101
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van de Grift YBC, Heijmans N, van Amerongen R. How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b. J Mammary Gland Biol Neoplasia 2020; 25:319-335. [PMID: 33625717 PMCID: PMC7960620 DOI: 10.1007/s10911-020-09474-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
An increasing number of '-omics' datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific '-omics' datasets and thereby expand the in silico toolbox.
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Affiliation(s)
- Yorick Bernardus Cornelis van de Grift
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Nika Heijmans
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
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102
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Chin HG, Sun Z, Vishnu US, Hao P, Cejas P, Spracklin G, Estève PO, Xu SY, Long HW, Pradhan S. Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues. Clin Epigenetics 2020; 12:143. [PMID: 32962734 PMCID: PMC7507628 DOI: 10.1186/s13148-020-00921-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negates the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for the FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high-resolution genomic feature studies.
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Affiliation(s)
- Hang Gyeong Chin
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Zhiyi Sun
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | | | - Pengying Hao
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215-5450, USA
- Translational Oncology Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ) and CIBERONC, La Paz University Hospital, Madrid, Spain
| | - George Spracklin
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | | | - Shuang-Yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215-5450, USA
| | - Sriharsa Pradhan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
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103
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Symmetric neural progenitor divisions require chromatin-mediated homologous recombination DNA repair by Ino80. Nat Commun 2020; 11:3839. [PMID: 32737294 PMCID: PMC7395731 DOI: 10.1038/s41467-020-17551-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
Chromatin regulates spatiotemporal gene expression during neurodevelopment, but it also mediates DNA damage repair essential to proliferating neural progenitor cells (NPCs). Here, we uncover molecularly dissociable roles for nucleosome remodeler Ino80 in chromatin-mediated transcriptional regulation and genome maintenance in corticogenesis. We find that conditional Ino80 deletion from cortical NPCs impairs DNA double-strand break (DSB) repair, triggering p53-dependent apoptosis and microcephaly. Using an in vivo DSB repair pathway assay, we find that Ino80 is selectively required for homologous recombination (HR) DNA repair, which is mechanistically distinct from Ino80 function in YY1-associated transcription. Unexpectedly, sensitivity to loss of Ino80-mediated HR is dependent on NPC division mode: Ino80 deletion leads to unrepaired DNA breaks and apoptosis in symmetric NPC-NPC divisions, but not in asymmetric neurogenic divisions. This division mode dependence is phenocopied following conditional deletion of HR gene Brca2. Thus, distinct modes of NPC division have divergent requirements for Ino80-dependent HR DNA repair.
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104
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Baumgarten N, Hecker D, Karunanithi S, Schmidt F, List M, Schulz MH. EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res 2020; 48:W193-W199. [PMID: 32459338 PMCID: PMC7319550 DOI: 10.1093/nar/gkaa382] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022] Open
Abstract
A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM's activity and its estimated cell type-specific contribution to its target gene's expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https://epiregio.de/.
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Affiliation(s)
- Nina Baumgarten
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Dennis Hecker
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
| | - Sivarajan Karunanithi
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
| | - Florian Schmidt
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Genome Institute of Singapore, 60 Biopolis Street, Genome, 02-01, 138672, Singapore
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
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105
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Policastro RA, Raborn RT, Brendel VP, Zentner GE. Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq. Genome Res 2020; 30:910-923. [PMID: 32660958 PMCID: PMC7370879 DOI: 10.1101/gr.261545.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/18/2020] [Indexed: 01/07/2023]
Abstract
Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5' ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
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Affiliation(s)
| | | | - Volker P Brendel
- Department of Biology
- Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA
| | - Gabriel E Zentner
- Department of Biology
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, Indiana 46202, USA
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106
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Broekema RV, Bakker OB, Jonkers IH. A practical view of fine-mapping and gene prioritization in the post-genome-wide association era. Open Biol 2020; 10:190221. [PMID: 31937202 PMCID: PMC7014684 DOI: 10.1098/rsob.190221] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/05/2019] [Indexed: 12/17/2022] Open
Abstract
Over the past 15 years, genome-wide association studies (GWASs) have enabled the systematic identification of genetic loci associated with traits and diseases. However, due to resolution issues and methodological limitations, the true causal variants and genes associated with traits remain difficult to identify. In this post-GWAS era, many biological and computational fine-mapping approaches now aim to solve these issues. Here, we review fine-mapping and gene prioritization approaches that, when combined, will improve the understanding of the underlying mechanisms of complex traits and diseases. Fine-mapping of genetic variants has become increasingly sophisticated: initially, variants were simply overlapped with functional elements, but now the impact of variants on regulatory activity and direct variant-gene 3D interactions can be identified. Moreover, gene manipulation by CRISPR/Cas9, the identification of expression quantitative trait loci and the use of co-expression networks have all increased our understanding of the genes and pathways affected by GWAS loci. However, despite this progress, limitations including the lack of cell-type- and disease-specific data and the ever-increasing complexity of polygenic models of traits pose serious challenges. Indeed, the combination of fine-mapping and gene prioritization by statistical, functional and population-based strategies will be necessary to truly understand how GWAS loci contribute to complex traits and diseases.
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Affiliation(s)
| | | | - I. H. Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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