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Literature DB >> 26272294

Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape.

Deborah R Winter¹, Steffen Jung¹, Ido Amit¹.

Abstract

Recent technological advances have enabled researchers to accurately and efficiently assay the chromatin dynamics of scarce cell populations. In this Opinion article, we advocate the application of these technologies to central questions in immunology. Unlike changes to other molecular structures in the cell, chromatin features can reveal the past (developmental history), present (current activity) and future (potential response to challenges) of a given immune cell type; chromatin profiling is therefore an important new tool for studying the immune-regulatory networks of health and disease.

Mesh：

Substances：
Chromatin

Year: 2015 PMID： 26272294 DOI： 10.1038/nri3884

Source DB: PubMed Journal: Nat Rev Immunol ISSN： 1474-1733 Impact factor: 53.106

77 in total

1. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Authors: Alan P Boyle; Lingyun Song; Bum-Kyu Lee; Darin London; Damian Keefe; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Terrence S Furey
Journal: Genome Res Date: 2010-11-24 Impact factor: 9.043

2. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors: Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal: Nat Genet Date: 2007-02-04 Impact factor: 38.330

Review 3. Nuclease hypersensitive sites in chromatin.

Authors: D S Gross; W T Garrard
Journal: Annu Rev Biochem Date: 1988 Impact factor: 23.643

4. Latent enhancers activated by stimulation in differentiated cells.

Authors: Renato Ostuni; Viviana Piccolo; Iros Barozzi; Sara Polletti; Alberto Termanini; Silvia Bonifacio; Alessia Curina; Elena Prosperini; Serena Ghisletti; Gioacchino Natoli
Journal: Cell Date: 2013-01-17 Impact factor: 41.582

5. Variation in the human immune system is largely driven by non-heritable influences.

Authors: Petter Brodin; Vladimir Jojic; Tianxiang Gao; Sanchita Bhattacharya; Cesar J Lopez Angel; David Furman; Shai Shen-Orr; Cornelia L Dekker; Gary E Swan; Atul J Butte; Holden T Maecker; Mark M Davis
Journal: Cell Date: 2015-01-15 Impact factor: 41.582

6. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors: Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal: Cell Date: 2014-12-11 Impact factor: 41.582

7. Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

Authors: Hong Ji; Lauren I R Ehrlich; Jun Seita; Peter Murakami; Akiko Doi; Paul Lindau; Hwajin Lee; Martin J Aryee; Rafael A Irizarry; Kitai Kim; Derrick J Rossi; Matthew A Inlay; Thomas Serwold; Holger Karsunky; Lena Ho; George Q Daley; Irving L Weissman; Andrew P Feinberg
Journal: Nature Date: 2010-08-15 Impact factor: 49.962

8. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.

Authors: Kairong Cui; Chongzhi Zang; Tae-Young Roh; Dustin E Schones; Richard W Childs; Weiqun Peng; Keji Zhao
Journal: Cell Stem Cell Date: 2009-01-09 Impact factor: 24.633

9. Genome-wide mapping of in vivo protein-DNA interactions.

Authors: David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal: Science Date: 2007-05-31 Impact factor: 47.728

10. BLUEPRINT to decode the epigenetic signature written in blood.

Authors: David Adams; Lucia Altucci; Stylianos E Antonarakis; Juan Ballesteros; Stephan Beck; Adrian Bird; Christoph Bock; Bernhard Boehm; Elias Campo; Andrea Caricasole; Fredrik Dahl; Emmanouil T Dermitzakis; Tariq Enver; Manel Esteller; Xavier Estivill; Anne Ferguson-Smith; Jude Fitzgibbon; Paul Flicek; Claudia Giehl; Thomas Graf; Frank Grosveld; Roderic Guigo; Ivo Gut; Kristian Helin; Jonas Jarvius; Ralf Küppers; Hans Lehrach; Thomas Lengauer; Åke Lernmark; David Leslie; Markus Loeffler; Elizabeth Macintyre; Antonello Mai; Joost H A Martens; Saverio Minucci; Willem H Ouwehand; Pier Giuseppe Pelicci; Hèléne Pendeville; Bo Porse; Vardhman Rakyan; Wolf Reik; Martin Schrappe; Dirk Schübeler; Martin Seifert; Reiner Siebert; David Simmons; Nicole Soranzo; Salvatore Spicuglia; Michael Stratton; Hendrik G Stunnenberg; Amos Tanay; David Torrents; Alfonso Valencia; Edo Vellenga; Martin Vingron; Jörn Walter; Spike Willcocks
Journal: Nat Biotechnol Date: 2012-03-07 Impact factor: 54.908

12 in total

Review 1. Genome-Wide Approaches to Defining Macrophage Identity and Function.

Authors: Gregory J Fonseca; Jason S Seidman; Christopher K Glass
Journal: Microbiol Spectr Date: 2016-10

2. A Beginner's Guide to Analysis of RNA Sequencing Data.

Authors: Clarissa M Koch; Stephen F Chiu; Mahzad Akbarpour; Ankit Bharat; Karen M Ridge; Elizabeth T Bartom; Deborah R Winter
Journal: Am J Respir Cell Mol Biol Date: 2018-08 Impact factor: 6.914

3. Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses.

Authors: Rosanne C van Deuren; Peer Arts; Giulio Cavalli; Martin Jaeger; Marloes Steehouwer; Maartje van de Vorst; Christian Gilissen; Leo A B Joosten; Charles A Dinarello; Musa M Mhlanga; Vinod Kumar; Mihai G Netea; Frank L van de Veerdonk; Alexander Hoischen
Journal: Genome Med Date: 2021-05-25 Impact factor: 15.266

Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape.

1. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

2. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Review 3. Nuclease hypersensitive sites in chromatin.

4. Latent enhancers activated by stimulation in differentiated cells.

5. Variation in the human immune system is largely driven by non-heritable influences.

6. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

7. Comprehensive methylome map of lineage commitment from haematopoietic progenitors.

8. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation.

9. Genome-wide mapping of in vivo protein-DNA interactions.

10. BLUEPRINT to decode the epigenetic signature written in blood.

Review 1. Genome-Wide Approaches to Defining Macrophage Identity and Function.

2. A Beginner's Guide to Analysis of RNA Sequencing Data.

3. Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses.

Review 4. Big Data Offers Novel Insights for Oncolytic Virus Immunotherapy.

Review 5. Insights into the pathogenesis of Langerhans cell histiocytosis: the development of targeted therapies.

6. Rapid Recall Ability of Memory T cells is Encoded in their Epigenome.

7. Chromatin landscapes and genetic risk for juvenile idiopathic arthritis.

8. Epigenetic landscapes reveal transcription factors that regulate CD8⁺ T cell differentiation.

Review 9. Thinking BIG rheumatology: how to make functional genomics data work for you.

Review 10. Mathematical Models for Immunology: Current State of the Art and Future Research Directions.