Articles

Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions

Characterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of ...

Authors: Xinyi Yang and Martin Vingron

Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida

Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embe...

Authors: Sunjoo Joo, Ming Hsiu Wang, Gary Lui, Jenny Lee, Andrew Barnas, Eunsoo Kim, Sebastian Sudek, Alexandra Z. Worden and Jae-Hyeok Lee

From plant immunity to food security: an interview with Ksenia Krasileva

Ksenia Krasileva is an Assistant Professor at UC Berkeley, studying innate immunity in plants. Ksenia’s work combines plant genomics and plant-microbe interactions with new technologies, spanning basic studies...

Authors: Ksenia Krasileva

15 years of BMC Biology

Authors: Christian Matheou, Graham P. Bell, Penelope Austin, Vitor Sousa and Mirna Kvajo

Studying the microbiome and its complexities: an interview with Alan Walker

Alan Walker is a Senior Lecturer at the University of Aberdeen, UK, studying the intestinal microbiota and its interactions with the host’s diet. In this interview, Alan discusses his research interests, earli...

Authors: Alan W. Walker

Unraveling rain forest biodiversity: an interview with Thomas Couvreur

Thomas Couvreur is a researcher and botanist at the Institut de Recherche pour le Développement (IRD), based in Montpellier, France, studying tropical biosystems. He is using diverse approaches—from taxonomy, ...

Authors: Thomas L. P. Couvreur

Horizons in evolutionary genomics: an interview with David Ferrier

David Ferrier is a Reader at the University of St Andrews and Deputy Director of the Scottish Oceans Institute, where his lab studies how the diversity of form in the animal kingdom evolved, with an emphasis o...

Authors: David E. K. Ferrier

Systems biology of meristems: an interview with Teva Vernoux

Teva Vernoux is a plant developmental biologist and holds positions as the Director of the Institute for Reproduction and Development of Plants at ENS de Lyon, and as a Research Director at Centre National de ...

Authors: Teva Vernoux

Communicating through scents: an interview with Jane Hurst

Jane Hurst is a William Prescott Professor of Animal Science at the University of Liverpool, UK, studying scent communication in mammals and its role in behaviours. In this interview, Jane discusses how scents...

Authors: Jane Hurst

Open questions: respiratory chain supercomplexes—why are they there and what do they do?

In the mitochondrial inner membrane the respiratory enzymes associate to form supramolecular assemblies known as supercomplexes. The existence of supercomplexes is now widely accepted—but what functional or st...

Authors: Judy Hirst

On microbes, aging and the worm: an interview with David Weinkove

David Weinkove is an associate professor at Durham University, UK, studying host–microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiolog...

Authors: David Weinkove

Open questions: why are babies rarely born with cancer?

Childhood cancer is fundamentally a disease of dysregulated development. Why does it rarely occur during the fetal period, a time of enormous growth and development?

Authors: Michelle Monje

Startling responses of zebrafish: an interview with Harold Burgess

Harold Burgess is a Senior Investigator at the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), part of the National Institutes of Health. Work in his lab combines genetic ...

Authors: Harold A. Burgess

Evolving eukaryotes: an interview with Joel Dacks

Joel Dacks is an Associate Professor and Canada Research Chair in Evolutionary Cell Biology at the University of Alberta, a Scientific Associate at the Natural History Museum (London), and the current Presiden...

Authors: Joel B. Dacks

Dissecting the forces that shape crops: an interview with Ryohei Terauchi

Ryohei Terauchi is a Professor at Kyoto University and a Group Leader at the Iwate Biotechnology Research Center, Japan, studying the evolution of crops and their pathogens. In this interview, Ryohei describes...

Authors: Ryohei Terauchi

Open questions: why should we care about ER-phagy and ER remodelling?

The endoplasmic reticulum (ER) is one of the most complex organelles in the eukaryotic cell. Recent findings suggest that a process called ER-phagy plays a major role in maintaining the ER’s shape and function.

Authors: Ivan Dikic

Open questions: what are the genes underlying antagonistic coevolution?

Although the idea of coevolution was first presented 150 years ago, we still only vaguely understand the genetic basis of its workings. Identifying the genes responsible for coevolutionary interactions would e...

Authors: Dieter Ebert

When a physicist wanders into biology…: an interview with KC Huang

Kerwyn Casey (“KC”) Huang is an Associate Professor at Stanford University, studying the physical nature of biological systems and the underpinnings of fundamental processes such as cell shape determination, c...

Authors: Kerwyn Casey Huang

From bacterial genomics to clinical epidemiology: an interview with Bill Hanage

Bill Hanage is an Associate Professor of Epidemiology at Harvard School of Public Health, where he studies fundamental and applied epidemiology using genomic and evolutionary methods. Bill spoke to us about th...

Authors: William P. Hanage

Host-parasite interactions: an interview with Emily Troemel

Emily Troemel is a Professor at the University of California San Diego, where her lab uses Caenorhabditis elegans to study host–pathogen interactions and the shaping of the immune response. In this interview, Emi...

Authors: Emily Troemel

Evolutionary development and morphological modifications of the brain: an interview with Angelika Stollewerk

Angelika Stollewerk is a Reader at Queen Mary University of London, where her lab uses a diverse range of species to study the evolution of the arthropod nervous system. Angelika spoke to us about social spide...

Authors: Angelika Stollewerk

Correction to: The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches

Reinvestigation of the raw data revealed an unfortunate error in Ugelvig et al. 2008 [1].

Authors: Line V. Ugelvig, Falko P. Drijfhout, Daniel J. C. Kronauer, Jacobus J. Boomsma, Jes S. Pedersen and Sylvia Cremer

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA pres...

Authors: Cesare de Filippo, Matthias Meyer and Kay Prüfer

Microtubule polyglutamylation and acetylation drive microtubule dynamics critical for platelet formation

Upon maturation in the bone marrow, polyploid megakaryocytes elongate very long and thin cytoplasmic branches called proplatelets. Proplatelets enter the sinusoids blood vessels in which platelets are ultimate...

Authors: Juliette van Dijk, Guillaume Bompard, Julien Cau, Shinji Kunishima, Gabriel Rabeharivelo, Julio Mateos-Langerak, Chantal Cazevieille, Patricia Cavelier, Brigitte Boizet-Bonhoure, Claude Delsert and Nathalie Morin

Open questions: knowing who’s who in multicellular animals is not always as simple as we imagine

The ability of certain tumor cells of mammals and molluscs to spread from the original host to others reopens the question of distinguishing self from non-self. It is part of a wider phenomenon of cellular par...

Authors: Robin A. Weiss

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage

High throughput methods for profiling the transcriptomes of single cells have recently emerged as transformative approaches for large-scale population surveys of cellular diversity in heterogeneous primary tis...

Authors: Aparna Bhaduri, Tomasz J Nowakowski, Alex A Pollen and Arnold R Kriegstein

Food perception without ingestion leads to metabolic changes and irreversible developmental arrest in C. elegans

Developmental physiology is very sensitive to nutrient availability. For instance, in the nematode Caenorhabditis elegans, newly hatched L1-stage larvae require food to initiate postembryonic development. In addi...

Authors: Rebecca E. W. Kaplan, Amy K. Webster, Rojin Chitrakar, Joseph A. Dent and L. Ryan Baugh

UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells

H3.3 is an ancient and conserved H3 variant and plays essential roles in transcriptional regulation. HIRA complex, which is composed of HIRA, UBN1 or UBN2, and Cabin1, is a H3.3 specific chaperone complex. How...

Authors: Chaoyang Xiong, Zengqi Wen, Juan Yu, Jun Chen, Chao-Pei Liu, Xiaodong Zhang, Ping Chen, Rui-Ming Xu and Guohong Li

VOPP1 promotes breast tumorigenesis by interacting with the tumor suppressor WWOX

The WW domain-containing oxidoreductase (WWOX) gene, frequently altered in breast cancer, encodes a tumor suppressor whose function is mediated through its interactions with cancer-related proteins, such as the p...

Authors: Florian Bonin, Karim Taouis, Paula Azorin, Ambre Petitalot, Zakia Tariq, Sebastien Nola, Nadège Bouteille, Sandrine Tury, Sophie Vacher, Ivan Bièche, Khadija Ait Rais, Gaelle Pierron, Laetitia Fuhrmann, Anne Vincent-Salomon, Etienne Formstecher, Jacques Camonis…

Cell type-specific expression profiling unravels the development and evolution of stinging cells in sea anemone

Cnidocytes are specialized cells that define the phylum Cnidaria. They possess an “explosive” organelle called cnidocyst that is important for prey capture and anti-predator defense. An extraordinary morpholog...

Authors: Kartik Sunagar, Yaara Y Columbus-Shenkar, Arie Fridrich, Nadya Gutkovich, Reuven Aharoni and Yehu Moran

Synaptic coupling of inner ear sensory cells is controlled by brevican-based extracellular matrix baskets resembling perineuronal nets

Perineuronal nets (PNNs) are specialized aggregations of extracellular matrix (ECM) molecules surrounding specific neurons in the central nervous system (CNS). PNNs are supposed to control synaptic transmissio...

Authors: Mandy Sonntag, Maren Blosa, Sophie Schmidt, Katja Reimann, Kerstin Blum, Tobias Eckrich, Gudrun Seeger, Dietmar Hecker, Bernhard Schick, Thomas Arendt, Jutta Engel and Markus Morawski

Brevican “nets” voltage-gated calcium channels at the hair cell ribbon synapse

During hearing in mammals, “sensorineural” inner hair cells convert sound wave-generated mechanical input into electrical activity, resulting in glutamate release onto type I spiral ganglion neurons (SGNs) at ...

Authors: Thomas M. Coate and Katherine Conant

Loss of males from mixed-sex societies in termites

Sexual reproduction is the norm in almost all animal species, and in many advanced animal societies, both males and females participate in social activities. To date, the complete loss of males from advanced s...

Authors: Toshihisa Yashiro, Nathan Lo, Kazuya Kobayashi, Tomonari Nozaki, Taro Fuchikawa, Nobuaki Mizumoto, Yusuke Namba and Kenji Matsuura

The disposable male— the ultimate emancipation of females?

Sexual reproduction is costly compared to asexual reproduction, in particular because males generally contribute little to offspring. Research published today in BMC Biology shows that some populations of a termi...

Authors: Duur K. Aanen

Histone variants H2A.Z and H3.3 coordinately regulate PRC2-dependent H3K27me3 deposition and gene expression regulation in mES cells

The hierarchical organization of eukaryotic chromatin plays a central role in gene regulation, by controlling the extent to which the transcription machinery can access DNA. The histone variants H3.3 and H2A.Z...

Authors: Yan Wang, Haizhen Long, Juan Yu, Liping Dong, Michel Wassef, Baowen Zhuo, Xia Li, Jicheng Zhao, Min Wang, Cuifang Liu, Zengqi Wen, Luyuan Chang, Ping Chen, Qian-fei Wang, Xueqing Xu, Raphael Margueron…

Open questions: CRISPR biology

CRISPR-Cas systems, the purveyors of adaptive immunity in archaea and bacteria and sources of the new generation of genome engineering tools, have been studied in exquisite molecular detail. However, when it c...

Authors: Eugene V. Koonin

Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance

Defining the mechanisms that establish and regulate the transmission of epigenetic information from parent to offspring is critical for understanding disease heredity. Currently, the molecular pathways that re...

Authors: Jessica M. Stringer, Samuel C. Forster, Zhipeng Qu, Lexie Prokopuk, Moira K. O’Bryan, David K. Gardner, Stefan J. White, David Adelson and Patrick S. Western

The piRNA pathway responds to environmental signals to establish intergenerational adaptation to stress

piRNAs have a constitutive role in genome defence by silencing transposable elements in the germline. In the nematode Caenorhabditis elegans, piRNAs also induce epigenetic silencing of transgenes, which can be ma...

Authors: Tony Belicard, Pree Jareosettasin and Peter Sarkies

Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

Global analyses of gene expression during development reveal specific transcription patterns associated with the emergence of various cell types, tissues, and organs. These heterogeneous patterns are instrumen...

Authors: P. J. Fabre, M. Leleu, B. Mascrez, Q. Lo Giudice, J. Cobb and D. Duboule

Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

Two of the most widely cultivated rice strains are Oryza sativa indica and O. sativa japonica, and understanding the genetic basis of their agronomic traits is of importance for crop production. These two species...

Authors: Xiukun Li, Lian Wu, Jiahong Wang, Jian Sun, Xiuhong Xia, Xin Geng, Xuhong Wang, Zhengjin Xu and Quan Xu

Parkinson’s disease-linked Parkin mutations impair glutamatergic signaling in hippocampal neurons

Parkinson’s disease (PD)-associated E3 ubiquitin ligase Parkin is enriched at glutamatergic synapses, where it ubiquitinates multiple substrates, suggesting that its mutation/loss-of-function could contribute ...

Authors: Mei Zhu, Giuseppe P. Cortese and Clarissa L. Waites

Q&A: Array tomography

Array tomography encompasses light and electron microscopy modalities that offer unparalleled opportunities to explore three-dimensional cellular architectures in extremely fine structural and molecular detail...

Authors: Stephen J Smith

Ontogenetic and phylogenetic simplification during white stripe evolution in clownfishes

Biologists have long been fascinated by the striking diversity of complex color patterns in tropical reef fishes. However, the origins and evolution of this diversity are still poorly understood. Disentangling...

Authors: Pauline Salis, Natacha Roux, Olivier Soulat, David Lecchini, Vincent Laudet and Bruno Frédérich

Microdomain formation is a general property of bacterial membrane proteins and induces heterogeneity of diffusion patterns

Proteins within the cytoplasmic membrane display distinct localization patterns and arrangements. While multiple models exist describing the dynamics of membrane proteins, to date, there have been few systemat...

Authors: Daniella Lucena, Marco Mauri, Felix Schmidt, Bruno Eckhardt and Peter L. Graumann

Horizons in the evolution of aging

Between the 1930s and 50s, evolutionary biologists developed a successful theory of why organisms age, firmly rooted in population genetic principles. By the 1980s the evolution of aging had a secure experimen...

Authors: Thomas Flatt and Linda Partridge

Open questions: How many genes do we have?

Seventeen years after the initial publication of the human genome, we still haven’t found all of our genes. The answer turns out to be more complex than anyone had imagined when the Human Genome Project began.

Authors: Steven L. Salzberg

Targeting the Tie2–α_vβ₃ integrin axis with bi-specific reagents for the inhibition of angiogenesis

Increased activity of the receptor tyrosine kinase Tie2 has been implicated in the promotion of pathological angiogenesis. This activity is mainly mediated through angiopoietin (Ang)1- and Ang2-dependent activ...

Authors: Tomer Shlamkovich, Lidan Aharon, Dana Koslawsky, Yulia Einav and Niv Papo

A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Our understanding of the regulation of gene expression has benefited from the availability of high-throughput technologies that interrogate the whole genome for the binding of specific transcription factors an...

Authors: Alberto Santos-Zavaleta, Mishael Sánchez-Pérez, Heladia Salgado, David A. Velázquez-Ramírez, Socorro Gama-Castro, Víctor H. Tierrafría, Stephen J. W. Busby, Patricia Aquino, Xin Fang, Bernhard O. Palsson, James E. Galagan and Julio Collado-Vides

Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor

Division of labor between reproductive queens and workers that perform brood care is a hallmark of insect societies. However, studies of the molecular basis of this fundamental dichotomy are limited by the fac...

Authors: Romain Libbrecht, Peter R. Oxley and Daniel J. C. Kronauer

Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay

The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and th...

Authors: Joanna Koszela, Nhan T. Pham, David Evans, Stefan Mann, Irene Perez-Pi, Steven Shave, Derek F. J. Ceccarelli, Frank Sicheri, Mike Tyers and Manfred Auer