High Throughput Discovery

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

Thu, 06/21/2018 - 00:00
Wang X, Allen WE, Wright MA, Sylwestrak EL, Samusik N, Vesuna S, Evans K, Liu C, Ramakrishnan C1, Liu J, Nolan GP, Bava FA6, Deisseroth K.
Science. 2018 Jun 21. pii: eaat5691. doi: 10.1126/science.aat5691. [Epub ahead of print]
Theodore Roth
Time
12:00pm

 

Retrieving high-content gene-expression information while retaining 3D positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. Here we develop and apply a technology for 3D intact-tissue RNA sequencing, termed STARmap (Spatially-resolved Transcript Amplicon Readout Mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1,020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy and reproducibility. Moving to thick tissue blocks, we observed a molecularly-defined gradient distribution of excitatory-neuron subtypes across cubic millimeter-scale volumes (>30,000 cells), and discovered a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.

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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain by scGESTALT

Thu, 10/19/2017 - 00:00
Bushra Raj, Daniel E. Wagner, Aaron McKenna, Shristi Pandey1, Allon M. Klein, Jay Shendure, James A. Gagnon, Alexander F. Schier.
bioRxiv preprint first posted online Oct. 19, 2017; doi: http://dx.doi.org/10.1101/205534. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC 4.0 International license.
Malin Akerblom
Time
12:00pm

Hundreds of cell types are generated during development, but their lineage relationships are largely elusive. Here we report a technology, scGESTALT, which combines cell type identification by single-cell RNA sequencing with lineage recording by cumulative barcode editing. We sequenced ~60,000 transcriptomes from the juvenile zebrafish brain and identified more than 100 cell types and marker genes. We engineered an inducible system that combines early and late barcode editing and isolated thousands of single-cell transcriptomes and their associated barcodes. The large diversity of edited barcodes and cell types enabled the generation of lineage trees with hundreds of branches. Inspection of lineage trajectories identified restrictions at the level of cell types and brain regions and helped uncover gene expression cascades during differentiation. These results establish scGESTALT as a new and widely applicable tool to simultaneously characterize the molecular identities and lineage histories of thousands of cells during development and disease.

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A microRNA screen reveals that elevated hepatic ectodysplasin A expression contributes to obesity-induced insulin resistance in skeletal muscle

Fri, 12/01/2017 - 00:00
Awazawa M1,2,3, Gabel P1,2,3, Tsaousidou E1,2,3, Nolte H3, Krüger M3, Schmitz J1,2,3, Ackermann PJ1,2,3, Brandt C1,2,3, Altmüller J4,5, Motameny S4, Wunderlich FT1, Kornfeld JW1,3, Blüher M6, Brüning JC1,2,3,7.
Nat Med. 2017 Dec;23(12):1466-1473. doi: 10.1038/nm.4420. Epub 2017 Nov 6.
Roman Camarda
Time
12:00pm

Over 40% of microRNAs (miRNAs) are located in introns of protein-coding genes, and many of these intronic miRNAs are co-regulated with their host genes. In such cases of co-regulation, the products of host genes and their intronic miRNAs can cooperate to coordinately regulate biologically important pathways. Therefore, we screened intronic miRNAs dysregulated in the livers of mouse models of obesity to identify previously uncharacterized protein-coding host genes that may contribute to the pathogenesis of obesity-associated insulin resistance and type 2 diabetes mellitus. Our approach revealed that expression of both the gene encoding ectodysplasin A (Eda), the causal gene in X-linked hypohidrotic ectodermal dysplasia (XLHED), and its intronic miRNA, miR-676, was increased in the livers of obese mice. Moreover, hepatic EDA expression is increased in obese human subjects and reduced upon weight loss, and its hepatic expression correlates with systemic insulin resistance. We also found that reducing miR-676 expression in db/db mice increases the expression of proteins involved in fatty acid oxidation and reduces the expression of inflammatory signaling components in the liver. Further, we found that Eda expression in mouse liver is controlled via PPARγ and RXR-α, increases in circulation under conditions of obesity, and promotes JNK activation and inhibitory serine phosphorylation of IRS1 in skeletal muscle. In accordance with these findings, gain- and loss-of-function approaches reveal that liver-derived EDA regulates systemic glucose metabolism, suggesting that EDA is a hepatokine that can contribute to impaired skeletalmuscle insulin sensitivity in obesity.

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High-resolution interrogation of functional elements in the noncoding genome

Fri, 09/30/2016 - 00:00
Neville E. Sanjana1,2,*,†,‡, Jason Wright1,2,†, Kaijie Zheng1,2, Ophir Shalem1,2, Pierre Fontanillas1, Julia Joung1,2, Christine Cheng1,3, Aviv Regev1,3, Feng
Science. 2016 Sep 30;353(6307):1545-1549.
Kol Jia Yong (UPDATE: New Article)
Time
12:00pm
The noncoding genome affects gene regulation and disease, yet we lack tools for rapid identification and manipulation of noncoding elements. We developed a CRISPR screen using ~18,000 single guide RNAs targeting >700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma. We find that noncoding locations that modulate drug resistance also harbor predictive hallmarks of noncoding function. With a subset of regions at the CUL3 locus, we demonstrate that engineered mutations alter transcription factor occupancy and long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. Through our expansion of the potential of pooled CRISPR screens, we provide tools for genomic discovery and for elucidating biologically relevant mechanisms of gene regulation.
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Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

Mon, 10/31/2016 - 00:00
Shiyou Zhu, Wei Li, Jingze Liu, Chen-Hao Chen, Qi Liao, Ping Xu, Han Xu, Tengfei Xiao, Zhongzheng Cao, Jingyu Peng, Pengfei Yuan, Myles Brown, Xiaole Shirley Liu & Wensheng Wei
Nat Biotechnol. 2016 Dec;34(12):1279-1286. doi: 10.1038/nbt.3715. Epub 2016 Oct 31.
Gabriel Eades
Time
12:00pm
CRISPR–Cas9 screens have been widely adopted to analyze coding-gene functions, but high-throughput screening of non-coding elements using this method is more challenging because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. We report a highthroughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library. Applying our screening method, we identified 51 lncRNAs that can positively or negatively regulate human cancer cell growth. We validated 9 of 51 lncRNA hits using CRISPR–Cas9-mediated genomic deletion, functional rescue, CRISPR activation or inhibition and gene-expression profiling. Our high-throughput pgRNA genome deletion method will enable rapid identification of functional mammalian non-coding elements.
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Molecular recordings by directed CRISPR spacer acquisition

Thu, 06/09/2016 - 00:00
Shipman SL1, Nivala J2, Macklis JD3, Church GM4.
Science. 2016 Jun 9. pii: aaf1175. [Epub ahead of print]
James Blau
Time
12:00pm
The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR-Cas system of E. coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes. We then applied directed evolution to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device.
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CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs

Thu, 04/07/2016 - 00:00
Mandegar MA1, Huebsch N2, Frolov EB3, Shin E3, Truong A3, Olvera MP3, Chan AH3, Miyaoka Y3, Holmes K3, Spencer CI3, Judge LM2, Gordon DE4, Eskildsen TV5, Villalta JE6, Horlbeck MA6, Gilbert LA6, Krogan NJ4, Sheikh SP5, Weissman JS6, Qi LS7, So PL3, Conklin BR8.
Cell Stem Cell.
Vanille Greiner
Time
12:00pm
Developing technologies for efficient and scalable disruption of gene expression will provide powerful tools for studying gene function, developmental pathways, and disease mechanisms. Here, we develop clustered regularly interspaced short palindromic repeat interference (CRISPRi) to repress gene expression in human induced pluripotent stem cells (iPSCs). CRISPRi, in which a doxycycline-inducible deactivated Cas9 is fused to a KRAB repression domain, can specifically and reversibly inhibit gene expression in iPSCs and iPSC-derived cardiac progenitors, cardiomyocytes, and T lymphocytes. This gene repression system is tunable and has the potential to silence single alleles. Compared with CRISPR nuclease (CRISPRn), CRISPRi gene repression is more efficient and homogenous across cell populations. The CRISPRi system in iPSCs provides a powerful platform to perform genome-scale screens in a wide range of iPSC-derived cell types, dissect developmental pathways, and model disease.
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Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

Mon, 01/11/2016 - 00:00
Korkmaz G1, Lopes R1, Ugalde AP1, Nevedomskaya E2, Han R1, Myacheva K1, Zwart W2, Elkon R1, Agami R1,3.
Nat Biotechnol.
Elenora De Klerk
Time
12:00pm
Systematic identification of noncoding regulatory elements has, to date, mainly relied on large-scale reporter assays that do not reproduce endogenous conditions. We present two distinct CRISPR-Cas9 genetic screens to identify and characterize functional enhancers in their native context. Our strategy is to target Cas9 to transcription factor binding sites in enhancer regions. We identified several functional enhancer elements and characterized the role of two of them in mediating p53 (TP53) and ERa (ESR1) gene regulation. Moreover, we show that a genomic CRISPR-Cas9 tiling screen can precisely map functional domains within enhancer elements. Our approach expands the utility of CRISPR-Cas9 to elucidate the functions of the noncoding genome
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Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes

Mon, 07/06/2015 - 00:00
Pfender S1, Kuznetsov V1, Pasternak M1, Tischer T1, Santhanam B1, Schuh M1.
Nature
Federica Franciosi
Time
12:00pm
During fertilization, an egg and a sperm fuse to form a new embryo. Eggs develop from oocytes in a process called meiosis. Meiosis in human oocytes is highly error-prone1,2, and defective eggs are the leading cause of pregnancy loss and several genetic disorders such as Down’s syndrome3–5. Which genes safeguard accurate progression through meiosis is largely unclear. Here we develop high-content phenotypic screening methods for the systematic identification of mammalian meiotic genes. We targeted 774 genes by RNA interference within follicle-enclosed mouse oocytes to block protein expression from an early stage of oocyte development onwards. We then analysed the function of several genes simultaneously by high-resolution imaging of chromosomes and microtubules in live oocytes and scored each oocyte quantitatively for 50 phenotypes, generating a comprehensive resource of meiotic gene function. The screen generated an unprecedented annotated data set of meiotic progression in 2,241 mammalian oocytes, which allowed us to analyse systematically which defects are linked to abnormal chromosome segregation during meiosis, identifying progression into anaphase with misaligned chromosomes as well as defects in spindle organization as risk factors. This study demonstrates how high-content screens can be performed in oocytes, and allows systematic studies of meiosis in mammals.
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