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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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Dai R, Zhang M, Chu T, Kopp R, Zhang C, Liu K, Wang Y, Wang X, Chen C, Liu C. Precision and Accuracy of Single-Cell/Nuclei RNA Sequencing Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589216. [PMID: 38659857 PMCID: PMC11042208 DOI: 10.1101/2024.04.12.589216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Single-cell/nuclei RNA sequencing (sc/snRNA-Seq) is widely used for profiling cell-type gene expressions in biomedical research. An important but underappreciated issue is the quality of sc/snRNA-Seq data that would impact the reliability of downstream analyses. Here we evaluated the precision and accuracy in 18 sc/snRNA-Seq datasets. The precision was assessed on data from human brain studies with a total of 3,483,905 cells from 297 individuals, by utilizing technical replicates. The accuracy was evaluated with sample-matched scRNA-Seq and pooled-cell RNA-Seq data of cultured mononuclear phagocytes from four species. The results revealed low precision and accuracy at the single-cell level across all evaluated data. Cell number and RNA quality were highlighted as two key factors determining the expression precision, accuracy, and reproducibility of differential expression analysis in sc/snRNA-Seq. This study underscores the necessity of sequencing enough high-quality cells per cell type per individual, preferably in the hundreds, to mitigate noise in expression quantification.
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Affiliation(s)
- Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ming Zhang
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tianyao Chu
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Richard Kopp
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Chunling Zhang
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Kefu Liu
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, VA, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chao Chen
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Furong Laboratory, Changsha, Hunan, China
- Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, China
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA
- MOE Key Laboratory of Rare Pediatric Diseases & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY, USA
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Liu T, Li K, Wang Y, Li H, Zhao H. Evaluating the Utilities of Foundation Models in Single-cell Data Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.08.555192. [PMID: 38464157 PMCID: PMC10925156 DOI: 10.1101/2023.09.08.555192] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Foundation Models (FMs) have made significant strides in both industrial and scientific domains. In this paper, we evaluate the performance of FMs in single-cell sequencing data analysis through comprehensive experiments across eight downstream tasks pertinent to single-cell data. By comparing ten different single-cell FMs with task-specific methods, we found that single-cell FMs may not consistently excel in all tasks than task-specific methods. However, the emergent abilities and the successful applications of cross-species/cross-modality transfer learning of FMs are promising. In addition, we present a systematic evaluation of the effects of hyper-parameters, initial settings, and stability for training single-cell FMs based on a proposed scEval framework, and provide guidelines for pre-training and fine-tuning. Our work summarizes the current state of single-cell FMs and points to their constraints and avenues for future development.
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Wu Y, Gu Q, Wang Z, Tian Z, Wang Z, Liu W, Han J, Liu S. Electrochemiluminescence Analysis of Multiple Glycans on Single Living Cell with a Closed Bipolar Electrode Array Chip. Anal Chem 2024; 96:2165-2172. [PMID: 38284353 DOI: 10.1021/acs.analchem.3c05127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
The profiling of multiple glycans on a single cell is important for elucidating glycosylation mechanisms and accurately identifying disease states. Herein, we developed a closed bipolar electrode (BPE) array chip for live single-cell trapping and in situ galactose and sialic acid detection with the electrochemiluminescence (ECL) method. Methylene blue-DNA (MB-DNA) as well as biotin-DNA (Bio-DNA) codecorated AuNPs were prepared as nanoprobes, which were selectively labeled on the cell surface through chemoselective labeling techniques. The individual cell was captured and labeled in the microtrap of the cathodic chamber, under an appropriate potential, MB molecules on the cellular membrane underwent oxidation, triggering the reduction of [Ru(bpy)3]2+/TPA and consequently generating ECL signals in the anodic chamber. The abundance of MB groups on the single cell enabled selective monitoring of both sialic acid and galactosyl groups with high sensitivity using ECL. The sialic acid and galactosyl content per HepG2 cell were detected to be 0.66 and 0.82 fmol, respectively. Through comprehensive evaluation of these two types of glycans on a single cell, tumor cells, and normal cells could be effectively discriminated and the accuracy of single-cell heterogeneous analysis was improved. Additionally, dynamic monitoring of variations in galactosyl groups on the surface of the single cell was also achieved. This work introduced a straightforward and convenient approach for heterogeneity analysis among single cells.
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Affiliation(s)
- Yafeng Wu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qinglin Gu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Zhi Wang
- Wuxi Institute of Inspection, Testing and Certification, Wuxi 214125, China
| | - Zhaoyan Tian
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng 252059, China
| | - Zhaohan Wang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Weiwei Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Jianyu Han
- School of Energy and Environment, Southeast University, Nanjing 211189, China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, State Key Laboratory of Digital Medical Engineering, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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