Bing Ren
San Diego
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Articles by Bing Ren
Integrated differential transcript usage and transcript abundance analyses reveal isoform-level remodeling in clear cell renal cell carcinoma
Abstract Clear cell renal cell carcinoma (ccRCC) is characterized by transcriptional reprogramming driven by hypoxia signaling, metabolic rewiring, and immune modulation. While gene-level analyses have defined key features of ccRCC biology, they do not capture isoform-level variation arising from alternative splicing.
Aging-induced hepatocyte CD44 drives IL6/STAT3 signaling that associates with impaired function of neighboring T cells
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Abstract Liver cancer incidences increase dramatically beyond 55 years of age, suggesting that age-associated changes contribute critically to tumor initiation. However, the mechanisms linking liver aging and cancer initiation remain incompletely defined. This study investigated the role of CD44, a marker of liver tumor-initiating cells (TICs), in age-associated liver pathophysiology.
By Armin Gandhi, Kathryn Lande, Kelly Li, Michael LaPorte, K. Garrett Evensen, Marcos Garcia Teneche, Rouven Arnold, Adarsh Rajesh, Jessica Proulx, Shanshan Yin, Aaron Havas, Angela Y. Liou, Allen Lee, Helene Martini, Xue Lei, Charlene Miciano, Qian Yang, Sainath Mamde, Andrew Davis, Rebecca A. Porritt, Alessandra Sacco, João F. Passos, Kevin Tharp, Kevin Y. Yip, Allen Wang, Bing Ren, April Williams, Susan M Kaech, Peter Adams, Filipe A. Hoffmann, Shirong Tan, Benji Portillo, Elizabeth W. Smoot
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Nature
Verified
Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease–linked transcription factor
Structured Abstract Abstract Supplementary Materials References and Notes Information & Authors Metrics & Citations Check Access References Figures Tables Media Share Structured Abstract INTRODUCTION Haploinsufficient mutations of transcription factors (TFs) resulting in reduced gene dosage are an underlying cause of human genetic developmental disorders affecting diverse tissue and cell types.
Multimodal PCSC Sensors for Real-Time Temperature and Force Detection Using LRTNet
You are already at the latest version Multimodal sensors can collect multiple signals and have great potential in robotics and other technical fields. However, such sensors often encounter challenges of signal crosstalk and insufficient real-time performance, particularly in the detection of pressure and temperature, which significantly affect measurement accuracy. To address this issue, a multimodal PCSC sensor was developed.
Single-cell epigenomics uncovers heterochromatin instability and transcription factor dysfunction during mouse brain aging
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STAR★Methods REAGENT or RESOURCESOURCEIDENTIFIER Chemicals, peptides, and recombinant proteins Tn5 transposase QB3 Macrolab at UC Berkeley N/A SPRISelect reagent Beckman Coulter Cat# B23319 DRAQ7 Cell Signaling Cat# 7406 NEBNext High-Fidelity PCR Master Mix NEB Cat# M0541L LightCycler 480 SYBR Green I Master Mix Roche Cat# 04707516001 DTT nuclei permeabilization buffer Sigma-Aldrich Cat# 646563-10X IGEPAL-CA630 Sigma-Aldrich Cat#I8896 1X cOmplete EDTA-free protease inhibitor cocktail tablets...
By Maria Amaral, Sainath Mamde, MICHAEL Miller, Xiaomeng Hou, Jessica Arzavala, Julia Osteen, Nicholas Johnson, Qian Yang, Emily Eisner, Qiurui Zeng, Cindy Tatiana Báez-Becerra, Joseph Kern, Jonathan A. Rink, Ariana Barcoma, Silvia Cho, Stella Cao, Nora E. Emerson, Jasper Lee, Jackson Willier, Songpeng Zu, Quan Zhu, Sebastian Preissl, Allen Wang, Joseph R. Ecker, Bing Ren, Elizabeth Walker Smoot, Jacqueline Olness, Timothy Loe, Henry Jiao, Maria Margarita Behrens
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Cell Reports
Verified
Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain
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Results We refined and employed snmC-seq3,35,36 an advanced single-nucleus methylome sequencing technique, to achieve base-resolution profiling of genome-wide 5-methylcytosine (5mC) across eight brain regions in C57BL/6 male mice (Figure 1A).
By Qiurui Zeng, Wenliang Wang, Wei Tian, Amit Klein, Anna Bartlett Verified, Hanqing Liu, Joseph R. Nery, Rosa Castanon, Julia Osteen, Nicholas Johnson, Wubin Ding, Huaming Chen, Jordan Altshul, Mia Kenworthy, Cynthia Valadon, William Owens, Zhanghao Wu, Maria Amaral, Nathan R. Zemke, Yuru Song, Silvia Cho, Jonathan A. Rink, Jasper Lee, Nora E. Emerson, Yuancheng Lu, Bing Ren, M. Margarita Behrens, Joseph R. Ecker, Cindy Tatiana Báez-Becerra, Chumo Chen, Jackson Willier, Stella Cao, Ariana Barcoma, Jessica Arzavala
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Cell Press
Verified
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex
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Keywords enhancer-AAV DNA sequence model TF codes single-cell multiomics cortex prediction benchmark cross-species ATAC-seq Introduction The mammalian neocortex, responsible for higher-order cognitive functions and sensorimotor processing, includes the primary motor cortex (M1), which facilitates fine motor movement and is composed of diverse cell types with distinct molecular signatures.1,2 Some neurodegenerative diseases, including Parkinson’s disease, Huntington’s disease, and amyotrophic...
By Nelson Johansen, Niklas Kempynck, Nathan R. Zemke, Saroja Somasundaram, Seppe De Winter, Marcus J. Hooper, Deepanjali Dwivedi, Ruchi Lohia, Fabien Wehbe, Bocheng Li, Darina Abaffyová, Ethan J. Armand, Eren Can Ekşi, Nikolai Hecker, Gert Hulselmans, David Mauduit, John K. Mich, Gabriele Partel, Tanya L. Daigle, Boaz P. Levi, Kai Zhang, Yoshiaki Tanaka, Jesse Gillis, Jonathan T. Ting, Yoav Ben-Simon, Jeremy Miller, Joseph R. Ecker, Bing Ren, Stein Aerts, Ed Lein, Bosiljka Tasic, Trygve E. Bakken, Julie De Man, Vasilis Konstantakos
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Cell Press
Verified
Perturbing LSD1 and WNT rewires transcription to synergistically induce AML differentiation - Nature
Abstract Impaired differentiation is a hallmark of myeloid malignancies1,2. Therapies that enable cells to circumvent the differentiation block, such as all-trans retinoic acid (ATRA) and arsenic trioxide (ATO), are by and large curative in acute promyelocytic leukaemia3, but whether ‘differentiation therapy’ is a generalizable therapeutic approach for acute myeloid leukaemia (AML) and beyond remains incompletely understood.
The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project - Nature Genetics
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Abstract Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts.
By Lingzhao Fang, Jinyan Teng, Dailu Guan, Bingjie Li, Ying Yu, Jacqueline Smith, Konrad Rawlik, Ruidong Xiang, Amanda Chamberlain, Greger Larson, David E. MacHugh, Goutam Sahana, Zhihua Jiang, Guoqiang Yi, Yuwen Liu, Zhonglin Tang, Xiao Wang, Robert Young, Xia Shen, Charley Xia, Li Ma, John Cole, Cong-Jun Li, Benjamin Rosen, Nayan Bhowmik, Joan K. Lunney, Wansheng Liu, Xin Zhao, Eveline M. Ibeagha-Awemu, Yonglun Luo, Lin Lin, James E. Koltes, Christopher K. Tuggle, Elisabetta Giuffra, Marcel Amills, Alex Clop, Maria Ballester, Gwenola Tosser-Klopp, Ming Fang, Qishan Wang, Zhuocheng Hou, Fuping Zhao, Lin Jiang, Guiping Zhao, Zhengkui Zhou, Rong Zhou, Long Jin, Mingzhou Li, Delin Mo, Shuhong Zhao, Hui-Zeng Sun, Yu Jiang, Dongdong Wu, Kui Li, Ning Yang, Xiaoxiang Hu, Wen Huang, Jian Yang, Claudia Kasper, Xiang Zhou, Wei Li, Edward S. Buckler, Bing Ren, Michael C Schatz, Jingyi Li, Abraham A. Palmer, Laurent A. F. Frantz, Huaijun Zhou, Zhe Zhang, George Liu
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Nature
Verified
Sensory input, sex and function shape hypothalamic cell type development - Nature
Abstract Mammalian behaviour and physiology undergo major changes in early life. Young animals rely on conspecifics to meet their needs and start showing nutritional independence and sex-specific social interactions at weaning and puberty, respectively. How neuronal populations regulating homeostatic functions and social behaviours develop during these transitions remains unclear.
Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues - Nature Structural & Molecular Biology
Abstract While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain.
Built to be imperfect - Nature Cell Biology
Transcription factors (TFs) and cis-regulatory elements (CREs) drive organism development. Suboptimal binding of TFs to CREs is shown to be key for the specificity of gene expression. New work now indicates that a similar principle governs the activities of TFs and their regulatory specificity.
视点：国内法院破产程序中的船舶扣押与拍卖实务问题研究--海事海商X破产系列文章（六） - Lexology
我们在前面的文章中介绍了航运企业跨境破产时与船舶扣押相关的法律问题（参见：视点 | 航运企业跨境破产与船舶扣押的冲突与协调——海事海商X破产系列文章（四），实际上司法实务中，国内法院在处理破产航运企业船舶扣押和拍卖时存在的争议同样不少，破产法律和海商事法律在对船舶的保全和执行问题上产生了交叉和冲突，给司法实践带来诸多困境。本文将结合我们承办的有关案例、其他典型案例和实务界的研究成果，对国内法院破产程序中的船舶扣押和拍卖问题进行讨论。 一、破产程序中船舶扣押与拍卖问题的司法实务样本 对于破产程序中船舶扣押与拍卖的问题，司法实践存在不同的处理模式，主要包括： （一）因船舶优先权提起的诉讼，已进入拍卖程序的船舶，不中止执行 案例1：连润公司与谭权斌船员劳务合同纠纷执行异议一案，（2016）沪执复8号，上海海事法院、上海市高级人民法院...
视点：船舶修造企业特殊资产在破产程序中的处置问题 --海事海商X破产系列文章（五）
中国船舶修造业在全球范围内具备足够的竞争力和优势，特别是江苏省作为我国的船舶修造重要区域，江苏地区的船舶修造和海洋工程已是江苏的一张名片。来自江苏省人民政府的统计数据显示：2022年，全省船舶海工规模以上企业实现营业收入1440亿元、占全国比重超三分之一；造船三大指标连续14年居全国第一。2023年前10月，江苏省造船完工量、新接订单量、手持订单量分别达1627.1万、2807.6万、6110.7万载重吨，占世界市场份额四分之一。江苏已形成南通海工装备和豪华邮轮、泰州大型油船和集装箱船、扬州大型散货船和滚装船等特色基地，船舶海工产业规模总量全国领先、核心竞争力显著提升、国际影响力不断增强。[①]江苏省国防科工办已发布《江苏省南通市、泰州市、扬州市高技术船舶和海工装备国家先进制造业集群培育提升三年行动方案（2023—2025）》，全力打造打造地标性世界级船舶海工先进制造业集群。...
航运企业跨境破产与船舶扣押的冲突与协调--海事海商X破产系列文章（四） - Lexology
航运企业的业务类型和资产状况决定其容易引发跨境破产程序的冲突问题，例如，2016年，航运巨头韩国韩进海运株式会社（下称“韩进航运”）提出破产申请，韩国首尔中央地方法院进行了受理，后宣布鉴于韩进海运的清算价值超过继续经营价值，韩进海运正式进入破产重组[1]。部分债权人选择向韩国的破产管理人申报债权，部分债权人选择在其他国家扣押韩进海运所有的船舶或其他财产，再通过海事诉讼获得清偿。分布在不同国家的债权人纷纷申请扣押韩进海运所有的船舶，引发了全球性的破产程序与船舶扣押程序的冲突[2]。我国海事法院合计受理了相关海事海商纠纷案件40余件，涉案总标的达数十亿元人民币[3]。这其中涉及最重要的问题包括：从航运企业跨国破产程序的救济形式和范围出发，针对船舶优先权人的权利是否应受到跨界破产程序的影响；在外国破产程序被承认前，被扣押船舶是否受到跨界破产程序的影响；非债务人自有船舶是否受到跨界破产程序保护等问题。 航运企业跨境破产的特殊性...
A Fast IAA−Based SR−STAP Method for Airborne Radar
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Spatially organized cellular communities form the developing human heart - Nature
Abstract The heart, which is the first organ to develop, is highly dependent on its form to function1,2. However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart function remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization to resolve the identity of the cardiac cell types that develop the human heart.
海事赔偿责任限制制度在航运企业破产程序中的冲突与协调--海事海商破产交叉系列文章（三） - Lexology
海事赔偿责任限制制度是《海商法》中最为特殊的制度安排之一，在单独的海事诉讼程序中，按照《海商法》、《海诉法》及其司法解释，各家海事法院及其上级法院已构建起我国涉及海事赔偿责任限制制度的完整体系。但如果航运企业责任人设立海事赔偿责任限制基金后，又因难以清偿企业的到期债务，进行破产清算，基金程序将与破产程序并存，两者之间既有互相冲突的地方，又有立法空白的地方。本文结合我们承办的有关案例以及实务界的研究成果，对海事赔偿责任限制制度在航运企业破产程序中的冲突与协调进行分析和讨论。 一、海事赔偿责任限制及基金制度与破产程序冲突的缘由 海事赔偿责任限制(limitation of liability for maritime claims)，是海商法特有的，为保障船东就特定事项享有责任限制权利而设立的特别制度。该制度历史十分悠久，多数观点认为此项制度始于11世纪，甚至有观点认为意大利《阿马尔菲法》中就有关于船东有权限制其责任的记载[1]。但也有观点认为13世纪意大利巴塞罗那的《海事裁判集》才是海事赔偿责任限制制度的发端[2]。...
Penile Sebaceous Adenoma with Sporadic Loss of
Case Report, J Genet Disor Genet Rep Vol: 12 Issue: 5 Blaire A. Anderson1,2*, Shaofeng Yan1 and Bing Ren1 1Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, United States of America 2Department of Medicine, Dartmouth College, Hanover, United States of America *Corresponding Author: Blaire A.
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells - Nature Communications
Abstract The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains.
SnapATAC2: a fast, scalable and versatile tool for single-cell omics analysis
Abstract Single-cell omics technologies have ushered in a new era for analyzing gene regulation in specific cell types, both in complex tissues and during different disease conditions. Nevertheless, identifying cell types in these datasets pose a substantial computational challenge driven by the intricate and high dimensional nature of the data.
A Novel Fast Sparse Bayesian Learning STAP Algorithm for Conformal Array Radar
This is an early access version, the complete PDF, HTML, and XML versions will be available soon. Open AccessArticle by and * National Key Laboratory of Radar Signal Processing, Xidian University, Xi’an 710071, China * Author to whom correspondence should be addressed. Remote Sens.
Interpreting non-coding disease-associated human variants using single-cell epigenomics - Nature Reviews Genetics
Authors and Affiliations Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego School of Medicine, La Jolla, CA, USA Kyle J.
Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation
Many cell types undergo changes postnatally to acquire their specialized mature phenotypes, and the governing mechanisms are understudied. Here, Zhou et al. integrate cardiomyocyte-specific profiling of gene expressions, enhancers, and 3D genomes across murine development to identify interactions between dynamic enhancers and the changing 3D genomes regulating maturational gene expressions.
Realizations of vascularized tissues: From in vitro platforms to in vivo grafts
II. HUMAN VASCULAR SYSTEM AND DESIGN CONSIDERATIONS To be of relevance, the vascular system of an engineered vascularized tissue needs to recapitulate the physiological vascular characteristics and functionalities of in situ tissues.9,179. G. Yang, B. Mahadik, J. Y. Choi, and J. P. Fisher, Prog. Biomed. Eng. 2(1), 012002 (2020). https://doi.org/10.1088/2516-1091/ab563717. S. Fleischer, D. N. Tavakol, and G. Vunjak‐Novakovic, Adv. Funct. Mater. 30(37), 1910811 (2020).
Author Correction: A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH - Nature Biotechnology
Correction to: Nature Biotechnology https://doi.org/10.1038/s41587-022-01568-9. Published online 2 January 2023. In the version of this article initially published, the 4D Nucleome Web Portal accession number (4DNESU4Y9CBF) provided in the Data availability section was incorrect and has been replaced with accession numbers 4DNESIGBIXQS, 4DNESC5PKTQ9, 4DNES51KSIZ9, 4DNESNEKOCAP and 4DNESOXQX1JT in the HTML and PDF versions of the article.
Characterizing cis-regulatory elements using single-cell epigenomics - Nature Reviews Genetics
Abstract Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin.
A Test Method for Obstacle-Avoidance Performance of Unmanned Surface Vehicles Based on Mobile-Buoy–Shore Multisource-Sensing-Data Fusion
Open AccessArticle by Guoquan Xiao 1, Guihong Zheng 1, Bing Ren 1, Yue Wang 2, Xiaobin Hong 1,* and Zhigang Zhang 3,* 1 School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510641, China 2 Thurgood Marshall (Frmly Third) College, University of California, San Diego, CA 92093, USA 3 Guangdong Provincial Key Laboratory of Electronic Information Products Reliability Technology, Guangzhou 510610, China * Authors to whom correspondence should be addressed.
Author Correction: Perspectives on ENCODE - Nature
Correction to: Nature https://doi.org/10.1038/s41586-020-2449-8published online 29 July 2020 In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.
A Quantitative Evaluation Method for Obstacle Avoidance Performance of Unmanned Ship
Open AccessArticle by Guoquan Xiao , Bing Ren , Chao Tong and Xiaobin Hong * School of Mechanical & Automotive Engineering, South China University of Technology, Guangzhou 510641, China * Author to whom correspondence should be addressed.
Publisher Correction: Chromothripsis drives the evolution of gene amplification in cancer
Correction to: https://doi.org/10.1038/s41586-020-03064-zPublished online 23 December 2020 In Fig. 2i of this Article, owing to an error during the production process, a scale bar from 0 to 200 appeared in the top right of the panel. This scale bar has been removed and the original Article has been corrected online.
Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development
Correction to: Nature https://doi.org/10.1038/s41586-020-2093-3 Published online 29 July 2020 In this Article, there are several errors. In Figure 3i, minus signs were missing from the P values; they should read P = 2.8 × 10−100 and P = 3.1 × 10−11. In Fig. 5e, the maximum value on the horizontal axis should be 2.1 (not 35). In Extended Data Fig. 1a, the text under the table should cite Extended Data Fig. 10 (not Extended Data Fig. 6). In the legend of Extended Data Fig.
Chromothripsis drives the evolution of gene amplification in cancer
Abstract Focal chromosomal amplification contributes to the initiation of cancer by mediating overexpression of oncogenes1,2,3, and to the development of cancer therapy resistance by increasing the expression of genes whose action diminishes the efficacy of anti-cancer drugs.
A TypeScript Project Structure Guide
Directory structures and module resolution of TypeScript projects are not complex, until you start organizing things into separate units, putting them into different directories, and experimenting with some of the configuration options discussed here. This article provides an overall understanding of the mechanisms and configuration options that affect TypeScript project directory structures and module resolution, as well as some caveats in the hope of saving the reader from certain pitfalls.
A TypeScript Project Structure Guide
Directory structures and module resolution of TypeScript projects are not complex, until you start organizing things into separate units, putting them into different directories, and experimenting with some of the configuration options discussed here. This article provides an overall understanding of the mechanisms and configuration options that affect TypeScript project directory structures and module resolution, as well as some caveats in the hope of saving the reader from certain pitfalls.
Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development
Correction to: Nature https://doi.org/10.1038/s41586-020-2093-3Published online 29 July 2020 In this Article, a citation to He et al. (2020)1 was missing from three places in the main text. This has been added to the original Article as ref. 98, and occurs after the following text: “…used as input for RNA sequencing (RNA-seq)”, “…are reported in companion manuscripts”, and “…including deconvolution of whole-tissue data into distinct cell types”.
Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution
Abstract Determining the spatial organization of chromatin in cells mainly relies on crosslinking-based chromosome conformation capture techniques, but resolution and signal-to-noise ratio of these approaches is limited by interference from DNA-bound proteins. Here we introduce chemical-crosslinking assisted proximity capture (CAP-C), a method that uses multifunctional chemical crosslinkers with defined sizes to capture chromatin contacts.
Spatiotemporal DNA methylome dynamics of the developing mouse fetus
Abstract Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood.
Single-cell multimodal omics: the power of many
Advances in single-cell genomics technologies have enabled investigation of the gene regulation programs of multicellular organisms at unprecedented resolution and scale. Development of single-cell multimodal omics tools is another major step toward understanding the inner workings of biological systems. Fig. 1: Methods for single-cell multimodal omics analysis. Fig. 2: Challenges and opportunities in single-cell multimodal omics. References 1. Stuart, T. & Satija, R. Nat. Rev. Genet. 20, 257–272 (2019). 2.
Common DNA sequence variation influences 3-dimensional conformation of the human genome
David U. Gorkin1,2 na1, Yunjiang Qiu1,3 na1, Ming Hu4 na1, Kipper Fletez-Brant5,6, Tristin Liu1, Anthony D. Schmitt1,7, Amina Noor2, Joshua Chiou8,9, Kyle J. Gaulton8, Jonathan Sebat2,10, Yun Li11, Kasper D.
An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome
Abstract Simultaneous profiling of transcriptome and chromatin accessibility within single cells is a powerful approach to dissect gene regulatory programs in complex tissues. However, current tools are limited by modest throughput. We now describe an ultra high-throughput method, Paired-seq, for parallel analysis of transcriptome and accessible chromatin in millions of single cells.
A compendium of promoter-centered long-range chromatin interactions in the human genome
Abstract A large number of putative cis-regulatory sequences have been annotated in the human genome, but the genes they control remain poorly defined. To bridge this gap, we generate maps of long-range chromatin interactions centered on 18,943 well-annotated promoters for protein-coding genes in 27 human cell/tissue types.
DNA replication acts as an error correction mechanism to maintain centromere identity by restricting CENP-A to centromeres
Abstract Chromatin assembled with the histone H3 variant CENP-A is the heritable epigenetic determinant of human centromere identity. Using genome-wide mapping and reference models for 23 human centromeres, CENP-A binding sites are identified within the megabase-long, repetitive α-satellite DNAs at each centromere. CENP-A is shown in early G1 to be assembled into nucleosomes within each centromere and onto 11,390 transcriptionally active sites on the chromosome arms.
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By Ming Hu, Zheng Xu, Yun Li Verified, Shin Lin, Yiing Lin, Bing Ren, Anthony D. Schmitt, Inkyung Jung, Yunjiang Qiu, Catherine L. Tan, Cathy L. Barr
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secure.jbs.elsevierhealth.com
Chromatin Domains: The Unit of Chromosome Organization
The chromatin contact maps from diverse cell types and tissues indicate that TADs are relatively cell-type invariant, in contrast to other chromatin organization features. Furthermore, comparison of chromatin contact maps in related species also showed that TADs are preserved in syntenic sequences (Dixon et al., 2012xTopological domains in mammalian genomes identified by analysis of chromatin interactions.
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