A comprehensive approach to expression of L1 loci.

L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5΄ RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads. At least 99% of L1-related sequences found in RNA do not arise from the L1 promoter, instead representing pieces of L1 incorporated in other cellular RNAs. In any given cell type a relatively few active L1 loci contribute to the 'authentic' L1 transcripts that arise from the L1 promoter, with significantly different loci seen expressed in different tissues.

Baryon Asymmetry from a Composite Higgs Boson.

We study the nature of the electroweak phase transition (EWPT) in models where the Higgs boson emerges as a pseudo-Nambu-Goldstone boson of an approximate global symmetry of a new strongly interacting sector confining around the TeV scale. Our analysis focuses for the first time on the case where the EWPT is accompanied by the confinement phase transition of the strong sector. We describe the confinement in terms of the dilaton, the pseudo-Nambu-Goldstone boson of spontaneously broken conformal invariance of the strong sector. The dilaton can either be a mesonlike or a glueball-like state and we demonstrate a significant qualitative difference in their dynamics. We show that the EWPT can naturally be strongly first order, due to the nearly conformal nature of the dilaton potential. Furthermore, we examine the sizable scale variation of the Higgs potential parameters during the EWPT. In particular, we consider in detail the case of a varying top quark Yukawa coupling, and show that the resulting CP violation is sufficient for successful electroweak baryogenesis. We demonstrate that this source of CP violation is compatible with existing flavor and CP constraints. Our scenario can be tested in complementary ways: by measuring the CP-odd top Yukawa coupling in electron electric dipole moment experiments, by searching for dilaton production and deviations in Higgs couplings at colliders, and through gravitational waves at LISA.

The serendipity of electroweak baryogenesis.

The origin of the matter-antimatter asymmetry of the universe remains unexplained in the Standard Model (SM) of particle physics. The origin of the flavour structure is another major puzzle of the theory. In this article, we report on recent work attempting to link the two themes through the appealing framework of electroweak (EW) baryogenesis. We show that Yukawa couplings of SM fermions can be the source of CP violation for EW baryogenesis if they vary at the same time as the Higgs is acquiring its vacuum expectation value, offering new avenues for EW baryogenesis. The advantage of this approach is that it circumvents the usual severe bounds from electric dipole moments. These ideas apply if the mechanism explaining the flavour structure of the SM is connected to EW symmetry breaking, as motivated for instance in Randall-Sundrum or Composite Higgs models. We compute the resulting baryon asymmetry for different configurations of the Yukawa coupling variation across the bubble wall and show that it can naturally be of the right order.This article is part of the Theo Murphy meeting issue 'Higgs cosmology'.

Baryogenesis from strong CP violation and the QCD axion.

We show that strong CP violation from the QCD axion can be responsible for the matter antimatter asymmetry of the Universe in the context of cold electroweak baryogenesis if the electroweak phase transition is delayed below the GeV scale. This can occur naturally if the Higgs couples to a O(100) GeV dilaton, as expected in some models where the Higgs is a pseudo-Nambu-Goldstone boson of a new strongly interacting sector at the TeV scale. The existence of such a second scalar resonance with a mass and properties similar to the Higgs boson will soon be tested at the LHC. In this context, the QCD axion would not only solve the strong CP problem, but also the matter antimatter asymmetry and dark matter.

Tye7 regulates yeast Ty1 retrotransposon sense and antisense transcription in response to adenylic nucleotides stress.

Transposable elements play a fundamental role in genome evolution. It is proposed that their mobility, activated under stress, induces mutations that could confer advantages to the host organism. Transcription of the Ty1 LTR-retrotransposon of Saccharomyces cerevisiae is activated in response to a severe deficiency in adenylic nucleotides. Here, we show that Ty2 and Ty3 are also stimulated under these stress conditions, revealing the simultaneous activation of three active Ty retrotransposon families. We demonstrate that Ty1 activation in response to adenylic nucleotide depletion requires the DNA-binding transcription factor Tye7. Ty1 is transcribed in both sense and antisense directions. We identify three Tye7 potential binding sites in the region of Ty1 DNA sequence where antisense transcription starts. We show that Tye7 binds to Ty1 DNA and regulates Ty1 antisense transcription. Altogether, our data suggest that, in response to adenylic nucleotide reduction, TYE7 is induced and activates Ty1 mRNA transcription, possibly by controlling Ty1 antisense transcription. We also provide the first evidence that Ty1 antisense transcription can be regulated by environmental stress conditions, pointing to a new level of control of Ty1 activity by stress, as Ty1 antisense RNAs play an important role in regulating Ty1 mobility at both the transcriptional and post-transcriptional stages.

Baryogenesis and dark matter through a Higgs asymmetry.

In addition to explaining the masses of elementary particles, the Higgs boson may have far-reaching implications for the generation of the matter content in the Universe. For instance, the Higgs boson plays a key role in two main theories of baryogenesis, namely, electroweak baryogenesis and leptogenesis. In this Letter, we propose a new cosmological scenario where the Higgs chemical potential mediates asymmetries between visible and dark matter sectors, either generating a baryon asymmetry from a dark matter asymmetry or vice versa. We illustrate this mechanism with a simple model with two new fermions coupled to the Higgs boson and discuss the associated signatures.

CRISPRing future medicines.

Introduction: The ability to engineer mammalian genomes in a quick and cost-effective way has led to rapid adaptation of CRISPR technology in biomedical research. CRISPR-based engineering has the potential to accelerate drug discovery, to support the reduction of high attrition rate in drug development and to enhance development of cell and gene-based therapies.Areas covered: How CRISPR technology is transforming drug discovery is discussed in this review. From target identification to target validation in both in vitro and in vivo models, CRISPR technology is positively impacting the early stages of drug development by providing a straightforward way to genome engineering. This property also attracted attention for CRISPR application in the cell and gene therapy area.Expert opinion: CRISPR technology is rapidly becoming the preferred tool for genome engineering and nowadays it is hard to imagine the drug discovery pipeline without this technology. With the years to come, CRISPR technology will undoubtedly be further refined and will flourish into a mature technology that will play a key role in supporting genome engineering requirements in the drug discovery pipeline as well as in cell and gene therapy development.

Transcription coupled repair and biased insertion of human retrotransposon L1 in transcribed genes.

BACKGROUND: L1 retrotransposons inserted within genes in the human genome show a strong bias against sense orientation with respect to the gene. One suggested explanation for this observation was the possibility that L1 inserted randomly, but that there was negative selection against sense-oriented insertions. However, multiple studies have now found that de novo and polymorphic L1 insertions, which have little opportunity for selection to act, also show the same bias. RESULTS: Here we show that the transcription-coupled sub-pathway of nucleotide excision repair does not affect the overall rate of insertion of L1 elements, which is in contrast with the regulation by the global sub-pathway of nucleotide excision repair. The transcription-coupled subpathway does cause a strong bias against insertion in the sense orientation relative to genes. CONCLUSIONS: This suggests that a major portion of the L1 orientation bias might be generated during the process of insertion through the action of transcription-coupled nucleotide excision repair.

The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition.

Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a "copy-and-paste" mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3' DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway. To determine if the NER pathway prevents the insertion of retroelements in the genome, we monitored the retrotransposition efficiencies of engineered L1 elements in NER-deficient cells and in their complemented versions. Core proteins of the NER pathway, XPD and XPA, and the lesion binding protein, XPC, are involved in limiting L1 retrotransposition. In addition, sequence analysis of recovered de novo L1 inserts and their genomic locations in NER-deficient cells demonstrated the presence of abnormally large duplications at the site of insertion, suggesting that NER proteins may also play a role in the normal L1 insertion process. Here, we propose new functions for the NER pathway in the maintenance of genome integrity: limitation of insertional mutations caused by retrotransposons and the prevention of potentially mutagenic large genomic duplications at the site of retrotransposon insertion events.

Insertion of Retrotransposons at Chromosome Ends: Adaptive Response to Chromosome Maintenance.

The telomerase complex is a specialized reverse transcriptase (RT) that inserts tandem DNA arrays at the linear chromosome ends and contributes to the protection of the genetic information in eukaryotic genomes. Telomerases are phylogenetically related to retrotransposons, encoding also the RT activity required for the amplification of their sequences throughout the genome. Intriguingly the telomerase gene is lost from the Drosophila genome and tandem retrotransposons replace telomeric sequences at the chromosome extremities. This observation suggests the versatility of RT activity in counteracting the chromosome shortening associated with genome replication and that retrotransposons can provide this activity in case of a dysfunctional telomerase. In this review paper, we describe the major classes of retroelements present in eukaryotic genomes in order to point out the differences and similarities with the telomerase complex. In a second part, we discuss the insertion of retroelements at the ends of chromosomes as an adaptive response for dysfunctional telomeres.

Altering Genomic Integrity: Heavy Metal Exposure Promotes Transposable Element-Mediated Damage.

Maintenance of genomic integrity is critical for cellular homeostasis and survival. The active transposable elements (TEs) composed primarily of three mobile element lineages LINE-1, Alu, and SVA comprise approximately 30% of the mass of the human genome. For the past 2 decades, studies have shown that TEs significantly contribute to genetic instability and that TE-caused damages are associated with genetic diseases and cancer. Different environmental exposures, including several heavy metals, influence how TEs interact with its host genome increasing their negative impact. This mini-review provides some basic knowledge on TEs, their contribution to disease, and an overview of the current knowledge on how heavy metals influence TE-mediated damage.

Development of a monoclonal antibody specific to the endonuclease domain of the human LINE-1 ORF2 protein.

BACKGROUND: LINE-1 (L1) retrotransposons are common occupants of mammalian genomes representing about a fifth of the genetic content. Ongoing L1 retrotransposition in the germ line and somatic tissues has contributed to structural genomic variations and disease-causing mutations in the human genome. L1 mobilization relies on the function of two, self-encoded proteins, ORF1 and ORF2. The ORF2 protein contains two characterized domains: endonuclease and reverse transcriptase. RESULTS: Using a bacterially purified endonuclease domain of the human L1 ORF2 protein, we have generated a monoclonal antibody specific to the human ORF2 protein. We determined that the epitope recognized by this monoclonal antibody includes amino acid 205, which is required for the function of the L1 ORF2 protein endonuclease. Using an in vitro L1 cleavage assay, we demonstrate that the monoclonal anti-ORF2 protein antibody partially inhibits L1 endonuclease activity without having any effect on the in vitro activity of the human AP endonuclease. CONCLUSIONS: Overall, our data demonstrate that this anti-ORF2 protein monoclonal antibody is a useful tool for human L1-related studies and that it provides a rationale for the development of antibody-based inhibitors of L1-induced damage.

Remodeling yeast gene transcription by activating the Ty1 long terminal repeat retrotransposon under severe adenine deficiency.

The Ty1 long terminal repeat (LTR) retrotransposon of Saccharomyces cerevisiae is a powerful model to understand the activation of transposable elements by stress and their impact on genome expression. We previously discovered that Ty1 transcription is activated under conditions of severe adenine starvation. The mechanism of activation is independent of the Bas1 transcriptional activator of the de novo AMP biosynthesis pathway and probably involves chromatin remodeling at the Ty1 promoter. Here, we show that the 5' LTR has a weak transcriptional activity and is sufficient for the activation by severe adenine starvation. Furthermore, we demonstrate that Ty1 insertions that bring Ty1 promoter sequences into the vicinity of a reporter gene confer adenine starvation regulation on it. We provide evidence that similar coactivation of genes adjacent to Ty1 sequences occurs naturally in the yeast genome, indicating that Ty1 insertions can mediate transcriptional control of yeast gene expression under conditions of severe adenine starvation. Finally, the transcription pattern of genes adjacent to Ty1 insertions suggests that severe adenine starvation facilitates the initiation of transcription at alternative sites, partly located in the 5' LTR. We propose that Ty1-driven transcription of coding and noncoding sequences could regulate yeast gene expression in response to stress.

Warped unification, proton stability, and dark matter.

We show that solving the problem of baryon-number violation in nonsupersymmetric grand unified theories (GUT's) in warped higher-dimensional spacetime can lead to a stable Kaluza-Klein particle. This exotic particle has gauge quantum numbers of a right-handed neutrino, but carries fractional baryon number and is related to the top quark within the higher-dimensional GUT. A combination of baryon number and SU(3) color ensures its stability. Its relic density can easily be of the right value for masses in the 10 GeV-few TeV range. An exciting aspect of these models is that the entire parameter space will be tested at near future dark matter direct detection experiments. Other exotic GUT partners of the top quark are also light and can be produced at high energy colliders with distinctive signatures.