Hyeshik Chang

Publication date: 5 April 2018
Source:Molecular Cell, Volume 70, Issue 1
Author(s): Hyeshik Chang, Jinah Yeo, Jeong-gyun Kim, Hyunjoon Kim, Jaechul Lim, Mihye Lee, Hyun Ho Kim, Jiyeon Ohk, Hee-Yeon Jeon, Hyunsook Lee, Hosung Jung, Kyu-Won Kim, V. Narry Kim
During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3′ modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.

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Teaser

An embryo begins its life with maternally deposited RNAs that undergo timely translation and degradation. Chang et al. show that terminal uridylyltransferases add uridine tails to trigger decay of short poly(A)-tailed RNAs and that uridylation is critical for temporal organization of transcriptome in early vertebrate embryos.

Publication date: 1 December 2016
Source:Cell, Volume 167, Issue 6
Author(s): Christoph A. Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A. Jaitin, Eyal David, Deborah R. Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day. This diurnal microbial behavior drives, in turn, the global programming of the host circadian transcriptional, epigenetic, and metabolite oscillations. Surprisingly, disruption of homeostatic microbiome rhythmicity not only abrogates normal chromatin and transcriptional oscillations of the host, but also incites genome-wide de novo oscillations in both intestine and liver, thereby impacting diurnal fluctuations of host physiology and disease susceptibility. As such, the rhythmic biogeography and metabolome of the intestinal microbiota regulates the temporal organization and functional outcome of host transcriptional and epigenetic programs.

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Teaser

Diurnal oscillations in microbial localization and metabolite production in the gut have a major impact on the circadian epigenetic and transcriptional landscape of host tissues, not only locally, but also at distant sites such as the liver.

The pressure to publish pushes down quality

Nature 533, 7602 (2016). http://www.nature.com/doifinder/10.1038/533147a

Author: Daniel Sarewitz

Scientists must publish less, says Daniel Sarewitz, or good research will be swamped by the ever-increasing volume of poor work.

Publication date: 5 May 2016
Source:Cell, Volume 165, Issue 4
Author(s): Caleb Weinreb, Adam J. Riesselman, John B. Ingraham, Torsten Gross, Chris Sander, Debora S. Marks
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA gene sequences. We mine the evolutionary sequence record to derive precise information about the function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions—e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by increasing sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA.

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Teaser

The evolutionary signals for RNA 3D structure and interactions are detected by applying new algorithms to the analysis of thousands of genomes. This approach pinpoints an important interaction for HIV genome transport and predicts 3D contacts for hundreds of RNAs with unknown structure.

Post-transcriptional regulation of mRNAs plays an essential role in the control of gene expression. mRNAs are regulated in ribonucleoprotein (RNP) complexes by RNA-binding proteins (RBPs) along with associated protein and noncoding RNA (ncRNA) cofactors. A global understanding of post-transcriptional control in any cell type requires identification of the components of all of its RNP complexes. We have previously shown that these complexes can be purified by immunoprecipitation using anti-RBP synthetic antibodies produced by phage display. To develop the large number of synthetic antibodies required for a global analysis of RNP complex composition, we have established a pipeline that combines (i) a computationally aided strategy for design of antigens located outside of annotated domains, (ii) high-throughput antigen expression and purification in Escherichia coli, and (iii) high-throughput antibody selection and screening. Using this pipeline, we have produced 279 antibodies against 61 different protein components of Drosophila melanogaster RNPs. Together with those produced in our low-throughput efforts, we have a panel of 311 antibodies for 67 RNP complex proteins. Tests of a subset of our antibodies demonstrated that 89% immunoprecipitate their endogenous target from embryo lysate. This panel of antibodies will serve as a resource for global studies of RNP complexes in Drosophila. Furthermore, our high-throughput pipeline permits efficient production of synthetic antibodies against any large set of proteins.

Nature Methods 13, 269 (2016). doi:10.1038/nmeth.3742

Authors: Andreas P Frei, Felice-Alessio Bava, Eli R Zunder, Elena W Y Hsieh, Shih-Yu Chen, Garry P Nolan & Pier Federico Gherardini

Nature Methods 13, 185 (2016). doi:10.1038/nmeth.3798

Scientific disagreement prompts a closer look at data and can promote unexpected insights.

A simple rule governs the evolution and development of hominin tooth size

Nature 530, 7591 (2016). doi:10.1038/nature16972

Authors: Alistair R. Evans, E. Susanne Daly, Kierstin K. Catlett, Kathleen S. Paul, Stephen J. King, Matthew M. Skinner, Hans P. Nesse, Jean-Jacques Hublin, Grant C. Townsend, Gary T. Schwartz & Jukka Jernvall

The variation in molar tooth size in humans and our closest relatives (hominins) has strongly influenced our view of human evolution. The reduction in overall size and disproportionate decrease in third molar size have been noted for over a century, and have been attributed to reduced selection for large dentitions owing to changes in diet or the acquisition of cooking. The systematic pattern of size variation along the tooth row has been described as a ‘morphogenetic gradient’ in mammal, and more specifically hominin, teeth since Butler and Dahlberg. However, the underlying controls of tooth size have not been well understood, with hypotheses ranging from morphogenetic fields to the clone theory. In this study we address the following question: are there rules that govern how hominin tooth size evolves? Here we propose that the inhibitory cascade, an activator–inhibitor mechanism that affects relative tooth size in mammals, produces the default pattern of tooth sizes for all lower primary postcanine teeth (deciduous premolars and permanent molars) in hominins. This configuration is also equivalent to a morphogenetic gradient, finally pointing to a mechanism that can generate this gradient. The pattern of tooth size remains constant with absolute size in australopiths (including Ardipithecus, Australopithecus and Paranthropus). However, in species of Homo, including modern humans, there is a tight link between tooth proportions and absolute size such that a single developmental parameter can explain both the relative and absolute sizes of primary postcanine teeth. On the basis of the relationship of inhibitory cascade patterning with size, we can use the size at one tooth position to predict the sizes of the remaining four primary postcanine teeth in the row for hominins. Our study provides a development-based expectation to examine the evolution of the unique proportions of human teeth.

Publication date: March 2016
Source:Trends in Biotechnology, Volume 34, Issue 3
Author(s): Jameson K. Rogers, George M. Church
Biotechnology is the manufacturing technology of the future. However, engineering biology is complex, and many possible genetic designs must be evaluated to find cells that produce high levels of a desired drug or chemical. Recent advances have enabled the design and construction of billions of genetic variants per day, but evaluation capacity remains limited to thousands of variants per day. Here we evaluate biological engineering through the lens of the design–build–test cycle framework and highlight the role that multiplexing has had in transforming the design and build steps. We describe a multiplexed solution to the ‘test’ step that is enabled by new research. Achieving a multiplexed test step will permit a fully multiplexed engineering cycle and boost the throughput of biobased product development by up to a millionfold.

Biologists urged to hug a preprint

Nature 530, 7590 (2016). http://www.nature.com/doifinder/10.1038/530265a

Authors: Ewen Callaway & Kendall Powell

ASAPbio meeting discusses the ins and outs of posting work online before peer review.

Marvin L. Minsky (1927–2016)

Nature 530, 7590 (2016). doi:10.1038/530282a

Author: Patrick Henry Winston

A founding father of artificial intelligence.

Physics: Post-PhD job stability

Nature 530, 7590 (2016). doi:10.1038/nj7590-373b

Fewer than one-third of physics PhD graduates take permanent jobs, and that is a record high.

RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.

Purine biosynthetic enzymes organize into dynamic cellular bodies called purinosomes. Little is known about the spatiotemporal control of these structures. Using super-resolution microscopy, we demonstrated that purinosomes colocalized with mitochondria, and these results were supported by isolation of purinosome enzymes with mitochondria. Moreover, the number of purinosome-containing cells responded to dysregulation of mitochondrial function and metabolism. To explore the role of intracellular signaling, we performed a kinome screen using a label-free assay and found that mechanistic target of rapamycin (mTOR) influenced purinosome assembly. mTOR inhibition reduced purinosome-mitochondria colocalization and suppressed purinosome formation stimulated by mitochondria dysregulation. Collectively, our data suggest an mTOR-mediated link between purinosomes and mitochondria, and a general means by which mTOR regulates nucleotide metabolism by spatiotemporal control over protein association. Authors: Jarrod B. French, Sara A. Jones, Huayun Deng, Anthony M. Pedley, Doory Kim, Chung Yu Chan, Haibei Hu, Raymond J. Pugh, Hong Zhao, Youxin Zhang, Tony Jun Huang, Ye Fang, Xiaowei Zhuang, Stephen J. Benkovic

In response to growth signals, mechanistic target of rapamycin complex 1 (mTORC1) stimulates anabolic processes underlying cell growth. We found that mTORC1 increases metabolic flux through the de novo purine synthesis pathway in various mouse and human cells, thereby influencing the nucleotide pool available for nucleic acid synthesis. mTORC1 had transcriptional effects on multiple enzymes contributing to purine synthesis, with expression of the mitochondrial tetrahydrofolate (mTHF) cycle enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) being closely associated with mTORC1 signaling in both normal and cancer cells. MTHFD2 expression and purine synthesis were stimulated by activating transcription factor 4 (ATF4), which was activated by mTORC1 independent of its canonical induction downstream of eukaryotic initiation factor 2α eIF2α phosphorylation. Thus, mTORC1 stimulates the mTHF cycle, which contributes one-carbon units to enhance production of purine nucleotides in response to growth signals. Authors: Issam Ben-Sahra, Gerta Hoxhaj, Stéphane J. H. Ricoult, John M. Asara, Brendan D. Manning

Publication date: 11 February 2016
Source:Cell, Volume 164, Issue 4
Author(s): Erin E. Heyer, Melissa J. Moore
Fully assembled ribosomes exist in two populations: polysomes and monosomes. While the former has been studied extensively, to what extent translation occurs on monosomes and its importance for overall translational output remain controversial. Here, we used ribosome profiling to examine the translational status of 80S monosomes in Saccharomyces cerevisiae. We found that the vast majority of 80S monosomes are elongating, not initiating. Further, most mRNAs exhibit some degree of monosome occupancy, with monosomes predominating on nonsense-mediated decay (NMD) targets, upstream open reading frames (uORFs), canonical ORFs shorter than ∼590 nt, and ORFs for which the total time required to complete elongation is substantially shorter than that required for initiation. Importantly, mRNAs encoding low-abundance regulatory proteins tend to be enriched in the monosome fraction. Our data highlight the importance of monosomes for the translation of highly regulated mRNAs.

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Ribosome profiling in Saccharomyces cerevisiae reveals that the vast majority of 80S monosomes actively contribute to the translation of nonsense-mediated decay targets, open reading frames for which elongation time is substantially shorter than initiation time, and mRNAs encoding low-abundance regulatory proteins.

Publication date: 11 February 2016
Source:Cell, Volume 164, Issue 4
Author(s): Xinping Yang, Jasmin Coulombe-Huntington, Shuli Kang, Gloria M. Sheynkman, Tong Hao, Aaron Richardson, Song Sun, Fan Yang, Yun A. Shen, Ryan R. Murray, Kerstin Spirohn, Bridget E. Begg, Miquel Duran-Frigola, Andrew MacWilliams, Samuel J. Pevzner, Quan Zhong, Shelly A. Trigg, Stanley Tam, Lila Ghamsari, Nidhi Sahni, Song Yi, Maria D. Rodriguez, Dawit Balcha, Guihong Tan, Michael Costanzo, Brenda Andrews, Charles Boone, Xianghong J. Zhou, Kourosh Salehi-Ashtiani, Benoit Charloteaux, Alyce A. Chen, Michael A. Calderwood, Patrick Aloy, Frederick P. Roth, David E. Hill, Lilia M. Iakoucheva, Yu Xia, Marc Vidal
While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative “isoforms” are functionally divergent (i.e., “functional alloforms”).

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Teaser

Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.

Related Articles

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.

Nat Methods. 2016 Jan 18;

Authors: Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP

Abstract
Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-utility analysis tasks.

PMID: 26780094 [PubMed - as supplied by publisher]

Translated regions distinct from annotated coding sequences have emerged as essential elements of the proteome. This includes upstream open reading frames (uORFs) present in mRNAs controlled by the integrated stress response (ISR) that show “privileged” translation despite inhibited eukaryotic initiation factor 2–guanosine triphosphate–initiator methionyl transfer RNA (eIF2·GTP·Met-tRNAiMet). We developed tracing translation by T cells to directly measure the translation products of uORFs during the ISR. We identified signature translation events from uORFs in the 5′ untranslated region of binding immunoglobulin protein (BiP) mRNA (also called heat shock 70-kilodalton protein 5 mRNA) that were not initiated at the start codon AUG. BiP expression during the ISR required both the alternative initiation factor eIF2A and non–AUG-initiated uORFs. We propose that persistent uORF translation, for a variety of chaperones, shelters select mRNAs from the ISR, while simultaneously generating peptides that could serve as major histocompatibility complex class I ligands, marking cells for recognition by the adaptive immune system. Authors: Shelley R. Starck, Jordan C. Tsai, Keling Chen, Michael Shodiya, Lei Wang, Kinnosuke Yahiro, Manuela Martins-Green, Nilabh Shastri, Peter Walter

Next-generation RNA sequencing (RNA-seq) has revolutionized our ability to analyze transcriptomes. Current RNA-seq methods are highly reproducible, but each has biases resulting from different modes of RNA sample preparation, reverse transcription, and adapter addition, leading to variability between methods. Moreover, the transcriptome cannot be profiled comprehensively because highly structured RNAs, such as tRNAs and snoRNAs, are refractory to conventional RNA-seq methods. Recently, we developed a new method for strand-specific RNA-seq using thermostable group II intron reverse transcriptases (TGIRTs). TGIRT enzymes have higher processivity and fidelity than conventional retroviral reverse transcriptases plus a novel template-switching activity that enables RNA-seq adapter addition during cDNA synthesis without using RNA ligase. Here, we obtained TGIRT-seq data sets for well-characterized human RNA reference samples and compared them to previous data sets obtained for these RNAs by the Illumina TruSeq v2 and v3 methods. We find that TGIRT-seq recapitulates the relative abundance of human transcripts and RNA spike-ins in ribo-depleted, fragmented RNA samples comparably to non-strand-specific TruSeq v2 and better than strand-specific TruSeq v3. Moreover, TGIRT-seq is more strand specific than TruSeq v3 and eliminates sampling biases from random hexamer priming, which are inherent to TruSeq. The TGIRT-seq data sets also show more uniform 5' to 3' gene coverage and identify more splice junctions, particularly near the 5' ends of mRNAs, than do the TruSeq data sets. Finally, TGIRT-seq enables the simultaneous profiling of mRNAs and lncRNAs in the same RNA-seq experiment as structured small ncRNAs, including tRNAs, which are essentially absent with TruSeq.

Nature Methods 13, 107 (2016). doi:10.1038/nmeth.3741

Authors: Laura C Lazzeroni, Ying Lu & Ilana Belitskaya-Lévy

Publication date: 28 January 2016
Source:Cell, Volume 164, Issue 3
Author(s): Ron Sender, Shai Fuchs, Ron Milo
It is often presented as common knowledge that, in the human body, bacteria outnumber human cells by a ratio of at least 10:1. Revisiting the question, we find that the ratio is much closer to 1:1.

Teaser

It is often presented as common knowledge that, in the human body, bacteria outnumber human cells by a ratio of at least 10:1. Revisiting the question, we find that the ratio is much closer to 1:1.

Publication date: 11 February 2016
Source:Cell, Volume 164, Issue 4
Author(s): Leonardo Morsut, Kole T. Roybal, Xin Xiong, Russell M. Gordley, Scott M. Coyle, Matthew Thomson, Wendell A. Lim
The Notch protein is one of the most mechanistically direct transmembrane receptors—the intracellular domain contains a transcriptional regulator that is released from the membrane when engagement of the cognate extracellular ligand induces intramembrane proteolysis. We find that chimeric forms of Notch, in which both the extracellular sensor module and the intracellular transcriptional module are replaced with heterologous protein domains, can serve as a general platform for generating novel cell-cell contact signaling pathways. Synthetic Notch (synNotch) pathways can drive user-defined functional responses in diverse mammalian cell types. Because individual synNotch pathways do not share common signaling intermediates, the pathways are functionally orthogonal. Thus, multiple synNotch receptors can be used in the same cell to achieve combinatorial integration of environmental cues, including Boolean response programs, multi-cellular signaling cascades, and self-organized cellular patterns. SynNotch receptors provide extraordinary flexibility in engineering cells with customized sensing/response behaviors to user-specified extracellular cues. Video Abstract

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Modular synthetic Notch receptors (synNotch) provide extraordinary flexibility in engineering mammalian cells with customized sensing/response behaviors to achieve combinatorial integration of user-specified environmental cues.

Publication date: 11 February 2016
Source:Cell, Volume 164, Issue 4
Author(s): Kole T. Roybal, Levi J. Rupp, Leonardo Morsut, Whitney J. Walker, Krista A. McNally, Jason S. Park, Wendell A. Lim
T cells can be re-directed to kill cancer cells using chimeric antigen receptors (CARs) or T cell receptors (TCRs). This approach, however, is constrained by the rarity of tumor-specific single antigens. Targeting antigens also found on bystander tissues can cause life-threatening adverse effects. A powerful way to enhance ON-target activity of therapeutic T cells is to engineer them to require combinatorial antigens. Here, we engineer a combinatorially activated T cell circuit in which a synthetic Notch receptor for one antigen induces the expression of a CAR for a second antigen. These dual-receptor AND-gate T cells are only armed and activated in the presence of dual antigen tumor cells. These T cells show precise therapeutic discrimination in vivo—sparing single antigen “bystander” tumors while efficiently clearing combinatorial antigen “disease” tumors. This type of precision dual-receptor circuit opens the door to immune recognition of a wider range of tumors. Video Abstract

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T cells engineered with dual-receptor circuits that recognize combinations of antigens can efficiently kill target tumor cells in vivo, while sparing bystander cells.

If you are a Williams or Johnson—among the most common surnames in the United States—it can be tricky to find you on the Internet, especially if you also have a common first name such as Mary or James. For academic researchers, whose careers are measured largely by authorship on papers, name ambiguity can be a killer. Some clarity, however, is now in sight. In a letter released online 7 January, some of the world's largest academic publishers and scientific societies announced that they will not just encourage, but ultimately require, researchers to sign up with ORCID, a nonprofit organization that assigns members a 16-digit identifier. Author: John Bohannon

Nature advance online publication 20 January 2016. doi:10.1038/nature16547

Authors: Alexander J. Westermann, Konrad U. Förstner, Fabian Amman, Lars Barquist, Yanjie Chao, Leon N. Schulte, Lydia Müller, Richard Reinhardt, Peter F. Stadler & Jörg Vogel

Codon influence on protein expression in E. coli correlates with mRNA levels

Nature 529, 7586 (2016). doi:10.1038/nature16509

Authors: Grégory Boël, Reka Letso, Helen Neely, W. Nicholson Price, Kam-Ho Wong, Min Su, Jon D. Luff, Mayank Valecha, John K. Everett, Thomas B. Acton, Rong Xiao, Gaetano T. Montelione, Daniel P. Aalberts & John F. Hunt

Degeneracy in the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, has an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the sequence features influencing

Paper craft

Nature 529, 7586 (2016). doi:10.1038/nj7586-427a

Authors: Dmitry Budker & Derek Jackson Kimball

Consensus with co-authors is vital when writing up research, say Dmitry Budker and Derek Jackson Kimball.

Publication date: 14 January 2016
Source:Cell, Volume 164, Issues 1–2
Author(s): Matthew W. Snyder, Martin Kircher, Andrew J. Hill, Riza M. Daza, Jay Shendure
Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo nucleosome occupancy and found that short cfDNA fragments harbor footprints of transcription factors. The cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin. Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how nucleosome footprints can be used to infer cell types contributing to cfDNA in pathological states such as cancer. Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible. PaperClip

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Teaser

Deep sequencing of circulating cell-free DNA yields a dense, genome-wide map of nucleosome occupancy that enables identification of its cell-types of origin, potentially enabling the noninvasive monitoring of a much broader set of clinical conditions than currently possible.

Amyloid-like protein aggregation is associated with neurodegeneration and other pathologies. The nature of the toxic aggregate species and their mechanism of action remain elusive. Here, we analyzed the compartment specificity of aggregate toxicity using artificial β-sheet proteins, as well as fragments of mutant huntingtin and TAR DNA binding protein–43 (TDP-43). Aggregation in the cytoplasm interfered with nucleocytoplasmic protein and RNA transport. In contrast, the same proteins did not inhibit transport when forming inclusions in the nucleus at or around the nucleolus. Protein aggregation in the cytoplasm, but not the nucleus, caused the sequestration and mislocalization of proteins containing disordered and low-complexity sequences, including multiple factors of the nuclear import and export machinery. Thus, impairment of nucleocytoplasmic transport may contribute to the cellular pathology of various aggregate deposition diseases. Authors: Andreas C. Woerner, Frédéric Frottin, Daniel Hornburg, Li R. Feng, Felix Meissner, Maria Patra, Jörg Tatzelt, Matthias Mann, Konstanze F. Winklhofer, F. Ulrich Hartl, Mark S. Hipp