The vast majority of multi-exon genes in humans undergo alternative splicing, which greatly increases the functional diversity of protein species. Predicting functions at the isoform level is essential to further our understanding of developmental abnormalities and cancers, which frequently exhibit aberrant splicing and dysregulation of isoform expression. However, determination of isoform function is very difficult, and efforts to predict isoform function have been limited in the functional genomics field. Now deep sequencing of RNA provides an unprecedented amount of expression data at the transcript level. We describe here emerging computational approaches that integrate such large-scale RNA-seq data for predicting functions of alternatively spliced isoforms, and we discuss their applications in developmental and cancer biology. We outline future directions for isoform function prediction, emphasizing the need for heterogeneous genomic data integration and tissue-specific, dynamic isoform-level network modeling, which will allow the field to realize its full potential.
Splice isoforms; genomic data integration; function prediction; cancers; development
SWI/SNF is a multi-subunit chromatin remodeling complex that performs fundamental roles in gene regulation, cell lineage specification, and organismal development. Mutations that inactivate SWI/SNF subunits are found in nearly 20% of human cancers, which indicates that the proper functioning of this complex is necessary to prevent tumor formation in diverse tissues. Recent studies show that SWI/SNF-mutant cancers depend on residual SWI/SNF complexes for their aberrant growth, thus revealing synthetic lethal interactions that could be exploited for therapeutic purposes. Other studies show that certain acute leukemias and small cell lung cancers, which lack SWI/SNF mutations, can be vulnerable to inhibition of the SWI/SNF ATPase subunit BRG1, while several normal and malignant cell types lack this sensitivity. Here, we review the emerging evidence that implicates SWI/SNF as a tumor dependency and candidate drug target in human cancer.
SWI/SNF; synthetic lethality; cancer therapy
Transcriptional regulation of gene expression is fundamental to most cellular processes, including determination of cellular fates. Quantitative studies of transcription in cultured cells have led to significant advances in identifying mechanisms underlying transcriptional control. Recent progress allowed implementation of these same quantitative methods in multicellular organisms to ask how transcriptional regulation unfolds both in vivo and at the single molecule level in the context of embryonic development. Here we review some of these advances in early Drosophila development, which bring the embryo on par with its single-celled counterparts. In particular, we discuss progress in methods to measure mRNA and protein distributions in fixed and living embryos, and we highlight some initial applications that lead to fundamental new insights about molecular transcription processes. We end with an outlook on how to further exploit the unique advantages that come with investigating transcriptional control in the developmental context of the embryo.
gene regulatory networks; embryogenesis; quantitative biology; single molecule FISH; live imaging
The first link between sirtuins and longevity was made 15 years ago in yeast. These initial studies sparked efforts by many laboratories working in diverse model organisms to elucidate the relationships between sirtuins, lifespan, and age-associated dysfunction. Here we discuss the current understanding of how sirtuins relate to aging. We focus primarily on mammalian sirtuins SIRT1, SIRT3, and SIRT6, the three sirtuins for which the most relevant data are available. Strikingly, a large body of evidence now indicates that these and other mammalian sirtuins suppress a variety of age-related pathologies and promote healthspan. Moreover, increased expression of SIRT1 or SIRT6 extends mouse lifespan. Overall, these data point to important roles for sirtuins in promoting mammalian health, and perhaps in modulating the aging process.
Aging; longevity; age-associated disease; NAD+; mitochondria; SIRT1; SIRT3; SIRT6
Eri1 is an evolutionarily conserved 3′–5′ exoribonuclease that participates in 5.8S rRNA 3′ end processing and turnover of replication-dependent histone mRNAs. Over the course of evolution, Eri1 has also been recruited into a variety of conserved and species-specific regulatory small RNA pathways that include endogenous small interfering RNAs and microRNAs. Recent advances in Eri1 biology illustrate the importance of RNA metabolism in epigenetic gene regulation and illuminate common principles and players in RNA biogenesis and turnover. In this review, we highlight Eri1 as a member of a growing class of ribosome- and histone mRNA-associated proteins that have been recruited into divergent RNA metabolic pathways. We summarize recent advances in the understanding of Eri1 function in these pathways and discuss how Eri1 impacts gene expression and physiology in a variety of eukaryotic species. This emerging view highlights the possibility for crosstalk and coregulation of diverse cellular processes regulated by RNA.
microRNA (miRNA); RNA interference (RNAi); histone mRNA; ribosomal RNA (rRNA); epigenetic regulation; gene expression
Spatial and temporal regulation of gene expression is achieved through instructions provided by the distal transcriptional regulatory elements known as enhancers. How enhancers transmit such information to their targets has been the subject of intense investigation. Recent advances in high throughput analysis of the mammalian transcriptome have revealed a surprising result indicating that a large number of enhancers are transcribed to noncoding RNAs. Although long noncoding RNAs were initially shown to confer epigenetic transcriptional repression, recent studies have uncovered a role for a class of such transcripts in gene-specific activation, often from distal genomic regions. In this review, we discuss recent findings on the role of long noncoding RNAs in transcriptional regulation, with an emphasis on new developments on the functional links between long noncoding RNAs and enhancers.
Post-publication peer review (PPPR) is transforming how the life sciences community evaluates published manuscripts and data. Unsurprisingly, however, PPPR is experiencing growing pains, and some elements of the process distinct from standard pre-publication review remain controversial. I discuss the rapid evolution of PPPR, its impact, and the challenges associated with it.
Human Heredity and Health in Africa (H3Africa) research seeks to promote fair collaboration between scientists in Africa and those from elsewhere. Here, we outline how concerns over inequality and exploitation led to a policy framework that places a firm focus on African leadership and capacity building as guiding principles for African genomics research.
Africa; genomics; ethics; fairness; H3Africa
Copy number variation (CNV) is a major source of genetic variation among humans. In addition to existing as benign polymorphisms, CNVs can also convey clinical phenotypes, including genomic disorders, sporadic diseases and complex human traits. CNV results from genomic rearrangements that can represent simple deletion or duplication of a genomic segment, or be more complex. Complex chromosomal rearrangements (CCRs) have been known for some time but their mechanisms have remained elusive. Recent technology advances and high-resolution human genome analyses have revealed that complex genomic rearrangements can account for a large fraction of non-recurrent rearrangements at a given locus. Various mechanisms, most of which are DNA-replication-based, for example fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR), have been proposed for generating such complex genomic rearrangements and are probably responsible for CCR.
Monoallelic gene expression is a remarkable process in which transcription occurs from only one of two homologous alleles in a diploid cell. Interestingly, between 0.5% to 15% of autosomal genes exhibit random monoallelic gene expression, in which different cells express only one allele independently of the underlying genomic sequence, in a cell-type specific manner. Recently, genome-wide studies have increased our understanding of the cell-type specific incidence of random monoallelic gene expression, and how the imbalance in allelic expression is distinguished within the cell and potentially maintained across cell generations. Monoallelic gene expression is likely generated through stochastic independent regulation of the two alleles upon differentiation, and has varied implications for the cell and organism, in particular with respect to disease.
monoallelic expression; stochastic gene regulation
The role of normal transcription and RNA processing in maintaining genome integrity is becoming increasingly appreciated in organisms ranging from bacteria to humans. Several mutations in RNA biogenesis factors have been implicated in human cancers, but the mechanisms and potential connections to tumor genome instability are not clear. Here we discuss how RNA processing defects could destabilize genomes through mutagenic R-loop structures and by altering expression of genes required for genome stability. A compelling body of evidence now suggests that researchers should be directly testing these mechanisms in models of human cancer.
RNA processing; R-loops; genome instability; cancer; transcriptome
Although genetics play an essential role in defining an organism’s development, morphology and physiology, epigenetic mechanisms play an essential role in modulating these properties by regulating gene expression. During development, epigenetic mechanisms establish stable gene expression patterns to ensure proper differentiation. Epigenetic mechanisms also allow organisms to adapt to environmental changes and previous experiences can impact the future responsiveness of an organism to a stimulus over long time scales and even over generations. Here we discuss the concept of epigenetic memory, defined as the stable propagation of a change in gene expression or potentially induced by developmental or environmental stimuli. We highlight three distinct paradigms of epigenetic memory that operate on different time scales.
Epigenetics; methylation; chromatin; memory; inheritance; nuclear pore complex
Chromatin remodelers use the energy of ATP hydrolysis to reposition or evict nucleosomes or to replace canonical histones with histone variants. By regulating nucleosome dynamics, remodelers gate access to the underlying DNA for replication, repair, and transcription. Nucleosomes are subject to extensive post-translational modifications that can recruit regulatory proteins or alter the local chromatin structure. Just as extensive cross-talk has been observed between different histone post-translational modifications, there is growing evidence for both coordinated and antagonistic functional relationships between nucleosome remodeling and modifying machineries. Defining the combined functions of the complexes that alter nucleosome interactions, position, and stability is key to understanding processes that require access to DNA, particularly with growing appreciation of their contributions to human health and disease. Here, we highlight recent advances in the interactions between histone modifications and the ISWI and CHD1 chromatin remodelers from studies in budding yeast, fission yeast, flies, and mammalian cells, with a focus on yeast.
chromatin; nucleosome; histone modification; ISWI; Chd1; yeast
Sport fishermen keep tension on their lines to prevent hooked fish from releasing. A molecular version of this angler’s trick, operating at kinetochores, ensures accuracy during mitosis: The mitotic spindle attaches randomly to chromosomes and then correctly bioriented attachments are stabilized due to the tension exerted on them by opposing microtubules. Incorrect attachments, which lack tension, are unstable and release quickly, allowing another chance for biorientation. Stabilization of molecular interactions by tension also occurs in other physiological contexts such as cell adhesion, motility, hemostasis, and tissue morphogenesis. Here we review models for the stabilization of kinetochore attachments with an eye toward emerging models for other force-activated systems. While attention in the mitosis field has focused mainly on one kinase-based mechanism, multiple mechanisms may act together to stabilize properly bioriented kinetochores and some principles governing other tension-sensitive systems may apply to kinetochores as well.
Cell division; Mitotic spindle; Meiosis; Chromosome; Biorientation; Aurora B; Tension; Mechanobiology; Mechanosensor; Catch bond
Genome-wide association studies (GWAS) have identified more than 8,900 genetic variants, mainly single nucleotide polymorphisms (SNPs), associated with hundreds of human traits and diseases, which define risk-associated loci. Variants that map to coding regions can affect protein sequence, translational rate and alternative splicing, all of which influence protein function. However, the vast majority of sequence variants map to non-coding intergenic and intronic regions, and it has been much more challenging to assess the functional nature of these variants. Recent work annotating the non-coding regions of the genome has contributed to post-GWAS studies by facilitating the identification of the functional targets of risk-associated loci. Many non-coding genetic variants within risk-associated loci alter gene expression by modulating the activity of cis-regulatory elements. Here, we review these recent findings and discuss their implication for the post-GWAS era and relate their importance to the interpretation of disease-associated mutations identified through whole-genome sequencing.
gwas; genetic risk variant; causal variant; missing heritability; functional genomic; noncoding
The availability of sequenced genomes from multiple related organisms
allows the detection and localization of functional genomic elements based on
the idea that such elements evolve more slowly than neutral sequences. Although
such comparative genomics methods have proven useful in discovering functional
elements and ascertaining levels of functional constraint in the genome as a
whole, here we outline limitations intrinsic to this approach that cannot be
overcome by sequencing more species. We argue that it is essential to supplement
comparative genomics with ultra-deep sampling of populations from closely
related species to enable substantially more powerful genomic scans for
functional elements. The convergence of sequencing technology and population
genetics theory has made such projects feasible and has exciting implications
for functional genomics.
•De novo genes frequently arise from noncoding DNA.•While most of the de novo genes are lost, a fraction of them becomes essential.•De novo genes are most likely involved in the response to a rapidly changing environment.
Although considered an extremely unlikely event, many genes emerge from previously noncoding genomic regions. This review covers the entire life cycle of such de novo genes. Two competing hypotheses about the process of de novo gene birth are discussed as well as the high death rate of de novo genes. Despite the high death rate, some de novo genes are retained and remain functional, even in distantly related species, through their integration into gene networks. Further studies combining gene expression with ribosome profiling in multiple populations across different species will be instrumental for an improved understanding of the evolutionary processes operating on de novo genes.
orphans; de novo genes; transcription; population genetics
The amount of genetic and genomic information obtainable from the human fetus during pregnancy is accelerating at an unprecedented rate. Two themes have dominated recent technological advances in prenatal diagnosis: interrogation of the fetal genome in increasingly high resolution and the development of non-invasive methods of fetal testing using cell-free DNA in maternal plasma. These two areas of advancement have now converged with several recent reports of non-invasive assessment of the entire fetal genome from maternal blood. However, technological progress is outpacing the ability of the healthcare providers and patients to incorporate these new tests into existing clinical care, and further complicates many of the economic and ethical dilemmas in prenatal diagnosis. This review summarizes recent work in this field and discusses the integration of these new technologies into the clinic and society.
To combat potentially deadly viral infections, prokaryotic microbes enlist small RNA-based adaptive immune systems (CRISPR-Cas systems) that protect through sequence-specific recognition and targeted destruction of viral nucleic acids (either DNA or RNA depending on the system). Here, we summarize rapid progress made in redirecting the nuclease activities of these microbial immune systems to bind and cleave DNA or RNA targets of choice, by reprogramming the small guide RNAs of the various CRISPR-Cas complexes. These studies have demonstrated the potential of Type II CRISPR-Cas systems both as efficient and versatile genome editing tools and as potent and specific regulators of gene expression in a very broad range of cell types (including human) and organisms. Progress is also being made in developing a Type III RNA-targeting CRISPR-Cas system as a novel gene knockdown platform to investigate gene function and modulate gene expression for metabolic engineering in microbes.
CRISPR; Cas; genome editing; RNA silencing; biotechnology; metabolic engineering
Heterochromatin Protein 1 (HP1a in Drosophila) is a conserved eukaryotic chromosomal protein that is prominently associated with pericentric heterochromatin and mediates the concomitant gene silencing. Mechanistic studies implicate HP1 family proteins as “hub proteins,” able to interact with a variety of chromosomal proteins through the chromo-shadow domain, as well as recognize key histone modification sites (primarily H3K9me2/3) through the chromo domain. Consequently, HP1 plays many important roles in chromatin architecture and impacts both gene expression and gene silencing, utilizing a variety of mechanisms. Clearly, HP1 function is altered by context, and potentially by post-translational modifications. Here, we report on recent ideas as to how this versatile protein accomplishes its diverse functions.
HP1a; chromo domain; silencing; gene expression
•Discovery of vaccine candidate antigens by parasite genome sequence analyses.•Genetic crosses, linkage group selection, and functional studies on parasites.•Characterizing developmental and epigenetic variation alongside allelic polymorphism.•Selection by naturally acquired immune responses helps to focus vaccine design.
More human death and disease is caused by malaria parasites than by all other eukaryotic pathogens combined. As early as the sequencing of the first human genome, malaria parasite genomics was prioritized to fuel the discovery of vaccine candidate antigens. This stimulated increased research on malaria, generating new understanding of the cellular and molecular mechanisms of infection and immunity. This review of recent developments illustrates how new approaches in parasite genomics, and increasingly large amounts of data from population studies, are helping to identify antigens that are promising lead targets. Although these results have been encouraging, effective discovery and characterization need to be coupled with more innovation and funding to translate findings into newly designed vaccine products for clinical trials.
Elucidation of the genetic pathways that control red blood cell development has been a central goal of erythropoiesis research over the past decade. Notably, data from several recent studies have provided new insights into the regulation of erythroid gene transcription. Transcription profiling demonstrates that erythopoiesis is mainly controlled by a small group of lineage-restricted transcription factors (Gata1, Tal1, and Klf1). Binding site mapping using ChIP-Seq indicates that most DNA bound Gata1 and Tal1 proteins are contained within higher order complexes (Ldb1-complexes) that include the nuclear adapters Ldb1 and Lmo2. Ldb1-complexes regulate Klf1 and Ldb1-complex binding sites frequently co-localize with Klf1 at erythroid genes and cis-regulatory elements indicating strong functional synergy between Gata1, Tal1, and Klf1. Together with new data demonstrating that Ldb1 can mediate long-range promoter/enhancer interactions, these findings provide a foundation for the first comprehensive models for the global regulation of erythroid gene transcription.
Erythropoiesis; Gata1; Tal1; Klf1; Ldb1-complexes; Transcriptional regulation; ChIP-Seq