Guttman, Mitchell

Combined from CaltechAUTHORS

• Wolin, Erica and Guo, Jimmy K., et el. (2023) SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress; PMCID PMC10274648; 10.1101/2023.06.05.543769
• Bhat, Prashant and Chow, Amy, et el. (2023) 3D genome organization around nuclear speckles drives mRNA splicing efficiency; 10.1101/2023.01.04.522632
• Mattick, John S. and Amaral, Paulo P., et el. (2023) Long non-coding RNAs: definitions, functions, challenges and recommendations; Nature Reviews Molecular Cell Biology; Vol. 24; No. 6; 430-447; PMCID PMC10213152; 10.1038/s41580-022-00566-8
• Goronzy, Isabel N. and Quinodoz, Sofia A., et el. (2022) Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription; Cell Reports; Vol. 41; No. 9; Art. No. 111730; PMCID PMC9793828; 10.1016/j.celrep.2022.111730
• Guo, Jimmy K. and Guttman, Mitchell (2022) Regulatory non-coding RNAs: everything is possible, but what is important?; Nature Methods; Vol. 19; No. 10; 1156-1159; 10.1038/s41592-022-01629-6
• Boninsegna, Lorenzo and Yildirim, Asli, et el. (2022) Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations; Nature Methods; Vol. 19; No. 8; 938-949; 10.1038/s41592-022-01527-x
• Quinodoz, Sofia A. and Guttman, Mitchell (2022) Essential Roles for RNA in Shaping Nuclear Organization; Cold Spring Harbor Perspectives in Biology; Vol. 14; No. 5; a039719; PMCID PMC9159268; 10.1101/cshperspect.a039719
• Jachowicz, Joanna W. and Strehle, Mackenzie, et el. (2022) Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome; Nature Structural and Molecular Biology; Vol. 29; No. 3; 239-249; PMCID PMC8969943; 10.1038/s41594-022-00739-1
• Guttman, Mitchell (2022) How non-coding RNAs shape nuclear structure to regulate gene expression; Biophysical Journal; Vol. 121; No. 3; 167a; 10.1016/j.bpj.2021.11.1898
• Arrastia, Mary V. and Jachowicz, Joanna W., et el. (2022) Single-cell measurement of higher-order 3D genome organization with scSPRITE; Nature Biotechnology; Vol. 40; No. 1; 64-73; 10.1038/s41587-021-00998-1
• Quinodoz, Sofia A. and Bhat, Prashant, et el. (2022) SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding; Nature Protocols; Vol. 17; No. 1; 36-75; 10.1038/s41596-021-00633-y
• Markaki, Yolanda and Chong, Johnny Gan, et el. (2021) Xist nucleates local protein gradients to propagate silencing across the X chromosome; Cell; Vol. 184; No. 25; 6174-6192; PMCID PMC8671326; 10.1016/j.cell.2021.10.022
• Quinodoz, Sofia A. and Jachowicz, Joanna W., et el. (2021) RNA promotes the formation of spatial compartments in the nucleus; Cell; Vol. 184; No. 23; 5775-5790; PMCID PMC9115877; 10.1016/j.cell.2021.10.014
• Bhat, Prashant and Honson, Drew, et el. (2021) Nuclear compartmentalization as a mechanism of quantitative control of gene expression; Nature Reviews. Molecular Cell Biology; Vol. 22; No. 10; 653-670; 10.1038/s41580-021-00387-1
• Takei, Yodai and Yun, Jina, et el. (2021) Integrated spatial genomics reveals global architecture of single nuclei; Nature; Vol. 590; No. 7845; 344-350; PMCID PMC7878433; 10.1038/s41586-020-03126-2
• Banerjee, Abhik K. and Blanco, Mario R., et el. (2020) SARS-CoV-2 disrupts splicing, translation, and protein trafficking to suppress host defenses; Cell; Vol. 183; No. 5; 1325-1339; PMCID PMC7543886; 10.1016/j.cell.2020.10.004
• Markaki, Yolanda and Chong, Johnny Gan, et el. (2020) Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome; 10.1101/2020.11.22.393546
• Pandya-Jones, Amy and Markaki, Yolanda, et el. (2020) A protein assembly mediates Xist localization and gene silencing; Nature; Vol. 587; No. 7832; 145-151; PMCID PMC7644664; 10.1038/s41586-020-2703-0
• Vangala, Pranitha and Murphy, Rachel, et el. (2020) High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection; Molecular Cell; Vol. 80; No. 2; 359-373; PMCID PMC7572724; 10.1016/j.molcel.2020.09.005
• Strehle, Mackenzie and Guttman, Mitchell (2020) Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation; Current Opinion in Cell Biology; Vol. 64; 139-147; 10.1016/j.ceb.2020.04.009
• McDonel, Patrick and Guttman, Mitchell (2019) Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression; Cold Spring Harbor Perspectives in Biology; Vol. 11; No. 12; Art. No. a032151; PMCID PMC6886450; 10.1101/cshperspect.a032151
• van Bemmel, Joke G. and Galupa, Rafael, et el. (2019) The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist; Nature Genetics; Vol. 51; No. 6; 1024-1034; PMCID PMC6551226; 10.1038/s41588-019-0412-0
• Cerase, Andrea and Armaos, Alexandros, et el. (2019) Phase separation drives X-chromosome inactivation: a hypothesis; Nature Structural & Molecular Biology; Vol. 26; No. 5; 331-334; 10.1038/s41594-019-0223-0
• Munschauer, Mathias and Nguyen, Celina T., et el. (2018) The NORAD lncRNA assembles a topoisomerase complex critical for genome stability; Nature; Vol. 561; No. 7721; 132-136; 10.1038/s41586-018-0453-z
• Quinodoz, Sofia A. and Ollikainen, Noah, et el. (2018) Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus; Cell; Vol. 174; No. 3; 744-757; PMCID PMC6548320; 10.1016/j.cell.2018.05.024
• McHugh, Colleen A. and Guttman, Mitchell (2017) RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells; ISBN 978-1-4939-7212-8; RNA Detection: Methods and Protocols; 473-488; 10.1007/978-1-4939-7213-5_31
• Dekker, Job and Belmont, Andrew S., et el. (2017) The 4D nucleome project; Nature; Vol. 549; No. 7671; 219-226; PMCID PMC5617335; 10.1038/nature23884
• Chen, Chun-Kan and Chow, Amy, et el. (2017) Response to Comment on "Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing"; Science; Vol. 356; No. 6343; Art. No. eaam5439; 10.1126/science.aam5439
• Guttman, Mitchell and Breuer, Manuel (2017) Cell scientist to watch – Mitchell Guttman; Journal of Cell Science; Vol. 130; No. 9; 1497-1499; 10.1242/jcs.203976
• Blanco, Mario R. and Guttman, Mitchell (2017) Re-evaluating the foundations of lncRNA–Polycomb function; EMBO Journal; Vol. 36; No. 8; 964-966; 10.15252/embj.201796796
• Szempruch, Anthony and Guttman, Mitchell (2017) Linking Protein and RNA Function within the Same Gene; Cell; Vol. 168; No. 5; 753-755; 10.1016/j.cell.2017.02.014
• Guttman, Mitchell (2017) How a lncRNA Shapes Chromatin Structure to Control Gene Expression; Biophysical Journal; Vol. 112; No. 3, Supp. 1; 158a; 10.1016/j.bpj.2016.11.868
• Cirillo, Davide and Blanco, Mario, et el. (2017) Quantitative predictions of protein interactions with long non-coding RNAs; Nature Methods; Vol. 14; No. 1; 5-6; 10.1038/nmeth.4100
• McHugh, C. A. and Guttman, M. (2016) Uncovering mechanisms of lncRNA function through comprehensive identification of direct lncRNA-interacting proteins; Molecular Biology of the Cell; Vol. 27; No. 25; M121; 10.1091/mbc.E16-10-0736
• Engreitz, Jesse M. and Ollikainen, Noah, et el. (2016) Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression; Nature Reviews. Molecular Cell Biology; Vol. 17; No. 12; 756-770; 10.1038/nrm.2016.126
• Engreitz, Jesse M. and Haines, Jenna E., et el. (2016) Local regulation of gene expression by lncRNA promoters, transcription, and splicing; Nature; Vol. 539; No. 7629; 452-455; PMCID PMC6853796; 10.1038/nature20149
• Chen, Chun-Kan and Blanco, Mario, et el. (2016) Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing; Science; Vol. 354; No. 6311; 468-472; 10.1126/science.aae0047
• Patil, Deepak P. and Chen, Chun-Kan, et el. (2016) m⁶A RNA methylation promotes XIST-mediated transcriptional repression; Nature; Vol. 537; No. 7620; 369-373; PMCID PMC5509218; 10.1038/nature19342
• Van Nostrand, Eric L. and Pratt, Gabriel A., et el. (2016) Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP); Nature Methods; Vol. 13; No. 6; 508-514; 10.1038/nmeth.3810
• Engreitz, Jesse M. and Haines, Jenna E., et el. (2016) Neighborhood regulation by lncRNA promoters, transcription, and splicing; 10.1101/050948
• Dekker, Job and Guttman, Mitchell, et el. (2016) A Guide to Packing Your DNA; Cell; Vol. 165; No. 2; 259-261; 10.1016/j.cell.2016.03.039
• Chen, Jenny and Shishkin, Alexander A., et el. (2016) Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs; Genome Biology; Vol. 17; Art. No. 19; PMCID PMC4739325; 10.1186/s13059-016-0880-9
• Paten, Benedict and Diekhans, Mark, et el. (2015) The NIH BD2K center for big data in translational genomics; Journal of the American Medical Informatics Association; Vol. 22; No. 6; 1143-1147; PMCID PMC5009913; 10.1093/jamia/ocv047
• McHugh, Colleen A. and Chen, Chun-Kan, et el. (2015) The Xist lncRNA interacts with SHARP to silence transcription through HDAC3; Nature; Vol. 521; No. 7551; 232-236; PMCID PMC4516396; 10.1038/nature14443
• Shishkin, Alexander A. and Giannoukos, Georgia, et el. (2015) Simultaneous generation of many RNA-seq libraries in a single reaction; Nature Methods; Vol. 12; No. 4; 323-325; PMCID PMC4712044; 10.1038/nmeth.3313
• Engreitz, Jesse and Lander, Eric S., et el. (2015) RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin; ISBN 978-1-4939-2252-9; Nuclear Bodies and Noncoding RNAs: Methods and Protocols; 183-197; 10.1007/978-1-4939-2253-6_11
• Quinodoz, Sofia and Guttman, Mitchell (2014) Long noncoding RNAs: an emerging link between gene regulation and nuclear organization; Trends in Cell Biology; Vol. 24; No. 11; 651-663; PMCID PMC4254690; 10.1016/j.tcb.2014.08.009
• Myskiw, Chad and Kadri, Sabah, et el. (2014) Analysis of long non-coding RNA expression and function in a mouse model of glioblastoma; Cancer Research; Vol. 74; No. 19 Suppleme; Art. No. 524; 10.1158/1538-7445.AM2014-524
• Ach, Robert A. and Tsang, Peter, et el. (2014) Use of complex oligonucleotide libraries for concurrent high-resolution fluorescence imaging of both DNA and RNA in various sample types; Cancer Research; Vol. 74; No. 19 Suppleme; Art. No. 1513; 10.1158/1538-7445.AM2014-1513
• Engreitz, Jesse M. and Sirokman, Klara, et el. (2014) RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites; Cell; Vol. 159; No. 1; 188-199; PMCID PMC4177037; 10.1016/j.cell.2014.08.018
• Schwartz, Schraga and Bernstein, Douglas A., et el. (2014) Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA; Cell; Vol. 159; No. 1; 148-162; PMCID PMC4180118; 10.1016/j.cell.2014.08.028
• Rinn, John and Guttman, Mitchell (2014) RNA and dynamic nuclear organization; Science; Vol. 345; No. 6202; 1240-1241; PMCID PMC4186717; 10.1126/science.1252966
• Hacisuleyman, Ezgi and Goff, Loyal A., et el. (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre; Nature Structural & Molecular Biology; Vol. 21; No. 2; 198-206; PMCID PMC3950333; 10.1038/nsmb.2764
• McHugh, Colleen A. and Russell, Pamela, et el. (2014) Methods for comprehensive experimental identification of RNA-protein interactions; Genome Biology; Vol. 15; No. 1; Art. No. 203; PMCID PMC4054858; 10.1186/gb4152
• Engreitz, Jesse M. and Pandya-Jones, Amy, et el. (2013) The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome; Science; Vol. 341; No. 6147; Art. No. 1237973; PMCID PMC3778663; 10.1126/science.1237973
• Guttman, Mitchell and Russell, Pamela, et el. (2013) Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins; Cell; Vol. 154; No. 1; 240-251; PMCID PMC3756563; 10.1016/j.cell.2013.06.009
• Gifford, Casey A. and Ziller, Michael J., et el. (2013) Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells; Cell; Vol. 153; No. 5; 1149-1163; PMCID PMC3709577; 10.1016/j.cell.2013.04.037
• Kirby, Andrew and Guttman, Mitchell (2013) Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing; Nature Genetics; Vol. 45; No. 3; 299-303; PMCID PMC3901305; 10.1038/ng.2543
• Garber, Manuel and Guttman, Mitchell (2012) A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals; Molecular Cell; Vol. 47; No. 5; 810-822; PMCID PMC3873101; 10.1016/j.molcel.2012.07.030
• Guttman, Mitchell and Rinn, John L. (2012) Modular regulatory principles of large non-coding RNAs; Nature; Vol. 482; No. 7385; 339-346; PMCID PMC4197003; 10.1038/nature10887
• Lindblad-Toh, Kerstin and Guttman, Mitchell (2011) A high-resolution map of human evolutionary constraint using 29 mammals; Nature; Vol. 478; No. 7370; 476-482; PMCID PMC3207357; 10.1038/nature10530
• Guttman, Mitchell and Donaghey, Julie, et el. (2011) lincRNAs act in the circuitry controlling pluripotency and differentiation; Nature; Vol. 477; No. 7364; 295-300; PMCID PMC3175327; 10.1038/nature10398
• Garber, Manuel and Grabherr, Manfred G., et el. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq; Nature Methods; Vol. 8; No. 6; 469-477; 10.1038/NMETH.1613
• Robinson, James T. and Thorvaldsdóttir, Helga, et el. (2011) Integrative genomics viewer; Nature Biotechnology; Vol. 29; No. 1; 24-26; PMCID PMC3346182; 10.1038/nbt.1754
• Loewer, Sabine and Cabili, Moran N., et el. (2010) Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells; Nature Genetics; Vol. 42; No. 12; 1113-1117; PMCID PMC3040650; 10.1038/ng.710
• Huarte, Maite and Guttman, Mitchell, et el. (2010) A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response; Cell; Vol. 142; No. 3; 409-419; PMCID PMC2956184; 10.1016/j.cell.2010.06.040
• Guttman, Mitchell and Garber, Manuel, et el. (2010) Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs; Nature Biotechnology; Vol. 28; No. 5; 503-510; PMCID PMC2868100; 10.1038/nbt.1633
• Ozsolak, Fatih and Goren, Alon, et el. (2010) Digital transcriptome profiling from attomole-level RNA samples; Genome Research; Vol. 20; No. 4; 519-525; PMCID PMC2847755; 10.1101/gr.102129.109
• Amit, Ido and Garber, Manuel, et el. (2009) Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses; Science; Vol. 326; No. 5950; 257-263; PMCID PMC2879337; 10.1126/science.1179050
• Khalil, Ahmad M. and Guttman, Mitchell, et el. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression; Proceedings of the National Academy of Sciences of the United States of America; Vol. 106; No. 28; 11667-11672; PMCID PMC2704857; 10.1073/pnas.0904715106
• Garber, Manuel and Guttman, Mitchell, et el. (2009) Identifying novel constrained elements by exploiting biased substitution patterns; Bioinformatics; Vol. 25; No. 12; i54-i62; PMCID PMC2687944; 10.1093/bioinformatics/btp190
• Guttman, Mitchell and Amit, Ido, et el. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals; Nature; Vol. 458; No. 7235; 223-227; PMCID PMC2754849; 10.1038/nature07672
• Guttman, Mitchell and Mies, Carolyn, et el. (2007) Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays; PLoS Genetics; Vol. 3; No. 8; Art. No. e143; PMCID PMC1950957; 10.1371/journal.pgen.0030143
• Nagi, Chandandeep and Guttman, Mitchell, et el. (2005) N-cadherin Expression in Breast Cancer: Correlation with an Aggressive Histologic Variant – Invasive Micropapillary Carcinoma; Breast Cancer Research and Treatment; Vol. 94; No. 3; 225-235; 10.1007/s10549-005-7727-5
• Suyama, Kimita and Shapiro, Irina, et el. (2002) A signaling pathway leading to metastasis is controlled by N-cadherin and the FGF receptor; Cancer Cell; Vol. 2; No. 4; 301-314; 10.1016/S1535-6108(02)00150-2