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Hunter S, Hendrix J, Freeman J, Dowell RD, Allen MA. Transcription dosage compensation does not occur in Down syndrome. BMC Biol 2023; 21:228. [PMID: 37946204 PMCID: PMC10636926 DOI: 10.1186/s12915-023-01700-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND The increase in DNA copy number in Down syndrome (DS; caused by trisomy 21) has led to the DNA dosage hypothesis, which posits that the level of gene expression is proportional to the gene's DNA copy number. Yet many reports have suggested that a proportion of chromosome 21 genes are dosage compensated back towards typical expression levels (1.0×). In contrast, other reports suggest that dosage compensation is not a common mechanism of gene regulation in trisomy 21, providing support to the DNA dosage hypothesis. RESULTS In our work, we use both simulated and real data to dissect the elements of differential expression analysis that can lead to the appearance of dosage compensation, even when compensation is demonstrably absent. Using lymphoblastoid cell lines derived from a family with an individual with Down syndrome, we demonstrate that dosage compensation is nearly absent at both nascent transcription (GRO-seq) and steady-state RNA (RNA-seq) levels. Furthermore, we link the limited apparent dosage compensation to expected allelic variation in transcription levels. CONCLUSIONS Transcription dosage compensation does not occur in Down syndrome. Simulated data containing no dosage compensation can appear to have dosage compensation when analyzed via standard methods. Moreover, some chromosome 21 genes that appear to be dosage compensated are consistent with allele specific expression.
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Affiliation(s)
- Samuel Hunter
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, 80301, USA
| | - Jo Hendrix
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
- Computational Bioscience, The University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Justin Freeman
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
| | - Robin D Dowell
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, 80301, USA
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
- Linda Crnic Institute for Down Syndrome, 80045, Aurora, USA
- Crnic Boulder Branch, BioFrontiers, Boulder, 80309, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA.
- Linda Crnic Institute for Down Syndrome, 80045, Aurora, USA.
- Crnic Boulder Branch, BioFrontiers, Boulder, 80309, USA.
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2
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Wang N, Wang Z, Danko CG, Chu T. Mapping Transcription Regulation with Run-on and Sequencing Data Using the Web-Based tfTarget Gateway. Methods Mol Biol 2023; 2599:215-226. [PMID: 36427152 DOI: 10.1007/978-1-0716-2847-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Run-on and sequencing assays like GRO-seq, PRO-seq, and ChRO-seq allow for joint profiling of transcription activity of transcriptional regulatory elements (TREs), i.e., promoters and active enhancers, and target genes. Variation in biological conditions, such as treated vs. control, results in changes in the activity of transcription factors (TFs), which induces concerted changes in TREs and target genes. By modeling the differences between two biological conditions, we developed the computational pipeline known as tfTarget that predicts a set of putative TREs and target genes responding to each TF under the biological condition of interest. In this chapter, we demonstrate the use of the new web-based tfTarget in mapping transcription regulation using run-on sequencing data.
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Affiliation(s)
- Nating Wang
- School of Software Technology, Dalian University of Technology, Dalian, China
| | - Zhong Wang
- School of Software Technology, Dalian University of Technology, Dalian, China
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Tinyi Chu
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA.
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3
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Hunter S, Sigauke RF, Stanley JT, Allen MA, Dowell RD. Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries. BMC Genomics 2022; 23:187. [PMID: 35255806 PMCID: PMC8900324 DOI: 10.1186/s12864-022-08352-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 01/25/2022] [Indexed: 11/20/2022] Open
Abstract
Background A variety of protocols exist for producing whole genome run-on transcription datasets. However, little is known about how differences between these protocols affect the signal within the resulting libraries. Results Using run-on transcription datasets generated from the same biological system, we show that a variety of GRO- and PRO-seq preparation methods leave identifiable signatures within each library. Specifically we show that the library preparation method results in differences in quality control metrics, as well as differences in the signal distribution at the 5 ′ end of transcribed regions. These shifts lead to disparities in eRNA identification, but do not impact analyses aimed at inferring the key regulators involved in changes to transcription. Conclusions Run-on sequencing protocol variations result in technical signatures that can be used to identify both the enrichment and library preparation method of a particular data set. These technical signatures are batch effects that limit detailed comparisons of pausing ratios and eRNAs identified across protocols. However, these batch effects have only limited impact on our ability to infer which regulators underlie the observed transcriptional changes. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-022-08352-8).
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Affiliation(s)
- Samuel Hunter
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
| | - Rutendo F Sigauke
- Computational Bioscience Program, Anschutz Medical Campus, University of Colorado, Aurora, 80045, USA
| | - Jacob T Stanley
- Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, 80301, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado, Boulder, 80309, USA. .,Computational Bioscience Program, Anschutz Medical Campus, University of Colorado, Aurora, 80045, USA. .,Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, 80301, USA. .,Department of Computer Science, University of Colorado, Boulder, 80309, USA.
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4
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Lozano R, Booth GT, Omar BY, Li B, Buckler ES, Lis JT, Del Carpio DP, Jannink JL. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. G3 (Bethesda) 2021; 11:6364897. [PMID: 34499719 PMCID: PMC8527479 DOI: 10.1093/g3journal/jkab273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/04/2021] [Indexed: 12/14/2022]
Abstract
Control of gene expression is fundamental at every level of cell function. Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have only been studied in a handful of research experiments in plants. PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally engaged RNA polymerase at both the 5' and 3' end of genes, consistent with paused or slowly moving Polymerase. In addition, we identified divergent transcription at intergenic sites. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many intergenic regulatory element (IRE) candidates. These sites showed distinct patterns of methylation and nucleotide conservation based on genomic evolutionary rate profiling (GERP). SNPs within these IRE candidates explained significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, strongly suggesting a functional importance of these sites. Maize GRO-Seq data showed RNA polymerase occupancy at IREs consistent with patterns in cassava. Furthermore, these IREs in maize significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation, and were enriched for reported eQTL. Our results suggest that bidirectional transcription can identify intergenic genomic regions in plants that play an important role in transcription regulation and whose identification has the potential to aid crop improvement.
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Affiliation(s)
- Roberto Lozano
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | | | - Bo Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing 100101, China
| | - Edward S Buckler
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.,United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Dunia Pino Del Carpio
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Jean-Luc Jannink
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,United States Department of Agriculture, Agricultural Research Service (USDA-ARS) R.W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Ma Q, Yang F, Mackintosh C, Jayani RS, Oh S, Jin C, Nair SJ, Merkurjev D, Ma W, Allen S, Wang D, Almenar-Queralt A, Garcia-Bassets I. Super-Enhancer Redistribution as a Mechanism of Broad Gene Dysregulation in Repeatedly Drug-Treated Cancer Cells. Cell Rep 2021; 31:107532. [PMID: 32320655 DOI: 10.1016/j.celrep.2020.107532] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/07/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
Cisplatin is an antineoplastic drug administered at suboptimal and intermittent doses to avoid life-threatening effects. Although this regimen shortly improves symptoms in the short term, it also leads to more malignant disease in the long term. We describe a multilayered analysis ranging from chromatin to translation-integrating chromatin immunoprecipitation sequencing (ChIP-seq), global run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and ribosome profiling-to understand how cisplatin confers (pre)malignant features by using a well-established ovarian cancer model of cisplatin exposure. This approach allows us to segregate the human transcriptome into gene modules representing distinct regulatory principles and to characterize that the most cisplatin-disrupted modules are associated with underlying events of super-enhancer plasticity. These events arise when cancer cells initiate without ultimately ending the program of drug-stimulated death. Using a PageRank-based algorithm, we predict super-enhancer regulator ISL1 as a driver of this plasticity and validate this prediction by using CRISPR/dCas9-KRAB inhibition (CRISPRi) and CRISPR/dCas9-VP64 activation (CRISPRa) tools. Together, we propose that cisplatin reprograms cancer cells when inducing them to undergo near-to-death experiences.
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Affiliation(s)
- Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Carlos Mackintosh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ranveer Singh Jayani
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Soohwan Oh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chunyu Jin
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sreejith Janardhanan Nair
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wubin Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Allen
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 611137, China
| | - Angels Almenar-Queralt
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Galbraith MD, Andrysik Z, Sullivan KD, Espinosa JM. Global Analyses to Identify Direct Transcriptional Targets of p53. Methods Mol Biol 2021; 2267:19-56. [PMID: 33786783 DOI: 10.1007/978-1-0716-1217-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The transcription factor p53 controls a gene expression program with pleiotropic effects on cell biology including cell cycle arrest and apoptosis. Identifying direct p53 target genes within this network and determining how they influence cell fate decisions downstream of p53 activation is a prerequisite for designing therapeutic approaches that target p53 to effectively kill cancer cells. Here we describe a comprehensive multi-omics approach for identifying genes that are direct transcriptional targets of p53. We provide detailed procedures for measuring global RNA polymerase activity, defining p53 binding sites across the genome, and quantifying changes in steady-state mRNA in response to p53 activation.
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7
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Wang Y, Li J, Li J, Li P, Wang L, Di L. An Enhancer-Based Analysis Revealed a New Function of Androgen Receptor in Tumor Cell Immune Evasion. Front Genet 2020; 11:595550. [PMID: 33343635 PMCID: PMC7738566 DOI: 10.3389/fgene.2020.595550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cancer is characterized by dysregulation at multiple levels, such as gene transcription. Enhancers are well-studied transcription regulators that can enhance target transcripts through DNA loop formation mediated by chromosome folding. The gain or loss of the interaction between an enhancer and its target gene has a critical effect on gene expression. In this study, we analyzed GRO-seq data to identify active enhancers from seven common cancer cell lines and studied the function of these enhancers across multiple cancer types. By constructing an "enhancer effect score" (EES), we found a significant correlation between EES and tumor-infiltrating lymphocytes (TILs) in prostate cancer. Further analysis revealed that androgen receptor (AR) plays an important role in regulating the immune checkpoint gene PVR via its enhancer. These results suggest that AR contributes to prostate cancer aggressiveness by promoting cancer cell immune evasion.
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Affiliation(s)
| | | | | | | | | | - Lijun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China
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8
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Kaukonen D, Kaukonen R, Polit L, Hennessy BT, Lund R, Madden SF. Analysis of H3K4me3 and H3K27me3 bivalent promotors in HER2+ breast cancer cell lines reveals variations depending on estrogen receptor status and significantly correlates with gene expression. BMC Med Genomics 2020; 13:92. [PMID: 32620123 PMCID: PMC7333309 DOI: 10.1186/s12920-020-00749-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The role of histone modifications is poorly characterized in breast cancer, especially within the major subtypes. While epigenetic modifications may enhance the adaptability of a cell to both therapy and the surrounding environment, the mechanisms by which this is accomplished remains unclear. In this study we focus on the HER2 subtype and investigate two histone trimethylations that occur on the histone 3; the trimethylation located at lysine 4 (H3K4me3) found in active promoters and the trimethylation located at lysine 27 (H3K27me3) that correlates with gene repression. A bivalency state is the result of the co-presence of these two marks at the same promoter. METHODS In this study we investigated the relationship between these histone modifications in promoter regions and their proximal gene expression in HER2+ breast cancer cell lines. In addition, we assessed these patterns with respect to the presence or absence of the estrogen receptor (ER). To do this, we utilized ChIP-seq and matching RNA-seq from publicly available data for the AU565, SKBR3, MB361 and UACC812 cell lines. In order to visualize these relationships, we used KEGG pathway enrichment analysis, and Kaplan-Meyer plots. RESULTS We found that the correlation between the three types of promoter trimethylation statuses (H3K4me3, H3K27me3 or both) and the expression of the proximal genes was highly significant overall, while roughly a third of all genes are regulated by this phenomenon. We also show that there are several pathways related to cancer progression and invasion that are associated with the bivalent status of the gene promoters, and that there are specific differences between ER+ and ER- HER2+ breast cancer cell lines. These specific differences that are differentially trimethylated are also shown to be differentially expressed in patient samples. One of these genes, HIF1AN, significantly correlates with patient outcome. CONCLUSIONS This study highlights the importance of looking at epigenetic markings at a subtype specific level by characterizing the relationship between the bivalent promoters and gene expression. This provides a deeper insight into a mechanism that could lead to future targets for treatment and prognosis, along with oncogenesis and response to therapy of HER2+ breast cancer patients.
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Affiliation(s)
- Damien Kaukonen
- Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Riina Kaukonen
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Lélia Polit
- Institute Cochin, University Paris Descartes, Paris, France
| | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Riikka Lund
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
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Abstract
Next generation sequencing (NGS) is routinely used in gene expression analyses. In particular, RNA-seq has been the method of choice for highly sensitive genome-wide quantification of RNA expression. The method can be used in a wide variety of model systems, including studies to gain insight into underlying mechanisms of toxicologic processes and disease development induced by environmental toxicants. RNA-seq has also been coupled to many other molecular biology protocols to monitor specific aspects of the gene expression process. Here, we describe two such coupling-(a) global run-on sequencing (GRO-seq) that coupled it to the nuclear run-on (NRO), and (b) polysome profiling that coupled it to sucrose-gradient-based polysome isolation. Simultaneous RNA-seq, GRO-seq, and polysome profiling analyses enabled genome-wide analysis of the mode of stability control of individual RNA molecules.
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Affiliation(s)
- Degeng Wang
- Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA.
- The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, USA.
| | - Andrey L Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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10
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Morera AA, Ahmed NS, Schwartz JC. TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons. Biochim Biophys Acta Gene Regul Mech 2019; 1862:194434. [PMID: 31655156 DOI: 10.1016/j.bbagrm.2019.194434] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022]
Abstract
The 43-kDa transactive response DNA-binding protein (TDP-43) is an example of an RNA-binding protein that regulates RNA metabolism at multiple levels from transcription and splicing to translation. Its role in post-transcriptional RNA processing has been a primary focus of recent research, but its role in regulating transcription has been studied for only a few human genes. We characterized the effects of TDP-43 on transcription genome-wide and found that TDP-43 broadly affects transcription of protein-coding and noncoding RNA genes. Among protein-coding genes, the effects of TDP-43 were greatest for genes <30 thousand base pairs in length. Surprisingly, we found that the loss of TDP-43 resulted in increased evidence for transcription activity near repetitive Alu elements found within expressed genes. The highest densities of affected Alu elements were found in the shorter genes, whose transcription was most affected by TDP-43. Thus, in addition to its role in post-transcriptional RNA processing, TDP-43 plays a critical role in maintaining the transcriptional stability of protein-coding genes and transposable DNA elements.
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11
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Chu T, Wang Z, Chou SP, Danko CG. Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway. Curr Protoc Bioinformatics 2019; 66:e70. [PMID: 30589513 PMCID: PMC6584046 DOI: 10.1002/cpbi.70] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription is a chromatin mark that can be used effectively to identify the location of active enhancers and promoters, collectively known as transcriptional regulatory elements (TREs). We recently introduced dREG, a tool for the identification of TREs using run-on and sequencing (RO-seq) assays, including global run-on and sequencing (GRO-seq), precision run-on and sequencing (PRO-seq), and chromatin run-on and sequencing (ChRO-seq). In this protocol, we present step-by-step instructions for running dREG on an arbitrary run-on and sequencing dataset. Users provide dREG with bigWig files (in which each read is represented by a single base) representing the location of RNA polymerase in a cell or tissue sample of interest, and dREG returns a list of genomic regions that are predicted to be active TREs. Finally, we demonstrate the use of dREG regions in discovering transcription factors controlling response to a stimulus and predicting their target genes. Together, this protocol provides detailed instructions for running dREG on arbitrary run-on and sequencing data. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Tinyi Chu
- Baker Institute for Animal Health,Cornell University. Hungerford Hill Rd,Ithaca, NY 14853
| | - Zhong Wang
- Baker Institute for Animal Health,Cornell University. Hungerford Hill Rd,Ithaca, NY 14853
| | - Shao-Pei Chou
- Baker Institute for Animal Health,Cornell University. Hungerford Hill Rd,Ithaca, NY 14853
| | - Charles G. Danko
- Baker Institute for Animal Health,Cornell University. Hungerford Hill Rd,Ithaca, NY 14853
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12
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Jordán-Pla A, Pérez-Martínez ME, Pérez-Ortín JE. Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods. Methods 2019; 159-160:177-182. [PMID: 30716396 DOI: 10.1016/j.ymeth.2019.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 02/05/2023] Open
Abstract
The biogenesis of RNAs is a multi-layered and highly regulated process that involves a diverse set of players acting in an orchestrated manner throughout the transcription cycle. Transcription initiation, elongation and termination factors act on RNA polymerases to modulate their movement along the DNA template in a very precise manner, more complex than previously anticipated. Genome-scale run-on-based methodologies have been developed to study in detail the position of transcriptionally-engaged RNA polymerases. Genomic run-on (GRO), and its many variants and refinements made over the years, are helping the community to address an increasing amount of scientific questions, spanning an increasing range of organisms and systems. In this review, we aim to summarize the most relevant high throughput methodologies developed to study nascent RNA by run-on methods, compare their main features, advantages and limitations, while putting them in context with alternative ways of studying the transcriptional process.
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Affiliation(s)
- Antonio Jordán-Pla
- ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain.
| | - Maria E Pérez-Martínez
- ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - José E Pérez-Ortín
- ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
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Shivram H, Iyer VR. Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies. RNA 2018; 24:1266-1274. [PMID: 29950518 PMCID: PMC6097653 DOI: 10.1261/rna.066217.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
The quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Nonspecific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation of data (RT mispriming). This kind of artifact in RNA-seq based technologies is underappreciated and currently no adequate tools exist to computationally remove them from published data sets. We show that mispriming can occur with as little as two bases of complementarity at the 3' end of the primer followed by intermittent regions of complementarity. We also provide a computational pipeline that identifies cDNA reads produced from RT mispriming, allowing users to filter them out from any aligned data set. Using this analysis pipeline, we identify thousands of mispriming events in a dozen published data sets from diverse technologies including short RNA-seq, total/mRNA-seq, HITS-CLIP, and GRO-seq. We further show how RT mispriming can lead to misinterpretation of data. In addition to providing a solution to computationally remove RT-misprimed reads, we also propose an experimental solution to completely avoid RT-mispriming by performing RNA-seq using thermostable group II intron derived reverse transcriptase (TGIRT-seq).
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Affiliation(s)
- Haridha Shivram
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Vishwanath R Iyer
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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14
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Hait TA, Amar D, Shamir R, Elkon R. FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map. Genome Biol 2018; 19:56. [PMID: 29716618 PMCID: PMC5930446 DOI: 10.1186/s13059-018-1432-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/13/2018] [Indexed: 01/22/2023] Open
Abstract
Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer–promoter links. We show that current enhancer–promoter inference methods produce a high rate of false positive links. We introduce FOCS, a new inference method, and by benchmarking against ChIA-PET, HiChIP, and eQTL data show that it results in lower false discovery rates and at the same time higher inference power. By applying FOCS to 2630 samples taken from ENCODE, Roadmap Epigenomics, FANTOM5, and a new compendium of GRO-seq samples, we provide extensive enhancer–promotor maps (http://acgt.cs.tau.ac.il/focs). We illustrate the usability of our maps for deriving biological hypotheses.
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Affiliation(s)
- Tom Aharon Hait
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel
| | - David Amar
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.,Stanford Center for Inherited Cardiovascular Disease, Stanford University, Stanford, CA, 94305, USA
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, 69978, Tel Aviv, Israel.
| | - Ran Elkon
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel Aviv University, 69978, Tel Aviv, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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15
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Guzman C, D'Orso I. CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction. BMC Bioinformatics 2017; 18:363. [PMID: 28789639 PMCID: PMC5549294 DOI: 10.1186/s12859-017-1770-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 07/30/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) approaches are commonly used to identify key regulatory networks that drive transcriptional programs. Although these technologies are frequently used in biological studies, NGS data analysis remains a challenging, time-consuming, and often irreproducible process. Therefore, there is a need for a comprehensive and flexible workflow platform that can accelerate data processing and analysis so more time can be spent on functional studies. RESULTS We have developed an integrative, stand-alone workflow platform, named CIPHER, for the systematic analysis of several commonly used NGS datasets including ChIP-seq, RNA-seq, MNase-seq, DNase-seq, GRO-seq, and ATAC-seq data. CIPHER implements various open source software packages, in-house scripts, and Docker containers to analyze and process single-ended and pair-ended datasets. CIPHER's pipelines conduct extensive quality and contamination control checks, as well as comprehensive downstream analysis. A typical CIPHER workflow includes: (1) raw sequence evaluation, (2) read trimming and adapter removal, (3) read mapping and quality filtering, (4) visualization track generation, and (5) extensive quality control assessment. Furthermore, CIPHER conducts downstream analysis such as: narrow and broad peak calling, peak annotation, and motif identification for ChIP-seq, differential gene expression analysis for RNA-seq, nucleosome positioning for MNase-seq, DNase hypersensitive site mapping, site annotation and motif identification for DNase-seq, analysis of nascent transcription from Global-Run On (GRO-seq) data, and characterization of chromatin accessibility from ATAC-seq datasets. In addition, CIPHER contains an "analysis" mode that completes complex bioinformatics tasks such as enhancer discovery and provides functions to integrate various datasets together. CONCLUSIONS Using public and simulated data, we demonstrate that CIPHER is an efficient and comprehensive workflow platform that can analyze several NGS datasets commonly used in genome biology studies. Additionally, CIPHER's integrative "analysis" mode allows researchers to elicit important biological information from the combined dataset analysis.
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Affiliation(s)
- Carlos Guzman
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Present address: Bioinformatics and Systems Biology Graduate Program, University of California, La Jolla, San Diego, CA, 92093, USA.
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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16
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Abstract
Methodological advances that allow deeper characterization of non-coding elements in the genome have started to reveal the full spectrum of deregulation in cancer. We generated an inducible cell model to track transcriptional changes after induction of a well-known leukemia-inducing fusion gene, ETV6-RUNX1. Our data revealed widespread transcriptional alterations outside coding elements in the genome. This adds to the growing list of various alterations in the non-coding genome in cancer and pinpoints their role in diseased cellular state.
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Affiliation(s)
- Susanna Teppo
- a Tampere Center for Child Health Research, Faculty of Medicine and Life Sciences , University of Tampere and Tampere University Hospital , Tampere , Finland
| | - Merja Heinäniemi
- b Institute of Biomedicine, School of Medicine , University of Eastern Finland , Kuopio , Finland
| | - Olli Lohi
- a Tampere Center for Child Health Research, Faculty of Medicine and Life Sciences , University of Tampere and Tampere University Hospital , Tampere , Finland
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17
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Liu Y, Chen S, Wang S, Soares F, Fischer M, Meng F, Du Z, Lin C, Meyer C, DeCaprio JA, Brown M, Liu XS, He HH. Transcriptional landscape of the human cell cycle. Proc Natl Acad Sci U S A 2017; 114:3473-8. [PMID: 28289232 DOI: 10.1073/pnas.1617636114] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Steady-state gene expression across the cell cycle has been studied extensively. However, transcriptional gene regulation and the dynamics of histone modification at different cell-cycle stages are largely unknown. By applying a combination of global nuclear run-on sequencing (GRO-seq), RNA sequencing (RNA-seq), and histone-modification Chip sequencing (ChIP-seq), we depicted a comprehensive transcriptional landscape at the G0/G1, G1/S, and M phases of breast cancer MCF-7 cells. Importantly, GRO-seq and RNA-seq analysis identified different cell-cycle-regulated genes, suggesting a lag between transcription and steady-state expression during the cell cycle. Interestingly, we identified genes actively transcribed at early M phase that are longer in length and have low expression and are accompanied by a global increase in active histone 3 lysine 4 methylation (H3K4me2) and histone 3 lysine 27 acetylation (H3K27ac) modifications. In addition, we identified 2,440 cell-cycle-regulated enhancer RNAs (eRNAs) that are strongly associated with differential active transcription but not with stable expression levels across the cell cycle. Motif analysis of dynamic eRNAs predicted Kruppel-like factor 4 (KLF4) as a key regulator of G1/S transition, and this identification was validated experimentally. Taken together, our combined analysis characterized the transcriptional and histone-modification profile of the human cell cycle and identified dynamic transcriptional signatures across the cell cycle.
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18
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Abstract
Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers.
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Affiliation(s)
- Anusha Nagari
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - Shino Murakami
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Venkat S Malladi
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Expression, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-8511, USA.
- The Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, 75390-8511, USA.
- Program in Genetics, Development and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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19
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Abstract
The advent of next-generation sequencing (NGS) technologies has revolutionized the way we do research on gene expression. High-throughput transcriptomics became possible with the development of microarray technology, but its widespread application only occurred after the emergence of massive parallel sequencing. Especially, RNA sequencing (RNA-seq) has greatly increased our knowledge about the genome and led to the identification and annotation of novel classes of RNAs in different species. However, RNA-seq measures the steady-state level of a given RNA, which is the equilibrium between transcription, processing, and degradation. In recent years, a number of dedicated RNA-seq technologies were developed to measure specifically transcription events. Global run-on sequencing (GRO-seq) is the most widely used method to measure nascent RNA, and in recent years, it has been applied successfully to study the function and mechanism of action of noncoding RNAs. Here, we describe a detailed protocol of GRO-seq that can be readily applied to investigate different aspects of RNA biology in human cells.
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Affiliation(s)
- Rui Lopes
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
- Erasmus MC, Rotterdam University, Rotterdam, The Netherlands.
| | - Gozde Korkmaz
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands.
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20
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Abstract
Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. We generated an extensive catalog of nascent and steady-state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq, and RNA-seq and reanalyzed published maize data to capture characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts. Examining the promoters of coding and noncoding transcripts identified comparable chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-binding sites. Mapping of engaged RNA polymerases showed a lack of enhancer RNAs, promoter-proximal pausing, and divergent transcription in Arabidopsis seedlings and maize, which are commonly present in yeast and humans. In contrast, Arabidopsis and maize genes accumulate RNA polymerases in proximity of the polyadenylation site, a trend that coincided with longer genes and CpG hypomethylation. Lack of promoter-proximal pausing and a higher correlation of nascent and steady-state transcripts indicate Arabidopsis may regulate transcription predominantly at the level of initiation. Our findings provide insight into plant transcription and eukaryotic gene expression as a whole.
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21
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Heinäniemi M, Vuorenmaa T, Teppo S, Kaikkonen MU, Bouvy-Liivrand M, Mehtonen J, Niskanen H, Zachariadis V, Laukkanen S, Liuksiala T, Teittinen K, Lohi O. Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspots. eLife 2016; 5. [PMID: 27431763 PMCID: PMC4951197 DOI: 10.7554/elife.13087] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 06/09/2016] [Indexed: 12/11/2022] Open
Abstract
Progression of malignancy to overt disease requires multiple genetic hits. Activation-induced deaminase (AID) can drive lymphomagenesis by generating off-target DNA breaks at loci that harbor highly active enhancers and display convergent transcription. The first active transcriptional profiles from acute lymphoblastic leukemia (ALL) patients acquired here reveal striking similarity at structural variation (SV) sites. Specific transcriptional features, namely convergent transcription and Pol2 stalling, were detected at breakpoints. The overlap was most prominent at SV with recognition motifs for the recombination activating genes (RAG). We present signal feature analysis to detect vulnerable regions and quantified from human cells how convergent transcription contributes to R-loop generation and RNA polymerase stalling. Wide stalling regions were characterized by high DNAse hypersensitivity and unusually broad H3K4me3 signal. Based on 1382 pre-B-ALL patients, the ETV6-RUNX1 fusion positive patients had over ten-fold elevation in RAG1 while high expression of AID marked pre-B-ALL lacking common cytogenetic changes.
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Affiliation(s)
- Merja Heinäniemi
- School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Tapio Vuorenmaa
- School of Medicine, University of Eastern Finland, Kuopio, Finland.,A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Susanna Teppo
- School of Medicine, University of Tampere, Tampere, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Juha Mehtonen
- School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Olli Lohi
- School of Medicine, University of Tampere, Tampere, Finland.,Tampere University Hospital, Tampere, Finland
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22
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Lladser ME, Azofeifa JG, Allen MA, Dowell RD. RNA Pol II transcription model and interpretation of GRO-seq data. J Math Biol 2017; 74:77-97. [PMID: 27142882 DOI: 10.1007/s00285-016-1014-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 03/10/2016] [Indexed: 10/21/2022]
Abstract
A mixture model and statistical method is proposed to interpret the distribution of reads from a nascent transcriptional assay, such as global run-on sequencing (GRO-seq) data. The model is annotation agnostic and leverages on current understanding of the behavior of RNA polymerase II. Briefly, it assumes that polymerase loads at key positions (transcription start sites) within the genome. Once loaded, polymerase either remains in the initiation form (with some probability) or transitions into an elongating form (with the remaining probability). The model can be fit genome-wide, allowing patterns of Pol II behavior to be assessed on each distinct transcript. Furthermore, it allows for the first time a principled approach to distinguishing the initiation signal from the elongation signal; in particular, it implies a data driven method for calculating the pausing index, a commonly used metric that informs on the behavior of RNA polymerase II. We demonstrate that this approach improves on existing analyses of GRO-seq data and uncovers a novel biological understanding of the impact of knocking down the Male Specific Lethal (MSL) complex in Drosophilia melanogaster.
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23
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Zorca CE, Kim LK, Kim YJ, Krause MR, Zenklusen D, Spilianakis CG, Flavell RA. Myosin VI regulates gene pairing and transcriptional pause release in T cells. Proc Natl Acad Sci U S A 2015; 112:E1587-93. [PMID: 25770220 DOI: 10.1073/pnas.1502461112] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Naive CD4 T cells differentiate into several effector lineages, which generate a stronger and more rapid response to previously encountered immunological challenges. Although effector function is a key feature of adaptive immunity, the molecular basis of this process is poorly understood. Here, we investigated the spatiotemporal regulation of cytokine gene expression in resting and restimulated effector T helper 1 (Th1) cells. We found that the Lymphotoxin (LT)/TNF alleles, which encode TNF-α, were closely juxtaposed shortly after T-cell receptor (TCR) engagement, when transcription factors are limiting. Allelic pairing required a nuclear myosin, myosin VI, which is rapidly recruited to the LT/TNF locus upon restimulation. Furthermore, transcription was paused at the TNF locus and other related genes in resting Th1 cells and released in a myosin VI-dependent manner following activation. We propose that homologous pairing and myosin VI-mediated transcriptional pause release account for the rapid and efficient expression of genes induced by an external stimulus.
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24
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Abstract
Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.DOI: http://dx.doi.org/10.7554/eLife.02407.001.
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Affiliation(s)
- Iris Jonkers
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Hojoong Kwak
- Howard Hughes Medical Institute, University of Michigan, Ann Harbor, United States
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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25
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Hah N, Kraus WL. Hormone-regulated transcriptomes: lessons learned from estrogen signaling pathways in breast cancer cells. Mol Cell Endocrinol 2014; 382:652-664. [PMID: 23810978 PMCID: PMC3844033 DOI: 10.1016/j.mce.2013.06.021] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/15/2013] [Accepted: 06/17/2013] [Indexed: 12/21/2022]
Abstract
Recent rapid advances in next generation sequencing technologies have expanded our understanding of steroid hormone signaling to a genome-wide level. In this review, we discuss the use of a novel genomic approach, global nuclear run-on coupled with massively parallel sequencing (GRO-seq), to explore new facets of the steroid hormone-regulated transcriptome, especially estrogen responses in breast cancer cells. GRO-seq is a high throughput sequencing method adapted from conventional nuclear run-on methodologies, which is used to obtain a map of the position and orientation of all transcriptionally engaged RNA polymerases across the genome with extremely high spatial resolution. GRO-seq, which is an excellent tool for examining transcriptional responses to extracellular stimuli, has been used to comprehensively assay the effects of estrogen signaling on the transcriptome of ERα-positive MCF-7 human breast cancer cells. These studies have revealed new details about estrogen-dependent transcriptional regulation, including effects on transcription by all three RNA polymerases, complex transcriptional dynamics in response to estrogen signaling, and identification novel, unannotated non-coding RNAs. Collectively, these studies have been useful in discerning the molecular logic of the estrogen-regulated mitogenic response.
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Affiliation(s)
- Nasun Hah
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States.
| | - W Lee Kraus
- The Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States; Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
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26
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Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL. Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev 2013; 27:1146-58. [PMID: 23699410 DOI: 10.1101/gad.215459.113] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cascades of zygotic gene expression pattern the anterior-posterior (AP) and dorsal-ventral (DV) axes of the early Drosophila embryo. Here, we used the global run-on sequencing assay (GRO-seq) to map the genome-wide RNA polymerase distribution during early Drosophila embryogenesis, thus providing insights into how genes are regulated. We identify widespread promoter-proximal pausing yet show that the presence of paused polymerase does not necessarily equate to direct regulation through pause release to productive elongation. Our data reveal that a subset of early Zelda-activated genes is regulated at the level of polymerase recruitment, whereas other Zelda target and axis patterning genes are predominantly regulated through pause release. In contrast to other signaling pathways, we found that bone morphogenetic protein (BMP) target genes are collectively more highly paused than BMP pathway components and show that BMP target gene expression requires the pause-inducing negative elongation factor (NELF) complex. Our data also suggest that polymerase pausing allows plasticity in gene activation throughout embryogenesis, as transiently repressed and transcriptionally silenced genes maintain and lose promoter polymerases, respectively. Finally, we provide evidence that the major effect of pausing is on the levels, rather than timing, of transcription. These data are discussed in terms of the efficiency of transcriptional activation required across cell populations during developmental time constraints.
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Affiliation(s)
- Abbie Saunders
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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