抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

/pdf/initial-sequencing-and-comparative-analysis-of-the-mouse-5a9n62pifj.pdf

Initial sequencing and comparative analysis of the mouse genome.

Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.

/pdf/gene-regulation-by-long-non-coding-rnas-and-its-biological-25d7y97amp.pdf

Gene regulation by long non-coding RNAs and its biological functions.

Hippo Pathway in Organ Size Control, Tissue Homeostasis, and Cancer.

Physical access to DNA is a highly dynamic property of chromatin that plays an essential role in establishing and maintaining cellular identity. The organization of accessible chromatin across the genome reflects a network of permissible physical interactions through which enhancers, promoters, insulators and chromatin-binding factors cooperatively regulate gene expression. This landscape of accessibility changes dynamically in response to both external stimuli and developmental cues, and emerging evidence suggests that homeostatic maintenance of accessibility is itself dynamically regulated through a competitive interplay between chromatin-binding factors and nucleosomes. In this Review, we examine how the accessible genome is measured and explore the role of transcription factors in initiating accessibility remodelling; our goal is to illustrate how chromatin accessibility defines regulatory elements within the genome and how these epigenetic features are dynamically established to control gene expression.

Chromatin accessibility and the regulatory epigenome.

The mammalian vomeronasal organ (VNO), a part of the olfactory system, detects pheromones--chemical signals that modulate social and reproductive behaviours. But the molecular receptors in the VNO that detect these chemosensory stimuli remain undefined. Candidate pheromone receptors are encoded by two distinct and complex superfamilies of genes, V1r and V2r (refs 3 and 4), which code for receptors with seven transmembrane domains. These genes are selectively expressed in sensory neurons of the VNO. However, there is at present no functional evidence for a role of these genes in pheromone responses. Here, using chromosome engineering technology, we delete in the germ line of mice an approximately 600-kilobase genomic region that contains a cluster of 16 intact V1r genes. These genes comprise two of the 12 described V1r gene families, and represent approximately 12% of the V1r repertoire. The mutant mice display deficits in a subset of VNO-dependent behaviours: the expression of male sexual behaviour and maternal aggression is substantially altered. Electrophysiologically, the epithelium of the VNO of such mice does not respond detectably to specific pheromonal ligands. The behavioural impairment and chemosensory deficit support a role of V1r receptors as pheromone receptors.

/pdf/deficient-pheromone-responses-in-mice-lacking-a-cluster-of-4fbo5uk9d4.pdf

Deficient pheromone responses in mice lacking a cluster of vomeronasal receptor genes

Zygotic Genome Activation in Vertebrates.

During early development, animal embryos depend on maternally deposited RNA until zygotic genes become transcriptionally active. Before this maternal-to-zygotic transition, many species execute rapid and synchronous cell divisions without growth phases or cell cycle checkpoints. The coordinated onset of transcription, cell cycle lengthening, and cell cycle checkpoints comprise the midblastula transition (MBT). A long-standing model in the frog, Xenopus laevis, posits that MBT timing is controlled by a maternally loaded inhibitory factor that is titrated against the exponentially increasing amount of DNA. To identify MBT regulators, we developed an assay using Xenopus egg extract that recapitulates the activation of transcription only above the DNA-to-cytoplasm ratio found in embryos at the MBT. We used this system to biochemically purify factors responsible for inhibiting transcription below the threshold DNA-to-cytoplasm ratio. This unbiased approach identified histones H3 and H4 as concentration-dependent inhibitory factors. Addition or depletion of H3/H4 from the extract quantitatively shifted the amount of DNA required for transcriptional activation in vitro. Moreover, reduction of H3 protein in embryos induced premature transcriptional activation and cell cycle lengthening, and the addition of H3/H4 shortened post-MBT cell cycles. Our observations support a model for MBT regulation by DNA-based titration and suggest that depletion of free histones regulates the MBT. More broadly, our work shows how a constant concentration DNA binding molecule can effectively measure the amount of cytoplasm per genome to coordinate division, growth, and development.

https://www.pnas.org/content/pnas/112/10/E1086.full.pdf

Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition

RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.

Introduction: A finite number of signaling pathways are repurposed during animal development to regulate an extraordinary array of cellular decisions. Elucidating context-specific mechanisms is crucial for understanding how cellular diversity is generated and for defining potential avenues of pathway misregulation during disease. The Hippo tumor suppressor pathway has been primarily studied in growth control where it inhibits the oncogenic transcriptional coactivator Yorkie (Yki) (YAP/TAZ in vertebrates). The Hippo pathway also functions in nongrowth contexts such as postmitotic fate specification. In the Drosophila visual system, R8 photoreceptor neurons terminally differentiate into one of two alternative subtypes that express either blue-light–sensitive Rhodopsin5 (Rh5) or green-light–sensitive Rhodopsin6 (Rh6). These mutually exclusive cell fates are established by the Hippo pathway kinase warts and the growth regulator gene melted, which repress each other’s expression. However, the mechanisms underlying the context-specific use of the Hippo pathway in postmitotic fate decisions remain unclear. Context-speciﬁc regulation by the Hippo signaling in postmitotic photoreceptors. The Hippo pathway uses negative feedback through its transcriptional effector Yki for homeostatic control of proliferation. In Drosophila eyes, two alternative fates of blue- versus green-sensitive R8 photoreceptors are regulated by antagonism between the growth regulator Melted and the Hippo pathway. Contrary to the growth mechanism, Yki positive feedback and a cell-type–restricted transcription factor network promote repurposing of the Hippo pathway for binary fate decisions. Methods: To define the regulatory mechanisms of Hippo-dependent cell fate decisions in Drosophila photoreceptor neurons, we used a combination of genetic epistasis analyses, in vivo cis-regulatory studies, a candidate gene RNA interference screen, and cell culture–based transcription assays Results: We show that the transcriptional output of the Hippo pathway in photoreceptor differentiation, as in cell proliferation, is mediated through the factors Yki and Scalloped. In contrast to growth control, where Yki limits its own activity by negative feedback, we identify two Yki positive-feedback mechanisms: In blue-sensitive Rh5 photoreceptors, Yki represses its own negative regulator warts, downstream of melted; Yki also promotes melted expression, which subsequently represses warts to further promote Yki function. Yki cooperates with the transcription factors Orthodenticle (Otd) and Traffic Jam (Tj) to promote melted expression and Rh5 photoreceptor fate. Otd and Tj, othologs of the mammalian OTX/CRX and MAF/NRL transcription factors, form an evolutionarily conserved transcriptional module for generating photoreceptor subtype diversity. We also show that the transcription factors Senseless and Pph13 create a permissive environment for Warts/Hippo signaling to promote the alternative “default” green-sensitive Rh6 fate. Hence, Hippo pathway function integrates with four cell-type–restricted transcription factors, each promoting genetically different aspects of R8 subtypes, such that Yki activity ultimately coordinates the binary fate decision between blue- and green-sensitive photoreceptors. Discussion: This work illustrates how molecular signaling pathways can adopt context-specific regulation. Yki positive feedback in the photoreceptor fate decision is opposite to the negative feedback found in Hippo growth control. These distinct network-level feedback mechanisms provide context-appropriate functions: homeostasis to fine-tune growth regulation and an all-or-nothing fate decision to ensure robust differentiation of sensory neuron subtypes. Altering network-level systems properties, such as positive or negative feedback, within biochemically conserved pathways may be broadly used to co-opt signaling networks for use in cellular contexts as distinct as proliferation and terminal differentiation.

http://science.sciencemag.org/content/sci/342/6155/1238016.full.pdf

David Jukam

Papers

Deficient pheromone responses in mice lacking a cluster of vomeronasal receptor genes

Zygotic Genome Activation in Vertebrates.

Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts.

Opposite feedbacks in the Hippo pathway for growth control and neural fate