1
|
Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BDBD, Abedalthagafi MS, Mutlu O, Mangul S. Packaging and containerization of computational methods. Nat Protoc 2024:10.1038/s41596-024-00986-0. [PMID: 38565959 DOI: 10.1038/s41596-024-00986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.
Collapse
Affiliation(s)
- Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Brendan Lawlor
- Department of Computer Science, Munster Technological University, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Richard J Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sharon Waymost
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Neha Rajkumar
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Jaqueline Brito
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Nour Almadhoun
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Varuni Sarwal
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Can Firtina
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Tomasz Osinski
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Qiyang Hu
- Office of Advanced Research Computing, University of California, Los Angeles, CA, USA
| | - Derek Strong
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Byoung-Do B D Kim
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Onur Mutlu
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Serghei Mangul
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
2
|
Abdill RJ, Graham SP, Rubinetti V, Albert FW, Greene CS, Davis S, Blekhman R. Integration of 168,000 samples reveals global patterns of the human gut microbiome. bioRxiv 2023:2023.10.11.560955. [PMID: 37873416 PMCID: PMC10592789 DOI: 10.1101/2023.10.11.560955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Understanding the factors that shape variation in the human microbiome is a major goal of research in biology. While other genomics fields have used large, pre-compiled compendia to extract systematic insights requiring otherwise impractical sample sizes, there has been no comparable resource for the 16S rRNA sequencing data commonly used to quantify microbiome composition. To help close this gap, we have assembled a set of 168,484 publicly available human gut microbiome samples, processed with a single pipeline and combined into the largest unified microbiome dataset to date. We use this resource, which is freely available at microbiomap.org, to shed light on global variation in the human gut microbiome. We find that Firmicutes, particularly Bacilli and Clostridia, are almost universally present in the human gut. At the same time, the relative abundance of the 65 most common microbial genera differ between at least two world regions. We also show that gut microbiomes in undersampled world regions, such as Central and Southern Asia, differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America. Moreover, humans in these overlooked regions likely harbor hundreds of taxa that have not yet been discovered due to this undersampling, highlighting the need for diversity in microbiome studies. We anticipate that this new compendium can serve the community and enable advanced applied and methodological research.
Collapse
Affiliation(s)
- Richard J. Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Samantha P. Graham
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vincent Rubinetti
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Casey S. Greene
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Sean Davis
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
- Center for Health Artificial Intelligence (CHAI), University of Colorado School of Medicine, Aurora, CO, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
3
|
Park DS, Nguyen SC, Isenhart R, Shah PP, Kim W, Barnett RJ, Chandra A, Luppino JM, Harke J, Wai M, Walsh PJ, Abdill RJ, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki MT, Vahedi G, Phillips-Cremins JE, Jain R, Joyce EF. High-throughput Oligopaint screen identifies druggable 3D genome regulators. Nature 2023; 620:209-217. [PMID: 37438531 DOI: 10.1038/s41586-023-06340-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions1-3. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.
Collapse
Affiliation(s)
- Daniel S Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Randi Isenhart
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Parisha P Shah
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wonho Kim
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R Jordan Barnett
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditi Chandra
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer M Luppino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jailynn Harke
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - May Wai
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick J Walsh
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Richard J Abdill
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel Yang
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yemin Lan
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sora Yoon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Yunker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Shizuoka, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Phillips-Cremins
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Rajan Jain
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
4
|
Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol 2023; 24:16. [PMID: 36691074 PMCID: PMC9869549 DOI: 10.1186/s13059-023-02849-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Unlike many histone modifications and chromatin-associated proteins, lamina-associated domains (LADs) are mapped genome-wide in relatively few genetically normal human cell types, which limits our understanding of the role peripheral chromatin plays in development and disease. RESULTS To address this gap, we map LAMIN B1 occupancy across twelve human cell types encompassing pluripotent stem cells, intermediate progenitors, and differentiated cells from all three germ layers. Integrative analyses of this atlas with gene expression and repressive histone modification maps reveal that lamina-associated chromatin in all twelve cell types is organized into at least two subtypes defined by differences in LAMIN B1 occupancy, gene expression, chromatin accessibility, transposable elements, replication timing, and radial positioning. Imaging of fluorescently labeled DNA in single cells validates these subtypes and shows radial positioning of LADs with higher LAMIN B1 occupancy and heterochromatic histone modifications primarily embedded within the lamina. In contrast, the second subtype of lamina-associated chromatin is relatively gene dense, accessible, dynamic across development, and positioned adjacent to the lamina. Most genes gain or lose LAMIN B1 occupancy consistent with cell types along developmental trajectories; however, we also identify examples where the enhancer, but not the gene body and promoter, changes LAD state. CONCLUSIONS Altogether, this atlas represents the largest resource to date for peripheral chromatin organization studies and reveals an intermediate chromatin subtype.
Collapse
Affiliation(s)
- Parisha P. Shah
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Kathleen C. Keough
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Ketrin Gjoni
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Garrett T. Santini
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Richard J. Abdill
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Nadeera M. Wickramasinghe
- grid.59734.3c0000 0001 0670 2351Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Carolyn E. Dundes
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Ashley Karnay
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| | - Angela Chen
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Rachel E. A. Salomon
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Patrick J. Walsh
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Son C. Nguyen
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sean Whalen
- grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA
| | - Eric F. Joyce
- grid.25879.310000 0004 1936 8972Department of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kyle M. Loh
- grid.168010.e0000000419368956Department of Developmental Biology and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Nicole Dubois
- grid.59734.3c0000 0001 0670 2351Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Katherine S. Pollard
- grid.266102.10000 0001 2297 6811University of California, San Francisco, CA 94117 USA ,grid.249878.80000 0004 0572 7110Gladstone Institute of Data Science and Biotechnology, 1650 Owens Street, San Francisco, CA 94158 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
| | - Rajan Jain
- grid.25879.310000 0004 1936 8972Departments of Medicine and Cell and Developmental Biology, Penn CVI, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA ,Smilow TRC, 3400 Civic Center Blvd, Philadelphia, PA 19104 USA
| |
Collapse
|
5
|
Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression. PLoS Genet 2022; 18:e1010528. [PMID: 36449519 PMCID: PMC9744307 DOI: 10.1371/journal.pgen.1010528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/12/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; depletion of either is associated with changes in both chromatin folding and transcription across a wide range of cell types. However, a direct comparison of their individual and combined effects on gene expression in the same cell type is lacking. We find that NIPBL or WAPL depletion in human HCT116 cells each alter the expression of ~2,000 genes, with only ~30% of the genes shared between the conditions. We find that clusters of differentially expressed genes within the same topologically associated domain (TAD) show coordinated misexpression, suggesting some genomic domains are especially sensitive to both more or less cohesin. Finally, co-depletion of NIPBL and WAPL restores the majority of gene misexpression as compared to either knockdown alone. A similar set of NIPBL-sensitive genes are rescued following CTCF co-depletion. Together, this indicates that altered transcription due to reduced cohesin activity can be functionally offset by removal of either its negative regulator (WAPL) or the physical barriers (CTCF) that restrict loop-extrusion events.
Collapse
Affiliation(s)
- Jennifer M. Luppino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew Field
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Boston, Massachusetts, United States of America
| | - Son C. Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel S. Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Parisha P. Shah
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard J. Abdill
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yemin Lan
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rebecca Yunker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rajan Jain
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Boston, Massachusetts, United States of America
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eric F. Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
6
|
Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression. PLoS Genet 2022. [PMID: 36449519 DOI: 10.1101/2022.04.19.488785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; depletion of either is associated with changes in both chromatin folding and transcription across a wide range of cell types. However, a direct comparison of their individual and combined effects on gene expression in the same cell type is lacking. We find that NIPBL or WAPL depletion in human HCT116 cells each alter the expression of ~2,000 genes, with only ~30% of the genes shared between the conditions. We find that clusters of differentially expressed genes within the same topologically associated domain (TAD) show coordinated misexpression, suggesting some genomic domains are especially sensitive to both more or less cohesin. Finally, co-depletion of NIPBL and WAPL restores the majority of gene misexpression as compared to either knockdown alone. A similar set of NIPBL-sensitive genes are rescued following CTCF co-depletion. Together, this indicates that altered transcription due to reduced cohesin activity can be functionally offset by removal of either its negative regulator (WAPL) or the physical barriers (CTCF) that restrict loop-extrusion events.
Collapse
Affiliation(s)
- Jennifer M Luppino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Andrew Field
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Boston, Massachusetts, United States of America
| | - Son C Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel S Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Parisha P Shah
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard J Abdill
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Yemin Lan
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rebecca Yunker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rajan Jain
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Cell and Developmental Biology, Department of Medicine, Institute of Regenerative Medicine, Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Ludwig Center at Harvard, Boston, Massachusetts, United States of America
- The Eli and Edythe L. Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eric F Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
7
|
Abstract
The importance of sampling from globally representative populations has been well established in human genomics. In human microbiome research, however, we lack a full understanding of the global distribution of sampling in research studies. This information is crucial to better understand global patterns of microbiome-associated diseases and to extend the health benefits of this research to all populations. Here, we analyze the country of origin of all 444,829 human microbiome samples that are available from the world’s 3 largest genomic data repositories, including the Sequence Read Archive (SRA). The samples are from 2,592 studies of 19 body sites, including 220,017 samples of the gut microbiome. We show that more than 71% of samples with a known origin come from Europe, the United States, and Canada, including 46.8% from the US alone, despite the country representing only 4.3% of the global population. We also find that central and southern Asia is the most underrepresented region: Countries such as India, Pakistan, and Bangladesh account for more than a quarter of the world population but make up only 1.8% of human microbiome samples. These results demonstrate a critical need to ensure more global representation of participants in microbiome studies. The importance of sampling from globally representative populations has been well established in human genomics, but what about the microbiome? This study shows that metadata from almost half a million samples reveals worldwide human microbiome research is skewed heavily in favor of Europe and North America and excludes large but less developed nations in Asia and Africa.
Collapse
Affiliation(s)
- Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Elizabeth M. Adamowicz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
8
|
Carneiro CFD, Queiroz VGS, Moulin TC, Carvalho CAM, Haas CB, Rayêe D, Henshall DE, De-Souza EA, Amorim FE, Boos FZ, Guercio GD, Costa IR, Hajdu KL, van Egmond L, Modrák M, Tan PB, Abdill RJ, Burgess SJ, Guerra SFS, Bortoluzzi VT, Amaral OB. Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature. Res Integr Peer Rev 2020; 5:16. [PMID: 33292815 PMCID: PMC7706207 DOI: 10.1186/s41073-020-00101-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Preprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader's ability to independently interpret data and reproduce findings. METHODS In this observational study, we initially compared independent samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. After that, we performed paired comparisons between preprints from bioRxiv to their own peer-reviewed versions in journals. RESULTS Peer-reviewed articles had, on average, higher quality of reporting than preprints, although the difference was small, with absolute differences of 5.0% [95% CI 1.4, 8.6] and 4.7% [95% CI 2.4, 7.0] of reported items in the independent samples and paired sample comparison, respectively. There were larger differences favoring peer-reviewed articles in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information. Changes in reporting from preprints to peer-reviewed versions did not correlate with the impact factor of the publication venue or with the time lag from bioRxiv to journal publication. CONCLUSIONS Our results suggest that, on average, publication in a peer-reviewed journal is associated with improvement in quality of reporting. They also show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.
Collapse
Affiliation(s)
- Clarissa F D Carneiro
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil.
| | - Victor G S Queiroz
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Thiago C Moulin
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Carlos A M Carvalho
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Departamento de Patologia, Universidade do Estado do Pará, Belém, Pará, Brazil
- Centro Universitário Metropolitano da Amazônia, Instituto Euro-Americano de Educação, Ciência e Tecnologia, Belém, Pará, Brazil
| | - Clarissa B Haas
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Danielle Rayêe
- Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Evandro A De-Souza
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Felippe E Amorim
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Flávia Z Boos
- Programa de Pós-Graduação em Psicobiologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gerson D Guercio
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Igor R Costa
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Karina L Hajdu
- Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Martin Modrák
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pedro B Tan
- Biomedical Sciences Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Richard J Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Steven J Burgess
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Sylvia F S Guerra
- Centro Universitário Metropolitano da Amazônia, Instituto Euro-Americano de Educação, Ciência e Tecnologia, Belém, Pará, Brazil
- Seção de Virologia, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
- Departamento de Morfologia e Ciências Fisiológicas, Universidade do Estado do Pará, Belém, Pará, Brazil
| | - Vanessa T Bortoluzzi
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Olavo B Amaral
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| |
Collapse
|
9
|
Abstract
Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of 'contributor countries' (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.
Collapse
Affiliation(s)
- Richard J Abdill
- Department of Genetics, Cell Biology, and Development, University of MinnesotaMinneapolisUnited States
| | - Elizabeth M Adamowicz
- Department of Genetics, Cell Biology, and Development, University of MinnesotaMinneapolisUnited States
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of MinnesotaMinneapolisUnited States
- Department of Ecology, Evolution and Behavior, University of MinnesotaMinneapolisUnited States
| |
Collapse
|
10
|
Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AKM, Dayama G, Grieneisen L, Martin LS, Flint J, Eskin E, Blekhman R. Challenges and recommendations to improve the installability and archival stability of omics computational tools. PLoS Biol 2019; 17:e3000333. [PMID: 31220077 PMCID: PMC6605654 DOI: 10.1371/journal.pbio.3000333] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/02/2019] [Indexed: 01/07/2023] Open
Abstract
Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed "easy to install," and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.
Collapse
Affiliation(s)
- Serghei Mangul
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Thiago Mosqueiro
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dat Duong
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Keith Mitchell
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Varuni Sarwal
- Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Brian Hill
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jaqueline Brito
- Institute of Mathematics and Computer Science, University of São Paulo, São Paulo, Brazil
| | - Russell Jared Littman
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Benjamin Statz
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Angela Ka-Mei Lam
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
| | - Gargi Dayama
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lana S. Martin
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minnesota, United States of America
| |
Collapse
|
11
|
Abstract
Preprints have arrived. In increasing numbers, researchers across the life sciences are embracing the once-niche practice, shaking off decades of reluctance and posting hundreds of papers per week to preprint servers, sharing their findings with the community before embarking on the weary march through peer review. However, there are limited methods for individuals sifting through this avalanche of research to identify the preprints that are most relevant to their interests. Here, we describe Rxivist.org, a website that indexes all preprints posted to bioRxiv.org, the largest preprint server in the life sciences, and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods. In this work, we hope to make it easier for readers to find relevant research on bioRxiv and to improve the visibility of preprints currently being read and discussed online. This Community Page article describes Rxivist.org, a new website that indexes all preprints posted to bioRxiv.org and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods.
Collapse
Affiliation(s)
- Richard J. Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
12
|
Abstract
The growth of preprints in the life sciences has been reported widely and is driving policy changes for journals and funders, but little quantitative information has been published about preprint usage. Here, we report how we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. The rate of preprint uploads to bioRxiv continues to grow (exceeding 2,100 in October 2018), as does the number of downloads (1.1 million in October 2018). We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between the number of downloads a preprint has received and the impact factor of the journal in which it is published. We also describe Rxivist.org, a web application that provides multiple ways to interact with preprint metadata.
Collapse
Affiliation(s)
- Richard J Abdill
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, United States.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, United States
| |
Collapse
|