BioEssays

Cover image for Vol. 39 Issue 3

Edited By: Andrew Moore

Online ISSN: 1521-1878

Genome architecture and evolution


Genome architecture and evolution

Genome architecture describes the spatial arrangement of the functional and regulatory elements of a genome. This arrangement has an influence on gene expression and alterations may lead to disease. Below we have assembled our most recent content in this fascinating area. We will regularly update this special collection and wish you enjoyable reading.



Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome

Sequence-specific targeting of chromatin remodelers organizes precisely positioned nucleosomes throughout the genome

Gregory D. Bowman*, Jeffrey N. McKnight*

Nucleosomes exist at well-defined positions that are both reproducibly inherited after genome-disrupting events and predictably altered for transcriptional response to changing conditions. We postulate that nucleosome positioning fidelity and plasticity can be encoded in the DNA sequence and achieved by global cooperation of sequence-specific transcription factors with ATP-dependent chromatin remodelers.

BioEssays 2017, 39, No. 1, 0–0 [Insights & Perspectives]


Cajal body function in genome organization and transcriptome diversity

Cajal body function in genome organization and transcriptome diversity

Iain A. Sawyer, David Sturgill, Myong-Hee Sung, Gordon L. Hager*, Miroslav Dundr*

Nuclear architecture is largely non-random and is the product of many synergistic influences. Here, we propose that Cajal bodies contribute to the 3D structural organization of the nucleus by physically clustering target snRNA genes. In turn, this regulates spliceosomal component levels and shapes the transcriptome by regulating RNA splicing fidelity.

BioEssays 2016, 38, No. 12, 1197–1208 [Insights & Perspectives]


Shaping mitotic chromosomes: From classical concepts to molecular mechanisms

Shaping mitotic chromosomes: From classical concepts to molecular mechanisms

Marc Kschonsak, Christian H. Haering*

The structural rearrangements of chromatin fibers during mitotic chromosome condensation have remained one of the greatest outstanding mysteries of modern biology. Based on recent insights into the architecture and biophysical properties of mitotic chromosomes, we discuss how the actions of key molecular machines, including condensin I and II, topoisomerase II and cohesin, result in the formation of compact cylindrical chromosomes.

BioEssays 2015, 37, No. 7, 755–766 [Prospects & Overviews]


An Integrative Breakage Model of genome architecture, reshuffling and evolution

An Integrative Breakage Model of genome architecture, reshuffling and evolution

Marta Farré, Terence J. Robinson, Aurora Ruiz-Herrera*

Our understanding of genome reorganization and how these structural changes contribute to the speciation process and genetic disease is far from complete. In this report we propose a new multidisciplinary Integrative Breakage Model of genome evolution that is based on the high-level structural organization of genome (nucleome) and highlight the functional constrains that lead to genome reshuffling.

BioEssays 2015, 37, No. 5, 479–488 [Insights & Perspectives]


Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model

Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model

Robin Andersson*

Profiling of enhancer RNAs (eRNAs) likely represents a paradigm shift in enhancer genomics, yielding high specificity in the localization of active enhancers. The similarities between enhancers and promoters are discussed and their established distinctions are deconstructed. Based on this, a unified model of regulatory elements in transcriptional regulation is presented.

BioEssays 2015, 37, No. 3, 314–323 [Prospects & Overviews]


The shades of gray of the chromatin fiber

The shades of gray of the chromatin fiber

Juan Ausió*

The chromatin fiber consists of a string of nucleosomes connected by linker DNA regions. Over the years, its structure has long been controversial. Two recent papers provide key insights into the folding constraints and histone participation and to a more realistic view of its heterogeneous and dynamic organization.

BioEssays 2015, 37, No. 1, 46–51 [Prospects & Overviews]


Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction

Horizontal transfer of short and degraded DNA has evolutionary implications for microbes and eukaryotic sexual reproduction

Søren Overballe-Petersen, Eske Willerslev*

Natural transformation of short and damaged DNA changes our conception of evolution by allowing for recycling of genetic traits across time – a phenomenon we call anachronistic evolution. It may even have played a role in evolution of early life and eukaryotic sexual reproduction.

BioEssays 2014, 36, No. 10, 1005–1010 [Prospects & Overviews]


Making connections: Insulators organize eukaryotic chromosomes into independent cis-regulatory networks

Making connections: Insulators organize eukaryotic chromosomes into independent cis‐regulatory networks

Darya Chetverina, Tsutomu Aoki, Maksim Erokhin, Pavel Georgiev, Paul Schedl*

New insights into the properties and activities of insulators, together with the discovery that they are subject to stage and/or tissue specific regulation, requires us to rethink how they establish the domain/sub-domain organization of eukaryotic chromosomes and how they function to define and re-define gene regulatory networks during development.

BioEssays 2014, 36, No. 2, 163–172 [Prospects & Overviews]


Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution

Gerald Schönknecht*, Andreas P. M. Weber, Martin J. Lercher

Horizontal gene transfer is common among different species of bacteria and archaea, which often adapt through acquisition of new genes. Based on recent phylogenomic analyses, eukaryotic genomes have acquired numerous genes as well, and horizontal gene transfer may have contributed more to eukaryotic evolution than previously assumed.

BioEssays 2014, 36, No. 1, 9–20 [Insights & Perspectives]


Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

Elphège P. Nora*, Job Dekker, Edith Heard

It has been recently shown that chromosomes are segmented in a series of discrete Topologically Associating Domains, or TADs, which in mammals have an average size of 1 Megabase. Here we discuss how such an arrangement may provide a basis for domain-wide control of chromatin structure and transcriptional regulation.

BioEssays 2013, 35, No. 9, 818–828 [Prospects & Overviews]


Structural variations, the regulatory landscape of the genome and their alteration in human disease

Structural variations, the regulatory landscape of the genome and their alteration in human disease

Malte Spielmann, Stefan Mundlos*

The ENCODE data indicate that over 80% of the genome is biochemically active. The regulatory landscape of the genome is divided into topological domains containing cis-regulatory elements: enhancers, silencers, and insulators. Non-coding CNVs and mutations have to be taken into consideration for the investigation of human disease.

BioEssays 2013, 35, No. 6, 533–543 [Prospects & Overviews]


RNA-mediated genome rearrangement: Hypotheses and evidence

RNA‐mediated genome rearrangement: Hypotheses and evidence

Wenwen Fang, Laura F. Landweber*

RNA may mediate genome rearrangement by serving as a repair template for double-stranded DNA break repair (A), a scaffold to bring two genomic loci into proximity in space (B), or a recruiting agent for DNA repair complexesor chromatin modification complexes required for DNA repair (C).

BioEssays 2013, 35, No. 2, 84–87 [Insights & Perspectives]


Introns in UTRs: Why we should stop ignoring them

Introns in UTRs: Why we should stop ignoring them

Alicia A. Bicknell, Can Cenik, Hon N. Chua, Frederick P. Roth, Melissa J. Moore*

Whereas introns in coding regions are well-appreciated for their role in producing alternative protein isoforms, introns in untranslated regions (UTRs) have been largely ignored. Recent evidence shows that UTR introns are important for regulating gene expression; introns in 5′-UTRs control mRNA nuclear export, and introns in 3′-UTRs regulate mRNA stability.

BioEssays 2012, 34, No. 12, 1025–1034 [Insights & Perspectives]


Genome instability: Does genetic diversity amplification drive tumorigenesis?

Genome instability: Does genetic diversity amplification drive tumorigenesis?

Andrew B. Lane, Duncan J. Clarke*

Acute genome instability is a period of rapid volatility in which a catastrophic failure within a single cell cycle results in aneuploidy and complex chromosome rearrangements. If tolerated by the progeny, the massive genome damage can be exploited by cancer cells to gain a proliferative advantage and adaptability.

BioEssays 2012, 34, No. 11, 963–972 [Prospects & Overviews]


Mammalian chromosomes contain cis-acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes

Mammalian chromosomes contain cis‐acting elements that control replication timing, mitotic condensation, and stability of entire chromosomes

Mathew J. Thayer*

Mammalian chromosomes contain four types of cis-acting elementsthat function to regulate chromosome-wide replication timing, mitotic condensation and stability of individual chromosomes: origins of replication, telomeres, centrosomes and loci such as Xist and ASAR6 functioning as “inactivation/stability centers”.

BioEssays 2012, 34, No. 9, 760–770 [Prospects & Overviews]


The genome in space and time: Does form always follow function?

The genome in space and time: Does form always follow function?

Zhijun Duan*, Carl Anthony Blau*

Present evidence supports the idea that, in general, the spatial and temporal organization of a eukaryotic genome reflects and influences its function. However, the answer as to whether genome architecture is a hallmark of cell identity remains elusive.

BioEssays 2012, 34, No. 9, 800–810 [Prospects & Overviews]


Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA-binding protein occupancy

Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA‐binding protein occupancy

Igor F. Zhimulev*, Elena S. Belyaeva, Tatiana Yu Vatolina, Sergey A. Demakov

Recent genome-wide protein mapping efforts in Drosophila have provided information on the proteins associated with interbands as well as on the correspondence between the genomic maps and the polytene chromosome structure, and have shown that the polytene chromosome structure is likely to provide a good representation of the organisation of interphase chromatin in diploid cells.

BioEssays 2012, 34, No. 6, 498–508 [Prospects & Overviews]


Characterization of chromatin domains by 3D fluorescence microscopy: An automated methodology for quantitative analysis and nuclei screening

Characterization of chromatin domains by 3D fluorescence microscopy: An automated methodology for quantitative analysis and nuclei screening

Sylvain Cantaloube, Kelly Romeo, Patricia Le Baccon, Geneviève Almouzni, Jean-Pierre Quivy*

This method allows the quantitative analysis of the localisation of several endogenous markers (e.g. heterochromatin protein 1, HP1) at pericentric heterochromatin domains imaged via immunofluorescence microscopy.

BioEssays 2012, 34, No. 6, 509–517 [Prospects & Overviews]


How chromatin prevents genomic rearrangements: Locus colocalization induced by transcription factor binding

How chromatin prevents genomic rearrangements: Locus colocalization induced by transcription factor binding

Jérôme Déjardin*

The loosening of chromatin structures gives rise to unrestricted access to DNA and thus transcription factors (TFs) can bind to their otherwise masked target sequences. Regions bound by the same set of TFs tend to be located in close proximity and this might increase the probability of activating illegitimate genomic rearrangements.

BioEssays 2012, 34, No. 2, 90–93 [Insights & Perspectives]


Challenges in studying genomic structural variant formation mechanisms: The short-read dilemma and beyond

Challenges in studying genomic structural variant formation mechanisms: The short‐read dilemma and beyond

Megumi Onishi-Seebacher, Jan O. Korbel*

Structural variants (SVs) are responsible for a large degree of genetic variation among individuals and have also been implicated in a number of diseases and complex traits. However, short DNA reads typically generated by next-generation sequencing technologies can lead to a bias in the types of SVs most easily detected (short read dilemma). Novel approaches and integration of other sources of information will help overcome this dilemma.

BioEssays 2011, 33, No. 11, 840–850 [Prospects & Overviews]


Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica

Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica

Sreenivas Chavali*, David A. de Lima Morais, Julian Gough, M. Madan Babu

BioEssays 2011, 33, No. 8, 592–601 [Prospects & Overviews]

SEARCH

SEARCH BY CITATION