Wednesday, March 1, 2017

Nature Methods Contents: March 2017 Volume 14 pp 209 - 323

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Nature Methods

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March 2017 Volume 14, Issue 3

In This Issue
This Month
Research Highlights
Technology Feature
News and Views
Brief Communications


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In This Issue


In This Issue



Responsible referencing   p209
Careful construction of reference lists is the responsibility of every scientist.

This Month


The Author File: Bart Deplancke   p211
Vivien Marx
An engineered approach to study gene regulation, and why home is where the heart is.

Points of Significance: Interpreting P values   pp213 - 214
Naomi Altman and Martin Krzywinski
A P value measures a sample's compatibility with a hypothesis, not the truth of the hypothesis.



Should we ignore western blots when selecting antibodies for other applications?   p215
Fridtjof Lund-Johansen and Michael D Browning

See also: Correspondence by Uhlen

Response to: Should we ignore western blots when selecting antibodies for other applications?   pp215 - 216
Mathias Uhlen

See also: Correspondence by Lund-Johansen & Browning

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses   pp216 - 217
Shijie C Zheng, Stephan Beck, Andrew E Jaffe, Devin C Koestler, Kasper D Hansen et al.

See also: Correspondence by Rahmani et al. | Correspondence

Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation   pp218 - 219
Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu et al.

See also: Correspondence by Zheng et al. | Correspondence

Editor's note on Zheng et al. and Rahmani et al.   p219

See also: Correspondence by Zheng et al. | Correspondence by Rahmani et al.

Research Highlights


Taking nanoscopy to the limit
MINFLUX nanoscopy can obtain 1-nm localization precision with orders of magnitude fewer emitted photons.

Cerebral organoids enter the fold
Two groups use cerebral organoids to model brain development and disease.

Another player for RNA-guided RNA cleavage
Cas13b relies on activator and repressor proteins to regulate RNA cleavage.

Precision switches for protein control
Light- or drug-dependent switches enable precise control over signaling pathways in living cells.

Protein holography
Low-energy holography enables imaging single proteins and protein complexes.

Methods in Brief

Improved 3D single-molecule imaging | Cell-based fragment screening | Biomechanical properties measured in vivo | Faster Bayesian localization microscopy

Tools in Brief

CRiNCL unveils noncoding RNA functions | Crystal Skull—a panoramic view of the brain | Microbial genomes on a chip | Sequence covariation predicts the effects of mutation

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EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research   pp228 - 232
EV-TRACK Consortium:  Jan Van Deun, Pieter Mestdagh, Patrizia Agostinis, Ozden Akay et al.

Technology Feature


Cell biology: tracking a cell's cycle   pp233 - 236
Vivien Marx
The tools that clock a cell's everyday affairs reveal plenty that's out of the ordinary.

News and Views


Genetic screening enters the single-cell era   pp237 - 238
Daniel E Wagner and Allon M Klein
Four studies overcome the limitations of pooled and arrayed genetic screens by integrating single-cell transcriptomics.

See also: Article by Datlinger et al.

Stratifying tissue heterogeneity with scalable single-cell assays   pp238 - 239
Kun Zhang
Three methods dramatically improve the scale of single-cell genomic sequencing and structural assays, allowing for the hierarchical partitioning of cell populations within a tissue.

See also: Brief Communication by Ramani et al. | Article by Vitak et al.

Synthetic human proteomes for accelerating protein research   pp240 - 242
Yasset Perez-Riverol and Juan Antonio Vizcaino
The generation of synthetic human proteomes and future derived tools will expand knowledge in protein biology.

See also: Resource by Matsumoto et al. | Brief Communication by Zolg et al.



A guide to designing germline-dependent epigenetic inheritance experiments in mammals   pp243 - 249
Johannes Bohacek and Isabelle M Mansuy
This Review discusses key aspects of experimental design to evaluate intergenerational and transgenerational epigenetic inheritance. It describes advantages of patrilineal and matrilineal design, and it offers advice for selecting animals for breeding and for determining the weaning scheme and group size.



A large-scale targeted proteomics assay resource based on an in vitro human proteome   pp251 - 258
Masaki Matsumoto, Fumiko Matsuzaki, Kiyotaka Oshikawa, Naoki Goshima, Masatoshi Mori et al.
A large-scale resource, iMPAQT, provides multiple reaction monitoring (MRM)-mass spectrometry assays for targeted quantitative analysis of mTRAQ-labeled human proteins.

See also: News and Views by Perez-Riverol & Vizcaino

Brief Communications


Building ProteomeTools based on a complete synthetic human proteome   pp259 - 262
Daniel P Zolg, Mathias Wilhelm, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute et al.
The ProteomeTools project provides the proteomics community with a physical synthetic tryptic peptide resource and a digital LC-MS/MS data resource covering all human proteins.

See also: News and Views by Perez-Riverol & Vizcaino

Massively multiplex single-cell Hi-C   pp263 - 266
Vijay Ramani, Xinxian Deng, Ruolan Qiu, Kevin L Gunderson, Frank J Steemers et al.
Single-cell combinatorial indexed Hi-C (sciHi-C) is a streamlined protocol for generating thousands of high-quality single-cell chromosome conformation data sets that resemble bulk Hi-C data in aggregate.

See also: News and Views by Zhang

Effective detection of variation in single-cell transcriptomes using MATQ-seq   pp267 - 270
Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng and Chenghang Zong
MATQ-seq is a highly sensitive single-cell RNA-seq protocol that enables the detection of true subtle biological variations among single cells as well as the capture of nonpolyadenylated RNA.

Optogenetic inhibition of behavior with anion channelrhodopsins   pp271 - 274
Farhan Mohammad, James C Stewart, Stanislav Ott, Katarina Chlebikova, Jia Yi Chua et al.
Anion channelrhodopsins are light-sensitive chloride channels that can be used as optogenetic inhibitors. Mohammad et al. report their application in Drosophila, showing that various behaviors can be inhibited in a light-dependent manner.

Characterizing cell subsets using marker enrichment modeling   pp275 - 278
Kirsten E Diggins, Allison R  Greenplate, Nalin Leelatian, Cara E Wogsland and Jonathan M Irish
Marker enrichment modeling (MEM) provides an objective metric for characterizing cell populations from high-content single-cell analysis. The MEM score outperforms standard metrics and provides a machine-readeable label for cell subsets.

Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies   pp279 - 282
Michele Chirichella, Simonetta Lisi, Marco Fantini, Martina Goracci, Mariantonietta Calvello et al.
PISA, generates intrabodies that selectively bind and interfere with the intracellular function of an acetylated version of a target protein.

High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles   pp283 - 286
Michiel van de Waterbeemd, Kyle L Fort, Dmitriy Boll, Maria Reinhardt-Szyba, Andrew Routh et al.
Instrumental modifications enable native mass spectrometry analysis with unprecedented mass resolution, especially at high mass-to-charge ratios, as illustrated through the analysis of intact ribosome particles.

One-step generation of conditional and reversible gene knockouts   pp287 - 289
Amanda Andersson-Rolf, Roxana C Mustata, Alessandra Merenda, Jihoon Kim, Sajith Perera et al.
The combination of knocking one allele out with CRISPR-mediated NHEJ and targeting the other with a conditionally inactivating cassette allows rapid generation of conditional alleles.

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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination   pp290 - 296
Ali Punjani, John L Rubinstein, David J Fleet and Marcus A Brubaker
A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.

Pooled CRISPR screening with single-cell transcriptome readout   pp297 - 301
Paul Datlinger, Andre F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler et al.
CROP-seq enables pooled CRISPR screens for complex transcriptome signatures by making gRNA expression detectable in single-cell RNA sequencing.

See also: News and Views by Wagner & Klein

Sequencing thousands of single-cell genomes with combinatorial indexing   pp302 - 308
Sarah A Vitak, Kristof A Torkenczy, Jimi L Rosenkrantz, Andrew J Fields, Lena Christiansen et al.
Single-cell combinatorial indexed sequencing (SCI-seq) resolves genomic heterogeneity by generating thousands of low-pass single-cell libraries at once for somatic copy number variant detection.

See also: News and Views by Zhang

Single-cell mRNA quantification and differential analysis with Census   pp309 - 315
Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma et al.
The Census tool converts single-cell RNA-seq relative read counts to relative transcript counts for more accurate differential gene expression and analysis in the absence of spike-ins or molecular barcodes.

SMiLE-seq identifies binding motifs of single and dimeric transcription factors   pp316 - 322
Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern et al.
The Microfluidic-based Ligand Enrichment (SMiLE) sequencing strategy probes DNA binding of single and heterodimeric transcription factors over a wide affinity range.



Corrigendum: eC-CLEM: flexible multidimensional registration software for correlative microscopies   p323
Perrine Paul-Gilloteaux, Xavier Heiligenstein, Martin Belle, Marie-Charlotte Domart, Banafshe Larijani et al.



Erratum: Faster brain imaging   p323
Nina Vogt

Erratum: Epitranscriptome sequencing technologies: decoding RNA modifications   p323
Xiaoyu Li, Xushen Xiong and Chengqi Yi

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