Is this you? As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.
Claim your profile
Articles by Mitchell Guttman
LncRNA-splicing factor condensates regulate hypoxia-responsive pre-mRNA processing near nuclear speckles
Keywords nuclear domains gene regulation breast cancer RNA-binding protein RNA splicing phase separation nuclear organization Get full text access Log in, subscribe or purchase for full access. References 1. Höckel, M. ∙ Vaupel, P. Tumor hypoxia: definitions and current clinical, biologic, and molecular aspects J. Natl. Cancer Inst. 2001; 93:266-276 2. Vaupel, P. The role of hypoxia-induced factors in tumor progression Oncologist. 2004; 9:10-17 3. Nakayama, K. ∙ Kataoka, N.
An integrated view of the structure and function of the human 4D nucleome - Nature
|
Abstract The dynamic three-dimensional (3D) organization of the human genome (the 4D nucleome) is linked to genome function. Here we describe efforts by the 4D Nucleome Project1 to map and analyse the 4D nucleome in widely used H1 human embryonic stem cells and immortalized fibroblasts (HFFc6).
By Job Dekker, Johan H. Gibcus, Oliver J. Rando, Derek H. Janssens, Steven Henikoff, Alexander Kukalev, Willemin Andréa, Warren Winick-Ng, Ana Pombo, Miao Yu, PRADEEP KUMAR, Andrew S. Belmont, Takayo Sasaki, Bas van Steensel, Minji Jennifer Kim, Yijun Ruan, Sofia A Quinodoz, Prashant Bhat, Mitchell Guttman, Shu Chien, Yuan Liu, Sergey V. Venev, Dariusz Plewczynski, Christoph J. Thieme, Teresa Szczepińska, Mateusz Chiliński, Mattia Conte, Andrea Esposito, Ruochi Zhang, Xingzhao Wen, Andrea Maria Chiariello, Simona Bianco, Ming Hu, Yun Li, Peter J. Park, Clara Bakker, Ting Wang, Daofeng Li, Xiaotao Wang, Mario Nicodemi, Sheng Zhong, Jennifer E. Phillips-Cremins, David Gilbert, Katherine S. Pollard, Jian Ma, William Noble
|
Nature
Verified
Spatial multi-omics reveals cell-type-specific nuclear compartments - Nature
Abstract The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1,2,3. Understanding their relationships rests on identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci and transcriptional levels in individual cells, all in complex tissues.
Failing to account for RNA quantity inflates background and leads to the misleading appearance that PRC2 and GFP bind to RNA in vivo
Abstract We recently published biochemical and quantitative evidence that challenges the widespread claims that PRC2 binds directly to many RNAs in vivo. A recent preprint performs a re-analysis of some of our data using a different metric and claims to identify contradictory results: that PRC2 binds to more RNAs than the well-characterized PTBP1 and SAF-A RNA-binding proteins.
PRC2-RNA interactions: Viewpoint from Jimmy K. Guo, Mario R. Blanco, and Mitchell Guttman
Get full text access Log in, subscribe or purchase for full access. References 1. Laugesen, A. ∙ Højfeldt, J.W. ∙ Helin, K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation Mol. Cell. 2019; 74:8-18 2. Almeida, M. ∙ Bowness, J.S. ∙ Brockdorff, N. The many faces of Polycomb regulation by RNA Curr. Opin. Genet. Dev. 2020; 61:53-61 3. Guo, J.K. ∙ Guttman, M. Regulatory non-coding RNAs: everything is possible, but what is important? Nat. Methods. 2022; 19:1156-1159 4. Song, J.
Long non-coding RNAs: definitions, functions, challenges and recommendations - Nature Reviews Molecular Cell Biology
Abstract Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term ‘lncRNAs’ encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult.
Regulatory non-coding RNAs: everything is possible, but what is important? - Nature Methods
In recent years, the number of annotated noncoding RNAs (ncRNAs) and RNA-binding proteins (RBPs) has increased dramatically. The wide range of RBPs identified highlights the enormous potential for RNA in virtually all aspects of cell biology, from transcriptional regulation to metabolic control. Yet, there is a growing gap between what is possible and what has been demonstrated to be functionally important.
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations - Nature Methods
Abstract A multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional organization of genomes and key regulatory processes of genome function. Here, we develop a multimodal data integration approach to produce populations of single-cell genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction and spatial segregation of functionally related chromatin.
Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome - Nature Structural & Molecular Biology
Abstract Although thousands of long non-coding RNAs (lncRNAs) are encoded in mammalian genomes, their mechanisms of action are poorly understood, in part because they are often expressed at lower levels than their proposed targets. One such lncRNA is Xist, which mediates chromosome-wide gene silencing on one of the two X chromosomes (X) to achieve gene expression balance between males and females.
SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding - Nature Protocols
Abstract A fundamental question in gene regulation is how cell-type-specific gene expression is influenced by the packaging of DNA within the nucleus of each cell. We recently developed Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables mapping of higher-order interactions within the nucleus. SPRITE works by cross-linking interacting DNA, RNA and protein molecules and then mapping DNA–DNA spatial arrangements through an iterative split-and-pool barcoding method.
Corrigendum: The 4D nucleome project
This Perspective should have contained the following Acknowledgements section: ‘We would like to thank the National Institutes of Health (NIH) Common Fund, the Office of Strategic Coordination and the Office of the NIH Director for funding the 4D Nucleome Program, which has supported the work represented by this report (1U54DK107981, 1U54DK107965, 1U54DK107980, 1U54DK107977, 1U54DK107967, 1U54DK107979, 1U01EB021232, 1U01EB021240, 1U01EB021223, 1U01EB021239, 1U01EB021238, 1U01EB021230,...
Response to Comment on “Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing”
Wang et al. question whether Lamin B receptor is required for Xist-mediated silencing because they claim that our cells contain an inversion rather than a deletion. We present evidence that these cells contain a proper deletion and that the confusion is caused by DNA probes used in the experiment. Accordingly, the points raised have no effect on the conclusions in our paper.
The 4D nucleome project
The human genome contains over 20,000 genes and a larger number of regulatory elements. Large-scale studies over the last decade have catalogued these components of our genome and the cell types in which they are active. The ENCODE, Roadmap Epigenome, International Human Epigenome Consortium, EpiGeneSys (http://www.epigenesys.eu/en/) and FANTOM projects1, 2, 3, 4 have annotated thousands of genes and millions of candidate regulatory elements.
Show More
loading
Actions
Is this you?
As a journalist, you can create a free Muck Rack account to customize your profile, list your contact preferences, and upload a portfolio of your best work.Get in touch with Mitchell
Contact Mitchell, search articles and posts on X, monitor coverage, and track replies from one place.
Learn more about Muck Rack