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Epigenetic marks: from code to mechanisms

Epigenetic marks: from code to mechanisms Frontiers in Life Science, 2013 Vol. 7, Nos. 1–2, 1, http://dx.doi.org/10.1080/21553769.2013.854471 EDITORIAL It is now well-acknowledged that the structure and dynam- for a focused exchange on the current developments in ics of chromatin play a critical role in the regulation of all the epigenetic field. Thirteen speakers with backgrounds processes DNA undergoes, including replication, transcrip- in molecular and structural biology, biophysics, bioinfor- tion, recombination and repair. To understand how these matics and theoretical physics addressed this topic, giving reactions take place, one needs to integrate many regu- ample proof of the high activity the field currently sees. latory mechanisms at various time and space scales and About 120 participants subscribed to the meeting, show- decipher the complex interplay between numerous acting ing the vast interest of the scientific community into the factors. Through its local and dynamical physicochemi- challenging and interdisciplinary issues of epigenetics and cal heterogeneities, chromatin adds a layer of information, the control of gene expression. This occasion allowed us to commonly referred to as ‘epigenetic’. By creating microen- invite the guest speakers to contribute to this special issue vironments that promote or prevent the reading of genomic which consist in seven original papers (primary researches, sequence information, epigenetic factors actively partici- reviews and perspectives) each of which covers a dif- pate in the regulation of all biological processes involving ferent approach aimed at deciphering the still puzzling DNA. signification of the so-called ‘epigenetic marks’. Deciphering the epigenetic code is thus one of the most In the first paper, Bryan Turner sets the tone in his Per- exciting challenges currently faced by biologists. Among spective ‘Lamarck and the nucleosome’, where he puts the difficulties surrounding this tremendous task is the fact that, modern views on epigenetics in their historical context. contrary to genetic information, epigenetic information is The issue further contains review articles by Christophe highly dynamic (say, on a cellular life time scale), mak- Thiriet, Fred van Leeuwen and Ho-Ryun Chung and their ing ‘chromatin sequence’ much more difficult to grasp than collaborators, notably addressing recent findings in high- DNA sequence. However, recent progresses in microarrays throughput analyses of histone modification patterns. These and deep sequencing techniques have enabled first epige- are complemented by primary research papers by Alain nomic landscapes to emerge, with genome-scale profiling of Arneodo, François Roudier and Jörg Galle and their respec- transcription factor binding, nucleosome occupancy, chro- tive collaborators which address experimental and theoreti- matin remodelling targets, histone variants replacement cal approaches under development to decode the regulatory patterns and histone modifications distributions. As data meaning of epigenetic marks. accumulate at ever-growing speed, specific tools definitely We hope that this collection will both provide the need to be developed to analyse this huge amount of epi- uninitiated with an entry point to a highly dynamic but genetic information in an attempt to begin to break the complex field and the expert with an opportunity to have a ‘chromatin code’. At the same time, our understanding of fresh look at the viewpoints advocated by the researchers the mechanistic consequences of the various epigenetics from the different disciplines that have contributed. We profiles observed is still very poor. are both convinced that cracking the ‘chromatin code(s)’ This major biological problem provides a great com- will be considered in the future as a prime example of an mon playground for biologists, physicists, mathemati- interdisciplinary effort on an important biological problem. cians and bioinformaticians. While some researchers mainly focus on the mechanistic aspects of chro- Christophe Lavelle matin structure and dynamics, others address the National Museum of Natural History and genome-wide and ‘systemic’ aspects of gene regulation Nuclear Architecture and Dynamics and cell development. The special issue proposed here arises from a workshop we recently organized Ralf Blossey (http://www.iri.cnrs.fr/doc/chromatin_days_2012) which Nuclear Architecture and Dynamics and brought together a select group of international experts Interdisciplinary Research Institute © 2013 Taylor & Francis http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Frontiers in Life Science Taylor & Francis

Epigenetic marks: from code to mechanisms

Lavelle, Christophe; Blossey, Ralf
Frontiers in Life Science , Volume 7 (1-2): 1 – Jun 1, 2013
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Epigenetic marks: from code to mechanisms

Abstract

Frontiers in Life Science, 2013 Vol. 7, Nos. 1–2, 1, http://dx.doi.org/10.1080/21553769.2013.854471 EDITORIAL It is now well-acknowledged that the structure and dynam- for a focused exchange on the current developments in ics of chromatin play a critical role in the regulation of all the epigenetic field. Thirteen speakers with backgrounds processes DNA undergoes, including replication, transcrip- in molecular and structural biology, biophysics, bioinfor- tion, recombination and...
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Taylor & Francis
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© 2013 Taylor & Francis
ISSN
2689-5307
eISSN
2689-5293
DOI
10.1080/21553769.2013.854471
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Abstract

Frontiers in Life Science, 2013 Vol. 7, Nos. 1–2, 1, http://dx.doi.org/10.1080/21553769.2013.854471 EDITORIAL It is now well-acknowledged that the structure and dynam- for a focused exchange on the current developments in ics of chromatin play a critical role in the regulation of all the epigenetic field. Thirteen speakers with backgrounds processes DNA undergoes, including replication, transcrip- in molecular and structural biology, biophysics, bioinfor- tion, recombination and repair. To understand how these matics and theoretical physics addressed this topic, giving reactions take place, one needs to integrate many regu- ample proof of the high activity the field currently sees. latory mechanisms at various time and space scales and About 120 participants subscribed to the meeting, show- decipher the complex interplay between numerous acting ing the vast interest of the scientific community into the factors. Through its local and dynamical physicochemi- challenging and interdisciplinary issues of epigenetics and cal heterogeneities, chromatin adds a layer of information, the control of gene expression. This occasion allowed us to commonly referred to as ‘epigenetic’. By creating microen- invite the guest speakers to contribute to this special issue vironments that promote or prevent the reading of genomic which consist in seven original papers (primary researches, sequence information, epigenetic factors actively partici- reviews and perspectives) each of which covers a dif- pate in the regulation of all biological processes involving ferent approach aimed at deciphering the still puzzling DNA. signification of the so-called ‘epigenetic marks’. Deciphering the epigenetic code is thus one of the most In the first paper, Bryan Turner sets the tone in his Per- exciting challenges currently faced by biologists. Among spective ‘Lamarck and the nucleosome’, where he puts the difficulties surrounding this tremendous task is the fact that, modern views on epigenetics in their historical context. contrary to genetic information, epigenetic information is The issue further contains review articles by Christophe highly dynamic (say, on a cellular life time scale), mak- Thiriet, Fred van Leeuwen and Ho-Ryun Chung and their ing ‘chromatin sequence’ much more difficult to grasp than collaborators, notably addressing recent findings in high- DNA sequence. However, recent progresses in microarrays throughput analyses of histone modification patterns. These and deep sequencing techniques have enabled first epige- are complemented by primary research papers by Alain nomic landscapes to emerge, with genome-scale profiling of Arneodo, François Roudier and Jörg Galle and their respec- transcription factor binding, nucleosome occupancy, chro- tive collaborators which address experimental and theoreti- matin remodelling targets, histone variants replacement cal approaches under development to decode the regulatory patterns and histone modifications distributions. As data meaning of epigenetic marks. accumulate at ever-growing speed, specific tools definitely We hope that this collection will both provide the need to be developed to analyse this huge amount of epi- uninitiated with an entry point to a highly dynamic but genetic information in an attempt to begin to break the complex field and the expert with an opportunity to have a ‘chromatin code’. At the same time, our understanding of fresh look at the viewpoints advocated by the researchers the mechanistic consequences of the various epigenetics from the different disciplines that have contributed. We profiles observed is still very poor. are both convinced that cracking the ‘chromatin code(s)’ This major biological problem provides a great com- will be considered in the future as a prime example of an mon playground for biologists, physicists, mathemati- interdisciplinary effort on an important biological problem. cians and bioinformaticians. While some researchers mainly focus on the mechanistic aspects of chro- Christophe Lavelle matin structure and dynamics, others address the National Museum of Natural History and genome-wide and ‘systemic’ aspects of gene regulation Nuclear Architecture and Dynamics and cell development. The special issue proposed here arises from a workshop we recently organized Ralf Blossey (http://www.iri.cnrs.fr/doc/chromatin_days_2012) which Nuclear Architecture and Dynamics and brought together a select group of international experts Interdisciplinary Research Institute © 2013 Taylor & Francis

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Frontiers in Life Science – Taylor & Francis

Published: Jun 1, 2013

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