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1. High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

Author:
Raychowdhury, Raktima,   et al.   ; Rabani, Michal; Jovanovic, Marko; Rooney, Michael; Stumpo, Deborah J.; Pauli, Andrea; Hacohen, Nir; Schier, Alexander F.; Blackshear, Perry J.; Friedman, Nir; Amit, Ido; Regev, Aviv;     Show all 12 Authors
Source:
Cell 2014 v.159 pp. 1698-1710
ISSN:
0092-8674
Subject:
Danio rerio; dendritic cells; embryogenesis; gene expression regulation; genes; mice; models; non-coding RNA; sequence analysis; transcription (genetics)
Abstract:
... Cells control dynamic transitions in transcript levels by regulating transcription, processing, and/or degradation through an integrated regulatory strategy. Here, we combine RNA metabolic labeling, rRNA-depleted RNA-seq, and DRiLL, a novel computational framework, to quantify the level; editing sites; and transcription, processing, and degradation rates of each transcript at a splice junction res ...
DOI:
10.1016/j.cell.2014.11.015
PubMed:
25497548
PubMed Central:
PMC4272607

2. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation

Author:
Raychowdhury, Raktima,   et al.   ; Fields, Alexander P.; Rodriguez, Edwin H.; Jovanovic, Marko; Stern-Ginossar, Noam; Haas, Brian J.; Mertins, Philipp; Hacohen, Nir; Carr, Steven A.; Ingolia, Nicholas T.; Regev, Aviv; Weissman, Jonathan S.;     Show all 12 Authors
Source:
Molecular cell 2015 v.60 pp. 816-827
ISSN:
1097-2765
Subject:
dendritic cells; fibroblasts; genomics; humans; mice; protein synthesis; proteins; regression analysis; ribosomes
Abstract:
... A fundamental goal of genomics is to identify the complete set of expressed proteins. Automated annotation strategies rely on assumptions about protein-coding sequences (CDSs), e.g., they are conserved, do not overlap, and exceed a minimum length. However, an increasing number of newly discovered proteins violate these rules. Here we present an experimental and analytical framework, based on ribos ...
DOI:
10.1016/j.molcel.2015.11.013
PubMed:
26638175
PubMed Central:
PMC4720255

3. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Author:
Raychowdhury, Raktima,   et al.   ; Parnas, Oren; Jovanovic, Marko; Eisenhaure, Thomas M.; Herbst, Rebecca H.; Dixit, Atray; Ye, Chun Jimmie; Przybylski, Dariusz; Platt, Randall J.; Tirosh, Itay; Sanjana, Neville E.; Shalem, Ophir; Satija, Rahul; Mertins, Philipp; Carr, Steven A.; Zhang, Feng; Hacohen, Nir; Regev, Aviv;     Show all 18 Authors
Source:
Cell 2015 v.162 pp. 675-686
ISSN:
0092-8674
Subject:
dendritic cells; genes; lipopolysaccharides; mammals; messenger RNA; pathogens; tumor necrosis factors
Abstract:
... Finding the components of cellular circuits and determining their functions systematically remains a major challenge in mammalian cells. Here, we introduced genome-wide pooled CRISPR-Cas9 libraries into dendritic cells (DCs) to identify genes that control the induction of tumor necrosis factor (Tnf) by bacterial lipopolysaccharide (LPS), a key process in the host response to pathogens, mediated by ...
DOI:
10.1016/j.cell.2015.06.059
PubMed:
26189680
PubMed Central:
PMC4522370

4. A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

Author:
Raychowdhury, Raktima,   et al.   ; Garber, Manuel; Yosef, Nir; Goren, Alon; Thielke, Anne; Guttman, Mitchell; Robinson, James; Minie, Brian; Chevrier, Nicolas; Itzhaki, Zohar; Blecher-Gonen, Ronnie; Bornstein, Chamutal; Amann-Zalcenstein, Daniela; Weiner, Assaf; Friedrich, Dennis; Meldrim, James; Ram, Oren; Cheng, Christine; Gnirke, Andreas; Fisher, Sheila; Friedman, Nir; Wong, Bang; Bernstein, Bradley E.; Nusbaum, Chad; Hacohen, Nir; Regev, Aviv; Amit, Ido;     Show all 27 Authors
Source:
Molecular cell 2012 v.47 no.5 pp. 810-822
ISSN:
1097-2765
Subject:
DNA; cell differentiation; chromatin; dendritic cells; gene expression; gene induction; genes; mammals; models; pathogens; precipitin tests; transcription factors
Abstract:
... Understanding the principles governing mammalian gene regulation has been hampered by the difficulty in measuring in vivo binding dynamics of large numbers of transcription factors (TF) to DNA. Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions. HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 ch ...
DOI:
10.1016/j.molcel.2012.07.030
PubMed:
22940246
PubMed Central:
PMC3873101