/2022]
Abstract
Major advances in our understanding of cancer pathogenesis and therapy have come from efforts to catalog genomic alterations in cancer. A growing number of large-scale genomic studies have uncovered mutations that drive cancer by perturbing cotranscriptional and post-transcriptional regulation of gene expression. These include alterations that affect each phase of RNA processing, including splicing, transport, editing, and decay of messenger RNA. The discovery of these events illuminates a number of novel therapeutic vulnerabilities generated by aberrant RNA processing in cancer, several of which have progressed to clinical development. SIGNIFICANCE: There is increased recognition that genetic alterations affecting RNA splicing and polyadenylation are common in cancer and may generate novel therapeutic opportunities. Such mutations may occur within an individual gene or in RNA processing factors themselves, thereby influencing splicing of many downstream target genes. This review discusses the biological impact of these mutations on tumorigenesis and the therapeutic approaches targeting cells bearing these mutations.
Collapse
Affiliation(s)
- Esther A Obeng
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Connor Stewart
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
165
|
PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia. Nat Struct Mol Biol 2019; 26:999-1012. [PMID: 31611688 PMCID: PMC6858565 DOI: 10.1038/s41594-019-0313-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/03/2019] [Indexed: 12/28/2022]
Abstract
Protein arginine methyltransferase 5 (PRMT5) has emerged as a promising cancer drug target, and three PRMT5 inhibitors are currently in clinical trials for multiple malignancies. In this study, we investigated the role of PRMT5 in human acute myeloid leukemia (AML). Using an enzymatic dead version of PRMT5 and a PRMT5-specific inhibitor, we demonstrated the requirement of the catalytic activity of PRMT5 for the survival of AML cells. We then identified PRMT5 substrates using multiplexed quantitative proteomics and investigated their role in the survival of AML cells. We found that the function of the splicing regulator SRSF1 relies on its methylation by PRMT5 and that loss of PRMT5 leads to changes in alternative splicing of multiple essential genes. This explains the requirement of PRMT5 for leukemia cell survival. We show that PRMT5 regulates binding of SRSF1 to mRNAs and proteins and provide potential biomarkers for the treatment response to PRMT5 inhibitors.
Collapse
|
166
|
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. Proc Natl Acad Sci U S A 2019; 116:19490-19499. [PMID: 31501331 PMCID: PMC6765259 DOI: 10.1073/pnas.1912459116] [Citation(s) in RCA: 363] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The spatial organization of RNAs within cells and spatial patterning of cells within tissues play crucial roles in many biological processes. Here, we demonstrate that multiplexed error-robust FISH (MERFISH) can achieve near-genome-wide, spatially resolved RNA profiling of individual cells with high accuracy and high detection efficiency. Using this approach, we identified RNA species enriched in different subcellular compartments, observed transcriptionally distinct cell states corresponding to different cell-cycle phases, and revealed spatial patterning of transcriptionally distinct cells. Spatially resolved transcriptome quantification within cells further enabled RNA velocity and pseudotime analysis, which revealed numerous genes with cell cycle-dependent expression. We anticipate that spatially resolved transcriptome analysis will advance our understanding of the interplay between gene regulation and spatial context in biological systems. The expression profiles and spatial distributions of RNAs regulate many cellular functions. Image-based transcriptomic approaches provide powerful means to measure both expression and spatial information of RNAs in individual cells within their native environment. Among these approaches, multiplexed error-robust fluorescence in situ hybridization (MERFISH) has achieved spatially resolved RNA quantification at transcriptome scale by massively multiplexing single-molecule FISH measurements. Here, we increased the gene throughput of MERFISH and demonstrated simultaneous measurements of RNA transcripts from ∼10,000 genes in individual cells with ∼80% detection efficiency and ∼4% misidentification rate. We combined MERFISH with cellular structure imaging to determine subcellular compartmentalization of RNAs. We validated this approach by showing enrichment of secretome transcripts at the endoplasmic reticulum, and further revealed enrichment of long noncoding RNAs, RNAs with retained introns, and a subgroup of protein-coding mRNAs in the cell nucleus. Leveraging spatially resolved RNA profiling, we developed an approach to determine RNA velocity in situ using the balance of nuclear versus cytoplasmic RNA counts. We applied this approach to infer pseudotime ordering of cells and identified cells at different cell-cycle states, revealing ∼1,600 genes with putative cell cycle-dependent expression and a gradual transcription profile change as cells progress through cell-cycle stages. Our analysis further revealed cell cycle-dependent and cell cycle-independent spatial heterogeneity of transcriptionally distinct cells. We envision that the ability to perform spatially resolved, genome-wide RNA profiling with high detection efficiency and accuracy by MERFISH could help address a wide array of questions ranging from the regulation of gene expression in cells to the development of cell fate and organization in tissues.
Collapse
|
167
|
Ohtani M, Wachter A. NMD-Based Gene Regulation-A Strategy for Fitness Enhancement in Plants? PLANT & CELL PHYSIOLOGY 2019; 60:1953-1960. [PMID: 31111919 DOI: 10.1093/pcp/pcz090] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/22/2019] [Indexed: 05/20/2023]
Abstract
Post-transcriptional RNA quality control is a vital issue for all eukaryotes to secure accurate gene expression, both on a qualitative and quantitative level. Among the different mechanisms, nonsense-mediated mRNA decay (NMD) is an essential surveillance system that triggers degradation of both aberrant and physiological transcripts. By targeting a substantial fraction of all transcripts for degradation, including many alternative splicing variants, NMD has a major impact on shaping transcriptomes. Recent progress on the transcriptome-wide profiling and physiological analyses of NMD-deficient plant mutants revealed crucial roles for NMD in gene regulation and environmental responses. In this review, we will briefly summarize our current knowledge of the recognition and degradation of NMD targets, followed by an account of NMD's regulation and physiological functions. We will specifically discuss plant-specific aspects of RNA quality control and its functional contribution to the fitness and environmental responses of plants.
Collapse
Affiliation(s)
- Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Johannes von M�ller-Weg 6, Mainz, Germany
| |
Collapse
|
168
|
Corsini NS, Peer AM, Moeseneder P, Roiuk M, Burkard TR, Theussl HC, Moll I, Knoblich JA. Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation. Cell Stem Cell 2019; 22:543-558.e12. [PMID: 29625069 DOI: 10.1016/j.stem.2018.03.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 01/05/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Stem cell-specific transcriptional networks are well known to control pluripotency, but constitutive cellular processes such as mRNA splicing and protein synthesis can add complex layers of regulation with poorly understood effects on cell-fate decisions. Here, we show that the RNA binding protein HTATSF1 controls embryonic stem cell differentiation by regulating multiple aspects of RNA processing during ribosome biogenesis. HTATSF1, in a complex with splicing factor SF3B1, controls intron removal from ribosomal protein transcripts and regulates ribosomal RNA transcription and processing, thereby controlling 60S ribosomal abundance and protein synthesis. HTATSF1-dependent protein synthesis is essential for naive pre-implantation epiblast to transition into post-implantation epiblast, a stage with transiently low protein synthesis, and further differentiation toward neuroectoderm. Together, these results identify coordinated regulation of ribosomal RNA and protein synthesis by HTATSF1 and show that this essential mechanism controls protein synthesis during early mammalian embryogenesis.
Collapse
Affiliation(s)
- Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Angela M Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Paul Moeseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Mykola Roiuk
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Thomas R Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Hans-Christian Theussl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
169
|
Neugebauer KM. Nascent RNA and the Coordination of Splicing with Transcription. Cold Spring Harb Perspect Biol 2019; 11:11/8/a032227. [PMID: 31371351 DOI: 10.1101/cshperspect.a032227] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other processing events during its synthesis. This review discusses the development of three major methods that enable us to track the conversion of precursor messenger RNA (pre-mRNA) to messenger RNA (mRNA) products in vivo: live-cell imaging, metabolic labeling of RNA, and RNA-seq of purified nascent RNA. These approaches are complementary, addressing distinct issues of transcription rates and intron lifetimes alongside spatial information regarding the gene position of Pol II at which spliceosomes act. The findings will be placed in the context of active transcription units, each of which-because of the presence of nascent RNA, Pol II, and features of the chromatin environment-will recruit a potentially gene-specific constellation of RNA binding proteins and processing machineries.
Collapse
Affiliation(s)
- Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| |
Collapse
|
170
|
Lloyd JPB, Lang D, Zimmer AD, Causier B, Reski R, Davies B. The loss of SMG1 causes defects in quality control pathways in Physcomitrella patens. Nucleic Acids Res 2019; 46:5822-5836. [PMID: 29596649 PMCID: PMC6009662 DOI: 10.1093/nar/gky225] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 03/16/2018] [Indexed: 12/16/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is important for RNA quality control and gene regulation in eukaryotes. NMD targets aberrant transcripts for decay and also directly influences the abundance of non-aberrant transcripts. In animals, the SMG1 kinase plays an essential role in NMD by phosphorylating the core NMD factor UPF1. Despite SMG1 being ubiquitous throughout the plant kingdom, little is known about its function, probably because SMG1 is atypically absent from the genome of the model plant, Arabidopsis thaliana. By combining our previously established SMG1 knockout in moss with transcriptome-wide analysis, we reveal the range of processes involving SMG1 in plants. Machine learning assisted analysis suggests that 32% of multi-isoform genes produce NMD-targeted transcripts and that splice junctions downstream of a stop codon act as the major determinant of NMD targeting. Furthermore, we suggest that SMG1 is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. Consistent with this, smg1 plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The potential involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.
Collapse
Affiliation(s)
- James P B Lloyd
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Daniel Lang
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas D Zimmer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Barry Causier
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.,BIOSS - Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Brendan Davies
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, UK
| |
Collapse
|
171
|
Hansen MMK, Weinberger LS. Post-Transcriptional Noise Control. Bioessays 2019; 41:e1900044. [PMID: 31222776 PMCID: PMC6637019 DOI: 10.1002/bies.201900044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/22/2019] [Indexed: 01/01/2023]
Abstract
Recent evidence indicates that transcriptional bursts are intrinsically amplified by messenger RNA cytoplasmic processing to generate large stochastic fluctuations in protein levels. These fluctuations can be exploited by cells to enable probabilistic bet-hedging decisions. But large fluctuations in gene expression can also destabilize cell-fate commitment. Thus, it is unclear if cells temporally switch from high to low noise, and what mechanisms enable this switch. Here, the discovery of a post-transcriptional mechanism that attenuates noise in HIV is reviewed. Early in its life cycle, HIV amplifies transcriptional fluctuations to probabilistically select alternate fates, whereas at late times, HIV utilizes a post-transcriptional feedback mechanism to commit to a specific fate. Reanalyzing various reported post-transcriptional negative feedback architectures reveals that they attenuate noise more efficiently than classic transcriptional autorepression, leading to the derivation of an assay to detect post-transcriptional motifs. It is hypothesized that coupling transcriptional and post-transcriptional autoregulation enables efficient temporal noise control to benefit developmental bet-hedging decisions.
Collapse
Affiliation(s)
- Maike M. K. Hansen
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Leor S. Weinberger
- Gladstone|UCSF Center for Cell Circuitry, Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
172
|
Ding F, Elowitz MB. Constitutive splicing and economies of scale in gene expression. Nat Struct Mol Biol 2019; 26:424-432. [PMID: 31133700 DOI: 10.1038/s41594-019-0226-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/11/2019] [Indexed: 01/14/2023]
Abstract
In eukaryotic cells, many introns are constitutively, rather than alternatively, spliced and therefore do not contribute to isoform diversification. It has remained unclear what functional roles such constitutive splicing provides. To explore this issue, we asked how splicing affects the efficiency with which individual pre-messenger RNA transcripts are productively processed across different gene expression levels. We developed a quantitative single-molecule fluorescence in situ hybridization-based method to quantify splicing efficiency at transcription active sites in single cells. We found that both natural and synthetic genes in mouse and human cells exhibited an unexpected 'economy of scale' behavior in which splicing efficiency increased with transcription rate. Correlations between splicing efficiency and spatial proximity to nuclear speckles could explain this counterintuitive behavior. Functionally, economy of scale splicing represents a non-linear filter that amplifies the expression of genes when they are more strongly transcribed. These results indicate that constitutive splicing plays an active functional role in modulating gene expression.
Collapse
Affiliation(s)
- Fangyuan Ding
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
173
|
Viphakone N, Sudbery I, Griffith L, Heath CG, Sims D, Wilson SA. Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome. Mol Cell 2019; 75:310-323.e8. [PMID: 31104896 PMCID: PMC6675937 DOI: 10.1016/j.molcel.2019.04.034] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 02/25/2019] [Accepted: 04/29/2019] [Indexed: 11/29/2022]
Abstract
During gene expression, RNA export factors are mainly known for driving nucleo-cytoplasmic transport. While early studies suggested that the exon junction complex (EJC) provides a binding platform for them, subsequent work proposed that they are only recruited by the cap binding complex to the 5′ end of RNAs, as part of TREX. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are recruited to the whole mRNA co-transcriptionally via splicing but before 3′ end processing. Consequently, Alyref alters splicing decisions and Chtop regulates alternative polyadenylation. Alyref is recruited to the 5′ end of RNAs by CBC, and our data reveal subsequent binding to RNAs near EJCs. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to EJC sites but also on single-exon transcripts. Our study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome. 5′ cap binding complex CBC acts as a transient landing pad for Alyref Alyref is deposited upstream of the exon-exon junction next to the EJC Alyref can be deposited on introns and regulate splicing Chtop is mainly deposited on 3′ UTRs and influences poly(A) site choices
Collapse
Affiliation(s)
- Nicolas Viphakone
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - Ian Sudbery
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Llywelyn Griffith
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Catherine G Heath
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - David Sims
- MRC Computational Genomics Analysis and Training Programme (CGAT), MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS UK
| | - Stuart A Wilson
- Sheffield Institute For Nucleic Acids (SInFoNiA) and Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| |
Collapse
|
174
|
Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 2019; 569:503-508. [PMID: 31068700 DOI: 10.1038/s41586-019-1186-3] [Citation(s) in RCA: 1755] [Impact Index Per Article: 351.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 04/09/2019] [Indexed: 12/21/2022]
Abstract
Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets, and small-molecule and biological therapeutics and to identify new marker-driven cancer dependencies. To improve our understanding of the molecular features that contribute to cancer phenotypes, including drug responses, here we have expanded the characterizations of cancer cell lines to include genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression and reverse-phase protein array data for 1,072 cell lines from individuals of various lineages and ethnicities. Integration of these data with functional characterizations such as drug-sensitivity, short hairpin RNA knockdown and CRISPR-Cas9 knockout data reveals potential targets for cancer drugs and associated biomarkers. Together, this dataset and an accompanying public data portal provide a resource for the acceleration of cancer research using model cancer cell lines.
Collapse
|
175
|
Zuckerman B, Ulitsky I. Predictive models of subcellular localization of long RNAs. RNA (NEW YORK, N.Y.) 2019; 25:557-572. [PMID: 30745363 PMCID: PMC6467007 DOI: 10.1261/rna.068288.118] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/07/2019] [Indexed: 05/14/2023]
Abstract
Export to the cytoplasm is a key regulatory junction for both protein-coding mRNAs and long noncoding RNAs (lncRNAs), and cytoplasmic enrichment varies dramatically both within and between those groups. We used a new computational approach and RNA-seq data from human and mouse cells to quantify the genome-wide association between cytoplasmic/nuclear ratios of both gene groups and various factors, including expression levels, splicing efficiency, gene architecture, chromatin marks, and sequence elements. Splicing efficiency emerged as the main predictive factor, explaining up to a third of the variability in localization. Combination with other features allowed predictive models that could explain up to 45% of the variance for protein-coding genes and up to 34% for lncRNAs. Factors associated with localization were similar between lncRNAs and mRNAs with some important differences. Readily accessible features can thus be used to predict RNA localization.
Collapse
Affiliation(s)
- Binyamin Zuckerman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
176
|
Li HM, Ma XL, Li HG. Intriguing circles: Conflicts and controversies in circular RNA research. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1538. [PMID: 31034768 DOI: 10.1002/wrna.1538] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed RNA circles without a 5' cap or 3' tail. Since the landmark discovery of ciRS-7/CDR1as functioning as a miR-7 sponge in 2013, circRNAs have become a hot topic in RNA research. CircRNAs have been found to play active roles in cancer, cardiovascular diseases, neurological disorders, and many other diseases. They can function as microRNA (miRNA) sponges, protein scaffolds, and even translation templates. However, as circRNA research expands, many divergent views have emerged. For example, are most circRNAs competent in serving as miRNA sponges? What kinds of circRNAs are most likely to sponge miRNAs? Apart from sponging miRNAs, what could the functions of most circRNAs be? What are the features of circRNAs that are translatable? Many researchers have claimed that circRNAs are abundant, stable, conserved, and specific molecules, which hold great potential in serving as biomarkers. However, circRNA abundance is variable and some circRNAs are abundant while others are not. In addition, their stability and conservation may vary under different circumstances. Furthermore, it is unclear whether circRNA biogenesis is more likely to be regulated by RNA binding proteins or transcription factors. All of these are open questions that remain to be answered by researchers in this field. Discussing and investigating these questions will advance the understanding of this class of novel molecules and may propel inspiring new ideas for future studies. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA in Disease and Development > RNA in Disease RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Hui-Min Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xiu-Lan Ma
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Hong-Gang Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, P. R. China
| |
Collapse
|
177
|
DNA·RNA triple helix formation can function as a cis-acting regulatory mechanism at the human β-globin locus. Proc Natl Acad Sci U S A 2019; 116:6130-6139. [PMID: 30867287 DOI: 10.1073/pnas.1900107116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We have identified regulatory mechanisms in which an RNA transcript forms a DNA duplex·RNA triple helix with a gene or one of its regulatory elements, suggesting potential auto-regulatory mechanisms in vivo. We describe an interaction at the human β-globin locus, in which an RNA segment embedded in the second intron of the β-globin gene forms a DNA·RNA triplex with the HS2 sequence within the β-globin locus control region, a major regulator of globin expression. We show in human K562 cells that the triplex is stable in vivo. Its formation causes displacement from HS2 of major transcription factors and RNA Polymerase II, and consequently in loss of factors and polymerase that bind to the human ε- and γ-globin promoters, which are activated by HS2 in K562 cells. This results in reduced expression of these genes. These effects are observed when a small length of triplex-forming RNA is introduced into cells, or when a full-length intron-containing human β-globin transcript is expressed. Related results are obtained in human umbilical cord blood-derived erythroid progenitor-2 cells, in which β-globin expression is similarly affected by triplex formation. These results suggest a model in which RNAs conforming to the strict sequence rules for DNA·RNA triplex formation may participate in feedback regulation of genes in cis.
Collapse
|
178
|
Pai AA, Luca F. Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1503. [PMID: 30216698 PMCID: PMC6294667 DOI: 10.1002/wrna.1503] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/19/2018] [Accepted: 08/01/2018] [Indexed: 12/16/2022]
Abstract
RNA processing has emerged as a key mechanistic step in the regulation of the cellular response to environmental perturbation. Recent work has uncovered extensive remodeling of transcriptome composition upon environmental perturbation and linked the impacts of this molecular plasticity to health and disease outcomes. These isoform changes and their underlying mechanisms are varied-involving alternative sites of transcription initiation, alternative splicing, and alternative cleavage at the 3' end of the mRNA. The mechanisms and consequences of differential RNA processing have been characterized across a range of common environmental insults, including chemical stimuli, immune stimuli, heat stress, and cancer pathogenesis. In each case, there are perturbation-specific contributions of local (cis) regulatory elements or global (trans) factors and downstream consequences. Overall, it is clear that choices in isoform usage involve a balance between the usage of specific genetic elements (i.e., splice sites, polyadenylation sites) and the timing at which certain decisions are made (i.e., transcription elongation rate). Fine-tuned cellular responses to environmental perturbation are often dependent on the genetic makeup of the cell. Genetic analyses of interindividual variation in splicing have identified genetic effects on splicing that contribute to variation in complex traits. Finally, the increase in the number of tissue types and environmental conditions analyzed for RNA processing is paralleled by the need to develop appropriate analytical tools. The combination of large datasets, novel methods and conditions explored promises to provide a much greater understanding of the role of RNA processing response in human phenotypic variation. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Evolution and Genomics > Computational Analyses of RNA RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
Affiliation(s)
- Athma A Pai
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, and Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan
| |
Collapse
|
179
|
Chaudhary S, Khokhar W, Jabre I, Reddy ASN, Byrne LJ, Wilson CM, Syed NH. Alternative Splicing and Protein Diversity: Plants Versus Animals. FRONTIERS IN PLANT SCIENCE 2019; 10:708. [PMID: 31244866 PMCID: PMC6581706 DOI: 10.3389/fpls.2019.00708] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/13/2019] [Indexed: 05/11/2023]
Abstract
Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.
Collapse
Affiliation(s)
- Saurabh Chaudhary
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Waqas Khokhar
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Ibtissam Jabre
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Lee J. Byrne
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Cornelia M. Wilson
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Naeem H. Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
- *Correspondence: Naeem H. Syed,
| |
Collapse
|
180
|
Němec V, Hylsová M, Maier L, Flegel J, Sievers S, Ziegler S, Schröder M, Berger B, Chaikuad A, Valčíková B, Uldrijan S, Drápela S, Souček K, Waldmann H, Knapp S, Paruch K. Furo[3,2‐b]pyridine: A Privileged Scaffold for Highly Selective Kinase Inhibitors and Effective Modulators of the Hedgehog Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Václav Němec
- Department of Chemistry, CZ-OpenscreenMasaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Michaela Hylsová
- Department of Chemistry, CZ-OpenscreenMasaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Lukáš Maier
- Department of Chemistry, CZ-OpenscreenMasaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| | - Jana Flegel
- Max-Planck-Institute für Molekulare PhysiologieAbteilung Chemische Biologie Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sonja Sievers
- Max-Planck-Institute für Molekulare PhysiologieAbteilung Chemische Biologie Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Slava Ziegler
- Max-Planck-Institute für Molekulare PhysiologieAbteilung Chemische Biologie Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Martin Schröder
- Institute for Pharmaceutical ChemistryStructural Genomics ConsortiumJohann Wolfgang Goethe-University Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - Benedict‐Tilman Berger
- Institute for Pharmaceutical ChemistryStructural Genomics ConsortiumJohann Wolfgang Goethe-University Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - Apirat Chaikuad
- Institute for Pharmaceutical ChemistryStructural Genomics ConsortiumJohann Wolfgang Goethe-University Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - Barbora Valčíková
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
- Department of BiologyFaculty of MedicineMasaryk University Kamenice 5 Brno 625 00 Czech Republic
| | - Stjepan Uldrijan
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
- Department of BiologyFaculty of MedicineMasaryk University Kamenice 5 Brno 625 00 Czech Republic
| | - Stanislav Drápela
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
- Department of CytokineticsInstitute of Biophysics CAS Královopolská 135 Brno 612 65 Czech Republic
| | - Karel Souček
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
- Department of CytokineticsInstitute of Biophysics CAS Královopolská 135 Brno 612 65 Czech Republic
| | - Herbert Waldmann
- Max-Planck-Institute für Molekulare PhysiologieAbteilung Chemische Biologie Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Stefan Knapp
- Institute for Pharmaceutical ChemistryStructural Genomics ConsortiumJohann Wolfgang Goethe-University Max-von-Laue-Strasse 15 60438 Frankfurt am Main Germany
| | - Kamil Paruch
- Department of Chemistry, CZ-OpenscreenMasaryk University Kamenice 5 Brno 625 00 Czech Republic
- International Clinical Research CentreSt. Anne's University Hospital Pekařská 53 Brno 656 91 Czech Republic
| |
Collapse
|
181
|
Němec V, Hylsová M, Maier L, Flegel J, Sievers S, Ziegler S, Schröder M, Berger BT, Chaikuad A, Valčíková B, Uldrijan S, Drápela S, Souček K, Waldmann H, Knapp S, Paruch K. Furo[3,2-b]pyridine: A Privileged Scaffold for Highly Selective Kinase Inhibitors and Effective Modulators of the Hedgehog Pathway. Angew Chem Int Ed Engl 2018; 58:1062-1066. [PMID: 30569600 DOI: 10.1002/anie.201810312] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/16/2018] [Indexed: 12/15/2022]
Abstract
Reported is the identification of the furo[3,2-b]pyridine core as a novel scaffold for potent and highly selective inhibitors of cdc-like kinases (CLKs) and efficient modulators of the Hedgehog signaling pathway. Initially, a diverse target compound set was prepared by synthetic sequences based on chemoselective metal-mediated couplings, including assembly of the furo[3,2-b]pyridine scaffold by copper-mediated oxidative cyclization. Optimization of the subseries containing 3,5-disubstituted furo[3,2-b]pyridines afforded potent, cell-active, and highly selective inhibitors of CLKs. Profiling of the kinase-inactive subset of 3,5,7-trisubstituted furo[3,2-b]pyridines revealed sub-micromolar modulators of the Hedgehog pathway.
Collapse
Affiliation(s)
- Václav Němec
- Department of Chemistry, CZ-Openscreen, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Michaela Hylsová
- Department of Chemistry, CZ-Openscreen, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Lukáš Maier
- Department of Chemistry, CZ-Openscreen, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| | - Jana Flegel
- Max-Planck-Institute für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Sonja Sievers
- Max-Planck-Institute für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Slava Ziegler
- Max-Planck-Institute für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Martin Schröder
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Barbora Valčíková
- International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Stjepan Uldrijan
- International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Stanislav Drápela
- International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Královopolská 135, Brno, 612 65, Czech Republic
| | - Karel Souček
- International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Královopolská 135, Brno, 612 65, Czech Republic
| | - Herbert Waldmann
- Max-Planck-Institute für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Kamil Paruch
- Department of Chemistry, CZ-Openscreen, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,International Clinical Research Centre, St. Anne's University Hospital, Pekařská 53, Brno, 656 91, Czech Republic
| |
Collapse
|
182
|
Mabin JW, Woodward LA, Patton RD, Yi Z, Jia M, Wysocki VH, Bundschuh R, Singh G. The Exon Junction Complex Undergoes a Compositional Switch that Alters mRNP Structure and Nonsense-Mediated mRNA Decay Activity. Cell Rep 2018; 25:2431-2446.e7. [PMID: 30466796 DOI: 10.1016/j.celrep.2018.11.046] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/22/2018] [Accepted: 11/12/2018] [Indexed: 01/08/2023] Open
Abstract
The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition, and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. To illuminate consequences of EJC composition change, we purified EJCs from human cells via peripheral proteins RNPS1 and CASC3. We show that the EJC originates as an SR-rich mega-dalton-sized RNP that contains RNPS1 but lacks CASC3. Sometime before or during translation, the EJC undergoes compositional and structural remodeling into an SR-devoid monomeric complex that contains CASC3. Surprisingly, RNPS1 is important for nonsense-mediated mRNA decay (NMD) in general, whereas CASC3 is needed for NMD of only select mRNAs. The switch to CASC3-EJC slows down NMD. Overall, the EJC compositional switch dramatically alters mRNP structure and specifies two distinct phases of EJC-dependent NMD.
Collapse
Affiliation(s)
- Justin W Mabin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Lauren A Woodward
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Robert D Patton
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Zhongxia Yi
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mengxuan Jia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Department of Physics, The Ohio State University, Columbus, OH 43210, USA; Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| |
Collapse
|
183
|
Mao M, Hu Y, Yang Y, Qian Y, Wei H, Fan W, Yang Y, Li X, Wang Z. Modeling and Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning. Cell Syst 2018; 7:510-520.e4. [PMID: 30414922 DOI: 10.1016/j.cels.2018.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 05/10/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
Alternative splicing (AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in pre-mRNAs. The human genome encodes ∼1,500 RNA binding proteins (RBPs) that potentially regulate AS, yet their functions remain largely unknown. To explore their potential activities, we fused the putative functional domains of RBPs to a sequence-specific RNA-binding domain and systemically analyzed how these engineered factors affect splicing. We discovered that ∼80% of low-complexity domains in endogenous RBPs displayed distinct context-dependent activities in regulating splicing, indicating that AS is under more extensive regulation than previously expected. We developed a machine learning approach to classify and predict the activities of RBPs based on their sequence compositions and further validated this model using endogenous RBPs and synthetic polypeptides. These results represent a systematic inspection, modeling, prediction, and validation of how RBP sequences affect their activities in controlling splicing, paving the way for de novo engineering of artificial splicing factors.
Collapse
Affiliation(s)
- Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China; Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yue Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yajie Qian
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Huanhuan Wei
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| |
Collapse
|
184
|
de Francisco Amorim M, Willing EM, Szabo EX, Francisco-Mangilet AG, Droste-Borel I, Maček B, Schneeberger K, Laubinger S. The U1 snRNP Subunit LUC7 Modulates Plant Development and Stress Responses via Regulation of Alternative Splicing. THE PLANT CELL 2018; 30:2838-2854. [PMID: 30309899 PMCID: PMC6305971 DOI: 10.1105/tpc.18.00244] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/11/2018] [Accepted: 10/05/2018] [Indexed: 05/21/2023]
Abstract
Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNPs). The U1 snRNP, which binds to 5' splice sites, plays an essential role in early steps of the splicing reaction. Here, we show that Arabidopsis thaliana LETHAL UNLESS CBC7 (LUC7) proteins, which are encoded by a three-member gene family in Arabidopsis, are important for plant development and stress resistance. We show that LUC7 is a U1 snRNP accessory protein by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affect hundreds of alternative splicing events. Interestingly, LUC7 proteins specifically promote splicing of a subset of terminal introns. Splicing of LUC7-dependent introns is a prerequisite for nuclear export, and some splicing events are modulated by stress in a LUC7-dependent manner. Taken together, our results highlight the importance of the U1 snRNP component LUC7 in splicing regulation and suggest a previously unrecognized role of a U1 snRNP accessory factor in terminal intron splicing.
Collapse
Affiliation(s)
- Marcella de Francisco Amorim
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Eva-Maria Willing
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Emese X Szabo
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| | - Anchilie G Francisco-Mangilet
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| | | | - Boris Maček
- Proteome Centre, University of Tuebingen, 72076 Tuebingen, Germany
| | | | - Sascha Laubinger
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| |
Collapse
|
185
|
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: 28] [Impact Index Per Article: 4.7] [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.
Collapse
|
186
|
Palazzo AF, Lee ES. Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs. Front Genet 2018; 9:440. [PMID: 30386371 PMCID: PMC6199362 DOI: 10.3389/fgene.2018.00440] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/26/2022] Open
Abstract
Eukaryotes are divided into two major compartments: the nucleus where RNA is synthesized and processed, and the cytoplasm, where mRNA is translated into proteins. Although many different RNAs are made, only a subset is allowed access to the cytoplasm, primarily RNAs involved in protein synthesis (mRNA, tRNA, and rRNA). In contrast, nuclear retained transcripts are mostly long non-coding RNAs (lncRNAs) whose role in cell physiology has been a source of much investigation in the past few years. In addition, it is likely that many non-functional RNAs, which arise by spurious transcription and misprocessing of functional RNAs, are also retained in the nucleus and degraded. In this review, the main sequence features that dictate whether any particular mRNA or lncRNA is a substrate for retention in the nucleus, or export to the cytoplasm, are discussed. Although nuclear export is promoted by RNA-splicing due to the fact that the spliceosome can help recruit export factors to the mature RNA, nuclear export does not require splicing. Indeed, most stable unspliced transcripts are well exported and associate with these same export factors in a splicing-independent manner. In contrast, nuclear retention is promoted by specialized cis-elements found in certain RNAs. This new understanding of the determinants of nuclear retention and cytoplasmic export provides a deeper understanding of how information flow is regulated in eukaryotic cells. Ultimately these processes promote the evolution of complexity in eukaryotes by shaping the genomic content through constructive neutral evolution.
Collapse
|
187
|
Martin SES, Tan ZW, Itkonen HM, Duveau DY, Paulo JA, Janetzko J, Boutz PL, Törk L, Moss FA, Thomas CJ, Gygi SP, Lazarus MB, Walker S. Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. J Am Chem Soc 2018; 140:13542-13545. [PMID: 30285435 DOI: 10.1021/jacs.8b07328] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reversible glycosylation of nuclear and cytoplasmic proteins is an important regulatory mechanism across metazoans. One enzyme, O-linked N-acetylglucosamine transferase (OGT), is responsible for all nucleocytoplasmic glycosylation and there is a well-known need for potent, cell-permeable inhibitors to interrogate OGT function. Here we report the structure-based evolution of OGT inhibitors culminating in compounds with low nanomolar inhibitory potency and on-target cellular activity. In addition to disclosing useful OGT inhibitors, the structures we report provide insight into how to inhibit glycosyltransferases, a family of enzymes that has been notoriously refractory to inhibitor development.
Collapse
Affiliation(s)
- Sara E S Martin
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Zhi-Wei Tan
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Harri M Itkonen
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Damien Y Duveau
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Joao A Paulo
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - John Janetzko
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Paul L Boutz
- The David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Lisa Törk
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Frederick A Moss
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Michael B Lazarus
- Department of Pharmacological Sciences , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | - Suzanne Walker
- Department of Microbiology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| |
Collapse
|
188
|
Grau-Bové X, Ruiz-Trillo I, Irimia M. Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture. Genome Biol 2018; 19:135. [PMID: 30223879 PMCID: PMC6142364 DOI: 10.1186/s13059-018-1499-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/01/2018] [Indexed: 11/30/2022] Open
Abstract
Background Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode across non-animal eukaryotes, animals have unusually high rates of exon skipping. However, when and how this high prevalence of exon skipping evolved is unknown. Since exon skipping can greatly expand proteomes, answering these questions sheds light on the evolution of higher organismal complexity in metazoans. Results We used RNA-seq data to quantify exon skipping and intron retention frequencies across 65 eukaryotic species, with particular focus on early branching animals and unicellular holozoans. We found that only bilaterians have significantly increased their exon skipping frequencies compared to all other eukaryotic groups. Unlike in other eukaryotes, however, exon skipping in nearly all animals, including non-bilaterians, is strongly enriched for frame-preserving sequences, suggesting that exon skipping involvement in proteome expansion predated the increase in frequency. We also identified architectural features consistently associated with higher exon skipping rates within all studied eukaryotic genomes. Remarkably, these architectures became more prevalent during animal evolution, indicating co-evolution between genome architectures and exon skipping frequencies. Conclusion We suggest that the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events. Second, bilaterian ancestors dramatically increased their exon skipping frequencies, likely driven by the interplay between a shift in their genome architectures towards more exon definition and recruitment of frame-preserving exon skipping events to functionally diversify their cell-specific proteomes. Electronic supplementary material The online version of this article (10.1186/s13059-018-1499-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xavier Grau-Bové
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain.,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Avinguda Diagonal 643, 08028, Barcelona, Catalonia, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. .,Departament de Genètica, Microbiologia i Estadística, Universitat de Barelona, Avinguda Diagonal 643, 08028, Barcelona, Catalonia, Spain. .,ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Catalonia, Spain.
| | - Manuel Irimia
- Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain. .,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10-12, 08002, Barcelona, Catalonia, Spain.
| |
Collapse
|
189
|
Wang K, Wang L, Wang J, Chen S, Shi M, Cheng H. Intronless mRNAs transit through nuclear speckles to gain export competence. J Cell Biol 2018; 217:3912-3929. [PMID: 30194269 PMCID: PMC6219727 DOI: 10.1083/jcb.201801184] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 07/04/2018] [Accepted: 08/09/2018] [Indexed: 01/12/2023] Open
Abstract
Nuclear speckles (NSs) store splicing factors. Wang et al. show that many naturally intronless mRNAs associate with NSs and that speckle association enhances their export by facilitating TREX recruitment, suggesting that trafficking to NSs could be an important quality control step in intronless mRNA export. Nuclear speckles (NSs) serve as splicing factor storage sites. In this study, we unexpectedly found that many endogenous intronless mRNAs, which do not undergo splicing, associate with NSs. These associations do not require transcription, polyadenylation, or the polyA tail. Rather, exonic splicing enhancers present in intronless mRNAs and their binding partners, SR proteins, promote intronless mRNA localization to NSs. Significantly, speckle targeting of mRNAs promotes the recruitment of the TREX export complex and their TREX-dependent nuclear export. Furthermore, TREX, which accumulates in NSs, is required for releasing intronless mRNAs from NSs, whereas NXF1, which is mainly detected at nuclear pores, is not. Upon NXF1 depletion, the TREX protein UAP56 loses speckle concentration but coaccumulates with intronless mRNAs and polyA RNAs in the nucleoplasm, and these RNAs are trapped in NSs upon UAP56 codepletion. We propose that the export-competent messenger RNP assembly mainly occurs in NSs for intronless mRNAs and that entering NSs serves as a quality control step in mRNA export.
Collapse
Affiliation(s)
- Ke Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lantian Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianshu Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Suli Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Min Shi
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
190
|
Harahap NIF, Niba ETE, Ar Rochmah M, Wijaya YOS, Saito T, Saito K, Awano H, Morioka I, Iijima K, Lai PS, Matsuo M, Nishio H, Shinohara M. Intron-retained transcripts of the spinal muscular atrophy genes, SMN1 and SMN2. Brain Dev 2018; 40:670-677. [PMID: 29580671 DOI: 10.1016/j.braindev.2018.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 03/02/2018] [Accepted: 03/04/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND The SMN genes, SMN1 and SMN2, are highly homologous genes which are related to the development or clinical severity of spinal muscular atrophy. Some alternative splicing patterns of the SMN genes have been well documented. In 2007, an SMN1 transcript with a full sequence of intron 3 was reported as the first intron-retained SMN transcript. METHODS Intron-retained SMN transcripts in various cells and tissues were studied using reverse transcription (RT)-PCR. HeLa cells were used for subcellular localization of the transcripts and protein expression analysis with Western blotting. RESULTS Two intron-retained SMN transcripts were detected, which contain full sequences of intron 2b or intron 3. These transcripts were produced from SMN1 and SMN2, and ubiquitously expressed in human cells and tissues. Western blotting analysis showed no proteins derived from the intron-retained transcripts. Fractionation analysis showed that these intron-retained transcripts were localized mainly in the nucleus. Contrary to our expectation, the intron-retained transcript levels decreased during the treatment of cycloheximide, an inhibitor of nonsense-mediated decay (NMD), suggesting that they were not targets of NMD. CONCLUSION Intron 2b-retained SMN transcript and intron3-retained SMN transcript were ubiquitously expressed in human cells and tissues. The intron-retained transcripts were mainly localized in the nucleus and decreased through non-NMD pathway.
Collapse
Affiliation(s)
- Nur Imma Fatimah Harahap
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; Department of Clinical Pathology, Faculty of Medicine, Universitas Gadjah Mada, Radiopoetro Building 5th Floor, Jl. Farmako, Sekip Utara, Yogyakarta 55281, Indonesia
| | - Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Mawaddah Ar Rochmah
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; Department of Neurology, Faculty of Medicine, Universitas Gadjah Mada, Jl. Kesehatan No.1, Sekip, Yogyakarta 55281, Indonesia
| | - Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Toshio Saito
- Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama 5-1-1, Toyonaka, Osaka 560-8552, Japan
| | - Kayoko Saito
- Institute of Medical Genetics, School of Medicine, Tokyo Women's Medical University, 8-1 Kawadacho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Ichiro Morioka
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, 119228, Singapore
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani, Nishi, Kobe 6512180, Japan
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| |
Collapse
|
191
|
Parra M, Booth BW, Weiszmann R, Yee B, Yeo GW, Brown JB, Celniker SE, Conboy JG. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. RNA (NEW YORK, N.Y.) 2018; 24:1255-1265. [PMID: 29959282 PMCID: PMC6097662 DOI: 10.1261/rna.066951.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
During terminal erythropoiesis, the splicing machinery in differentiating erythroblasts executes a robust intron retention (IR) program that impacts expression of hundreds of genes. We studied IR mechanisms in the SF3B1 splicing factor gene, which expresses ∼50% of its transcripts in late erythroblasts as a nuclear isoform that retains intron 4. RNA-seq analysis of nonsense-mediated decay (NMD)-inhibited cells revealed previously undescribed splice junctions, rare or not detected in normal cells, that connect constitutive exons 4 and 5 to highly conserved cryptic cassette exons within the intron. Minigene splicing reporter assays showed that these cassettes promote IR. Genome-wide analysis of splice junction reads demonstrated that cryptic noncoding cassettes are much more common in large (>1 kb) retained introns than they are in small retained introns or in nonretained introns. Functional assays showed that heterologous cassettes can promote retention of intron 4 in the SF3B1 splicing reporter. Although many of these cryptic exons were spliced inefficiently, they exhibited substantial binding of U2AF1 and U2AF2 adjacent to their splice acceptor sites. We propose that these exons function as decoys that engage the intron-terminal splice sites, thereby blocking cross-intron interactions required for excision. Developmental regulation of decoy function underlies a major component of the erythroblast IR program.
Collapse
Affiliation(s)
- Marilyn Parra
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ben W Booth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Richard Weiszmann
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Brian Yee
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92037, USA
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - James B Brown
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - John G Conboy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| |
Collapse
|
192
|
Abstract
During erythropoiesis, hematopoietic stem and progenitor cells transition to erythroblasts en route to terminal differentiation into enucleated red blood cells. Transcriptome-wide changes underlie distinct morphological and functional characteristics at each cell division during this process. Many studies of gene expression have historically been carried out in erythroblasts, and the biogenesis of β-globin mRNA—the most highly expressed transcript in erythroblasts—was the focus of many seminal studies on the mechanisms of pre-mRNA splicing. We now understand that pre-mRNA splicing plays an important role in shaping the transcriptome of developing erythroblasts. Recent advances have provided insight into the role of alternative splicing and intron retention as important regulatory mechanisms of erythropoiesis. However, dysregulation of splicing during erythropoiesis is also a cause of several hematological diseases, including β-thalassemia and myelodysplastic syndromes. With a growing understanding of the role that splicing plays in these diseases, we are well poised to develop gene-editing treatments. In this review, we focus on changes in the developing erythroblast transcriptome caused by alternative splicing, the molecular basis of splicing-related blood diseases, and therapeutic advances in disease treatment using CRISPR/Cas9 gene editing.
Collapse
Affiliation(s)
- Kirsten A Reimer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520, USA
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520, USA
| |
Collapse
|
193
|
Furlanis E, Scheiffele P. Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing. Annu Rev Cell Dev Biol 2018; 34:451-469. [PMID: 30028642 DOI: 10.1146/annurev-cellbio-100617-062826] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Posttranscriptional mechanisms provide powerful means to expand the coding power of genomes. In nervous systems, alternative splicing has emerged as a fundamental mechanism not only for the diversification of protein isoforms but also for the spatiotemporal control of transcripts. Thus, alternative splicing programs play instructive roles in the development of neuronal cell type-specific properties, neuronal growth, self-recognition, synapse specification, and neuronal network function. Here we discuss the most recent genome-wide efforts on mapping RNA codes and RNA-binding proteins for neuronal alternative splicing regulation. We illustrate how alternative splicing shapes key steps of neuronal development, neuronal maturation, and synaptic properties. Finally, we highlight efforts to dissect the spatiotemporal dynamics of alternative splicing and their potential contribution to neuronal plasticity and the mature nervous system.
Collapse
|
194
|
Urbanski L, Leclair N, Anczuków O. Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1476. [PMID: 29693319 PMCID: PMC6002934 DOI: 10.1002/wrna.1476] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
Collapse
|
195
|
Wilusz JE. A 360° view of circular RNAs: From biogenesis to functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1478. [PMID: 29655315 PMCID: PMC6002912 DOI: 10.1002/wrna.1478] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022]
Abstract
The first circular RNA (circRNA) was identified more than 40 years ago, but it was only recently appreciated that circRNAs are common outputs of many eukaryotic protein-coding genes. Some circRNAs accumulate to higher levels than their associated linear mRNAs, especially in the nervous system, and have clear regulatory functions that result in organismal phenotypes. The pre-mRNA splicing machinery generates circRNAs via backsplicing reactions, which are often facilitated by intronic repeat sequences that base pair to one another and bring the intervening splice sites into close proximity. When spliceosomal components are limiting, circRNAs can become the preferred gene output, and backsplicing reactions are further controlled by exon skipping events and the combinatorial action of RNA binding proteins. This allows circRNAs to be expressed in a tissue- and stage-specific manner. Once generated, circRNAs are highly stable transcripts that often accumulate in the cytoplasm. The functions of most circRNAs remain unknown, but some can regulate the activities of microRNAs or be translated to produce proteins. Circular RNAs can further interface with the immune system as well as control gene expression events in the nucleus, including alternative splicing decisions. Circular RNAs thus represent a large class of RNA molecules that are tightly regulated, and it is becoming increasingly clear that they likely impact many biological processes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA.
Collapse
Affiliation(s)
- Jeremy E. Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| |
Collapse
|
196
|
Thompson MG, Muñoz-Moreno R, Bhat P, Roytenberg R, Lindberg J, Gazzara MR, Mallory MJ, Zhang K, García-Sastre A, Fontoura BMA, Lynch KW. Co-regulatory activity of hnRNP K and NS1-BP in influenza and human mRNA splicing. Nat Commun 2018; 9:2407. [PMID: 29921878 PMCID: PMC6008300 DOI: 10.1038/s41467-018-04779-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/17/2018] [Indexed: 11/17/2022] Open
Abstract
Three of the eight RNA segments encoded by the influenza A virus (IAV) undergo alternative splicing to generate distinct proteins. Previously, we found that host proteins hnRNP K and NS1-BP regulate IAV M segment splicing, but the mechanistic details were unknown. Here we show NS1-BP and hnRNP K bind M mRNA downstream of the M2 5′ splice site (5′ss). NS1-BP binds most proximal to the 5′ss, partially overlapping the U1 snRNP binding site, while hnRNP K binds further downstream and promotes U1 snRNP recruitment. Mutation of either or both the hnRNP K and NS1-BP-binding sites results in M segment mis-splicing and attenuated IAV replication. Additionally, we show that hnRNP K and NS1-BP regulate host splicing events and that viral infection causes mis-splicing of some of these transcripts. Therefore, our proposed mechanism of hnRNP K/NS1-BP mediated IAV M splicing provides potential targets of antiviral intervention and reveals novel host functions for these proteins. Alternative splicing of influenza A virus (IAV) M transcript is regulated by hnRNP K and NS1-BP, but mechanistic details are unknown. Here, Thompson et al. show how hnRNP K and NS1-BP bind M mRNA and that these proteins regulate splicing of host transcripts in both the absence and presence of IAV infection.
Collapse
Affiliation(s)
- Matthew G Thompson
- Departments of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Raquel Muñoz-Moreno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave., Box 1124, New York, NY, 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave., Box 1124, New York, NY, 10029, USA
| | - Prasanna Bhat
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Renat Roytenberg
- Departments of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - John Lindberg
- Departments of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Matthew R Gazzara
- Departments of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Michael J Mallory
- Departments of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA, 19104, USA
| | - Ke Zhang
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave., Box 1124, New York, NY, 10029, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave., Box 1124, New York, NY, 10029, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, 1468 Madison Ave., Box 1124, New York, NY, 10029, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Kristen W Lynch
- Departments of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Blvd, Philadelphia, PA, 19104, USA.
| |
Collapse
|
197
|
Herzel L, Straube K, Neugebauer KM. Long-read sequencing of nascent RNA reveals coupling among RNA processing events. Genome Res 2018; 28:1008-1019. [PMID: 29903723 PMCID: PMC6028129 DOI: 10.1101/gr.232025.117] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 05/24/2018] [Indexed: 12/13/2022]
Abstract
Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe. Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2, the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3′ end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation.
Collapse
Affiliation(s)
- Lydia Herzel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Korinna Straube
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| |
Collapse
|
198
|
Post-transcriptional regulation in planarian stem cells. Semin Cell Dev Biol 2018; 87:69-78. [PMID: 29870807 DOI: 10.1016/j.semcdb.2018.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 12/17/2022]
Abstract
Planarians are known for their immense regenerative abilities. A pluripotent stem cell population provides the cellular source for this process, as well as for the homeostatic cell turnover of the animals. These stem cells, known as neoblasts, present striking similarities at the morphological and molecular level to germ cells, but however, give rise to somatic tissue. Many RNA binding proteins known to be important for germ cell biology are also required for neoblast function, highlighting the importance of post-transcriptional regulation for stem cell control. Many of its aspects, including alternative splicing, alternative polyadenylation, translational control and mRNA deadenylation, as well as small RNAs such as microRNAs and piRNA are critical for stem cells. Their inhibition often abrogates both regeneration and cell turnover, resulting in lethality. Some of aspects of post-transcriptional regulation are conserved from planarian to mammalian stem cells.
Collapse
|
199
|
Abdelmoez MN, Iida K, Oguchi Y, Nishikii H, Yokokawa R, Kotera H, Uemura S, Santiago JG, Shintaku H. SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology. Genome Biol 2018; 19:66. [PMID: 29871653 PMCID: PMC5989370 DOI: 10.1186/s13059-018-1446-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells. These data provide unique insights into the regulatory network of messenger RNA from the nucleus toward the cytoplasm at the single-cell level.
Collapse
Affiliation(s)
- Mahmoud N Abdelmoez
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.,Microfluidics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Kei Iida
- Medical Research Support Center, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Oguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hidekazu Nishikii
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Hidetoshi Kotera
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA, USA
| | - Hirofumi Shintaku
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan. .,Microfluidics RIKEN Hakubi Research Team, RIKEN Cluster for Pioneering Research, Saitama, Japan.
| |
Collapse
|
200
|
Pendleton KE, Park SK, Hunter OV, Bresson SM, Conrad NK. Balance between MAT2A intron detention and splicing is determined cotranscriptionally. RNA (NEW YORK, N.Y.) 2018; 24:778-786. [PMID: 29563249 PMCID: PMC5959247 DOI: 10.1261/rna.064899.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/16/2018] [Indexed: 05/22/2023]
Abstract
Transcriptome analysis of human cells has revealed that intron retention controls the expression of a large number of genes with diverse cellular functions. Detained introns (DI) constitute a subgroup of transcripts with retained introns that are not exported to the cytoplasm but instead remain in the nucleus. Previous studies reported that the splicing of DIs in the CLK1 transcript is post-transcriptionally induced to produce mature mRNA in the absence of new transcription. Thus, CLK1-DI serves as a precursor or "reservoir" for the CLK1 mRNA. However, whether this is a universal mechanism for gene regulation by intron detention remains unknown. The MAT2A gene encodes S-adenosylmethionine (SAM) synthetase and it contains a DI that is regulated in response to intracellular SAM levels. We used three independent assays to assess the precursor-product relationship between MAT2A-DI and MAT2A mRNA. In contrast to CLK1-DI, these data support a model in which the MAT2A-DI transcript is not a precursor to mRNA but is instead a "dead-end" RNA fated for nuclear decay. Additionally, we show that in SAM-deprived conditions the cotranscriptional splicing of MAT2A detained introns increases. We conclude that polyadenylated RNAs with DIs can have at least two distinct fates. They can serve as nuclear reservoirs of pre-mRNAs available for rapid induction by the cell, or they constitute dead-end RNAs that are degraded in the nucleus.
Collapse
Affiliation(s)
- Kathryn E Pendleton
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sung-Kyun Park
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stefan M Bresson
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| |
Collapse
|