Publications

Preprints

Xist spatially amplifies SHARP recruitment to balance chromosome-wide silencing and specificity to the X chromosome

bioRxiv

Joanna W. Jachowicz*, Mackenzie Strehle*, Abhik K. Banerjee, Mario R. Blanco, Jasmine Thai, and Mitchell Guttman

2022

SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding

Nature Protocols

Sofia A. Quinodoz, Prashant Bhat, Peter Chovanec, Joanna W. Jachowicz, Noah Ollikainen, Elizabeth Detmar, Elizabeth Soehalim, and Mitchell Guttman

2021

RNA promotes the formation of spatial compartments in the nucleus

Cell

Sofia A. Quinodoz, Joanna W. Jachowicz*, Prashant Bhat*, Noah Ollikainen*, Abhik K. Banerjee**, Isabel N. Goronzy**, Mario R. Blanco, Peter Chovanec, Amy Chow, Yolanda Markaki, Jasmine Thai, Kathrin Plath, and Mitchell Guttman

Single-cell measurement of higher-order 3D genome organization with scSPRITE

Nature Biotechnology

Mary V. Arrastia, Joanna W. Jachowicz, Noah Ollikainen, Matthew S. Curtis, Charlotte Lai, Sofia A. Quinodoz, David A. Selck, Rustem F. Ismagilov & Mitchell Guttman (2021).

Essential Roles for RNA in Shaping Nuclear Organization

The Nucleus (2nd edition)

Sofia A. Quinodoz & Mitchell Guttman (2021).

Nuclear compartmentalization as a mechanism of quantitative control of gene expression

Nature Reviews Molecular Cell Biology

Prashant Bhat, Drew Honson, and Mitchell Guttman (2021).

Global architecture of the nucleus in single cells by DNA seqFISH+ and multiplexed immunofluorescence

Nature

Takei Y, Ollikainen N, Zheng S, Pierson N, White J, Shah S, Thoimassie J, Eng L, Guttman M, Yuan GC, Cai, L (2021).

2020

SARS-CoV-2 suppresses mRNA splicing, translation, and protein trafficking in a multipronged mechanism to evade host defenses

Cell

Banerjee AK, Blanco MR, Bruce EA, Honson DD, Chen L, Chow A, Bhat P, Ollikainen N, Quinodoz SA, Loney C, Thai J, Miller ZD, Lin AE, Schmidt MM, Stewart DG, Goldfarb D, De Lorenzo G, Rihn SJ, Voorhees R, Botten JW, Majumdar D, and Guttman M (2020)

High-resolution mapping of multiway enhancer promoter interactions regulating pathogen detection

Molecular Cell

Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel PE, Guttman M, Garber M (2020).

An Xist-dependent protein assembly mediates Xist localization and gene silencing

Nature

Pandya-Jones A, Markaki Y, Serizay J, Chitiashvilli T, Mancia W, Damianov A, Chronis C, Papp B, Chen CK, McKee R, Wang XJ, Chau A, Leonhardt H, Zheng S, Guttman M, Black DL, Plath K (2020).

Xist drives spatial compartmentalization of DNA and protein to orchestrate initiation and maintenance of X inactivation

Current Opinions in Cell Biology

Strehle M and Guttman M (2020).

2019

Phase separation drives X-chromosome inactivation: a hypothesis

Nature Structural and Molecular Biology

Cerase A, Armaos A, Neumayer C, Avner P, Guttman M, Tartaglia GG

Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression

RNA Worlds: New Tools for Deep Exploration edited by Thomas R. Cech, Joan A. Steitz, and John F. Atkins

Patrick McDonel and Mitchell Guttman (2019)

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

Nature Genetics

van Bemmel JG, Galupa R, Gard C, Servant N, Picard C, Davies J, Szempruch AJ, Zhan Y, Żylicz JJ, Nora EP, Lameiras S, de Wit E, Gentien D, Baulande S, Giorgetti L, Guttman M, Hughes JR, Higgs DR, Gribnau J, Heard E (2019)

2018

Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

Cell

Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai M, Shishkin A, Bhat P, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, McDonel P, Garber M, and Guttman M (2018).

Featured in:  Nature Methods | Epigenie

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Nature

Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, Schenone M, Guttman M, Carr SA, Lander ES (2018).

2017

The 4D nucleome project

Nature

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O’Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S (2017).

RAP-MS: A Method to Identify Proteins that Interact Directly with a Specific RNA Molecule in Cells

Methods Molecular Biology

McHugh CA and Guttman M (2017).

Re-evaluating the foundations of lncRNA-Polycomb function

EMBO Journal

Blanco MR and Guttman M (2017)

Linking Protein and RNA Function within the same gene

Cell

Szempruch A and Guttman M (2017).

2016

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

Science

Chen CK, Blanco M, Jackson C, Aznauryan E, Ollikainen N, Surka C., Chow A, Cerase A, McDonel PE, Guttman M (2016).

Featured in: Caltech

Long non-coding RNAs (lncRNAs) as spatial amplifiers that control nuclear architecture and gene expression

Nature Reviews Molecular Cell Biology

Engreitz JM, Ollikainen N, Guttman M (2016).

Quantitative predictions of protein interactions with long non-coding RNAs

Nature Methods

Cirillo D, Blanco MR, Armaos A, Buness A, Avner P, Guttman M, Cerase A, Tartaglia GG (2016).

Local regulation of gene expression by lncRNA promoters, transcription, and splicing

Nature

Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES (2016).

m6A RNA methylation promotes XIST-mediated transcriptional repression

Nature

Patil DP, Chen CK, Pickering BF, Chow A, Jackson C, Guttman M, Jaffrey SR (2016).

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites

Nature Methods

Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang M, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW (2016).

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Genome Biology

Chen J, Shishkin AA, Zhu X, Kadri S, Maza I, Guttman M, Hanna JH, Regev A, Garber M (2016).

2015

The Xist lncRNA directly interacts with SHARP to silence transcription through HDAC3

Nature

McHugh CA, Chen CK, Chow A, Surka CF, Tran C, McDonel P, Pandya-Jones A, Blanco MR, Burghard C, Moradian A, Sweredoski MJ, Shishkin AA, Su J, Lander ES, Hess S, Plath K, and Guttman M (2015).

Simultaneous generation of large numbers of strand-specific RNA-Seq cDNA libraries in a single reaction

Nature Methods

Shishkin AA, Giannoukos G, Kucukural A, Ciulla D, Busby M, Surka CF, Chen J, Bhattacharyya RP, Rudy RF, Patel MM, Novod N, Hung DT, Gnirke A, Garber M, Guttman M*, Jonathan Livny (2015).

Featured in:  Nature Methods

RNA Antisense Purification (RAP) for mapping RNA interactions with chromatin

Methods in Molecular Biology

Engreitz JM, Lander ES, and Guttman M (2015).

The NIH BD2K center for big data in translational genomics

J Am Med Inform Assoc.

Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van’t Veer L, Wold B, Haussler D (2015).

2014

RNA and the dynamics of nuclear organization

Science

Rinn JL and Guttman M (2014).

Long non-coding RNAs: An emerging link between gene regulation and nuclear organization

Trends in Cell Biology

Quinodoz S and Guttman M (2014).

RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites

Cell

Engreitz JM, Sirokman K, McDonel P, Shishkin A, Surka CF, Russell P, Grossman SR, Chow AY, Guttman M, Lander ES (2014).

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

Cell

Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A (2014).

Methods for comprehensive experimental identification of RNA–protein interactions

Genome Biology

McHugh CA, Russell P, and Guttman M (2014).

Topological Organization of Multi-chromosomal Regions by Firre

Nature Structural & Molecular Biology

Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz JM, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, and Rinn JL (2014).

2013

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X-chromosome

Science

Engreitz JM, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, and Guttman M. (2013). 

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

Cell

Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. (2013).

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Cell

Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek A, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn JL, Gnirke A, Lander ES, Bernestin BE, Meissner A. (2013).

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Nature Genetics

Kirby A, Gnirke A, Jaffe DB, Baresova V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hulkova H, Sovova J, Vyletal P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollack MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ. (2013). 

2012

Modular Regulatory Principles of Large Non-coding RNAs

Nature

Guttman M and Rinn JL. (2012).

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

Molecular Cell

Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. (2012)

2011

lincRNAs Act in the Circuitry Controlling Pluripotency and Differentiation

Nature

Guttman M, Donaghey J, Carey BW, Garber M, Grenier J, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. (2011).

Evolutionary Constraint in the Human Genome Based on 29 Eutherian Mammals

Nature

Lindblad-Toh K, Garber M, Or Zuk, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alfoldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney NJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. (2011).

Computational Methods for Transcriptome Annotation and Quantification using RNA-Seq

Nature Methods

Garber M, Grabherr MG, Guttman M, Trapnell C. (2011).

2010

Ab initio Reconstruction of Transcriptomes of Pluripotent and Lineage Committed Cells Reveals Gene Structures of Thousands of lincRNAs

Nature Biotechnology

Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A. (2010)

A Large intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Transcriptional Response

Cell

Huarte M, Guttman M, Feldser D, Garber M, Koziol M, Broz D, Khalil AM, Zuk O, Amit I, Rabani M, Attardi L, Regev A, Lander ES, Jacks T, Rinn JL. (2010)

Integrative Genomics Viewer

Nature Biotechnology

Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. (2010).

Large Intergenic Non-coding RNA-RoR Modulates Reprogramming of Human Induced Pluripotent Stem Cells

Nature Genetics

Loewer S, Cabili MN, Guttman M, Loh YH, Thomas K, Park IH, Garber M, Curran M, Onder T, Agarwal S, Manos PD, Datta S, Lander ES, Schlaeger TM, Daley GQ, Rinn JL. (2010).

Digital Transcriptome Profiling from Attomole-level RNA Samples

Genome Research

Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. (2010)

2009

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

Nature

Guttman M, Amit I, Garber M, French C, Lin M, Feldser D, Huarte M, Cabili M, Carey BW, Cassady J, Jaenisch R, Mikkelsen T, Jacks T, Hacohen N, Bernstein BEB, Kellis M, Regev A, Rinn JL, Lander ES. (2009)

Many Human Large Intergenic Noncoding RNAs Associate with Chromatin-Modifying Complexes and Affect Gene Expression

Proceedings of the National Academies of Science

Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. (2009)

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

Science

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. (2009)

Identifying Novel Constrained Elements by Exploiting Biased Substitution Patterns

Bioinformatics

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. (2009).

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