The nuclear RNA degradation landscape of mESCs.

Slides:

Advertisements

Similar presentations

Page Example problems: Page 324, #2,3,9. Transcription The process of making… RNA review Very similar to DNA except: Has a ribose sugar instead.

Advertisements

Pol II Docking and Pausing at Growth and Stress Genes in C. elegans

Fig. 1. In situ hybridization analysis for detecting endogenous mBest1 transcript in whole-brain region. In situ hybridization results from coronal (top.

Genetics Unit I-Part C Transcription

Recurrent inversion breaking intron 1 of the factor VIII gene is a frequent cause of severe hemophilia A by Richard D. Bagnall, Naushin Waseem, Peter M.

by Leighton J. Core, Joshua J. Waterfall, and John T. Lis

Grounded: Transcriptional Pausing in Naive mESCs

Ultraconserved Elements in the Human Genome

Volume 155, Issue 5, Pages (November 2013)

Expression profiling of snoRNAs in normal hematopoiesis and AML

Volume 11, Issue 2, Pages (August 2012)

Volume 44, Issue 3, Pages (November 2011)

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters by Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen,

Nat. Rev. Gastroenterol. Hepatol. doi: /nrgastro

Volume 19, Issue 3, Pages (April 2017)

LincRNAs expressed in specific subpopulations of mESCs and NPCs.

The ribozyme approach distinguishes RNA-dependent and RNA-independent functions of lincRNA genes. The ribozyme approach distinguishes RNA-dependent and.

Hyeshik Chang, Jaechul Lim, Minju Ha, V. Narry Kim Molecular Cell

A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation Michal Rabani, Lindsey Pieper, Guo-Liang Chew,

Regulation of RNA Pol II directionality by FACT.

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes Michael S. Werner, Alexander J. Ruthenburg Cell.

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock Reut Shalgi, Jessica A. Hurt, Susan Lindquist,

Volume 15, Issue 8, Pages (May 2016)

Volume 66, Issue 1, Pages e5 (April 2017)

Dynamic change of transcription pausing through modulating NELF protein stability regulates granulocytic differentiation by Xiuli Liu, Aishwarya A. Gogate,

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

Transcriptome changes in Cnot6l knockout oocytes and zygotes.

Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes Michael S. Werner, Alexander J. Ruthenburg Cell.

Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2 Lukas M. Simon, Edward S. Chen, Leonard C. Edelstein,

Volume 5, Issue 6, Pages (December 2013)

Hyeshik Chang, Jaechul Lim, Minju Ha, V. Narry Kim Molecular Cell

Fine-Resolution Mapping of TF Binding and Chromatin Interactions

Volume 150, Issue 5, Pages (August 2012)

Fine-Resolution Mapping of TF Binding and Chromatin Interactions

Volume 26, Issue 1, Pages (April 2007)

Stefan Bresson, Alex Tuck, Desislava Staneva, David Tollervey

Volume 44, Issue 3, Pages (November 2011)

Volume 11, Issue 6, Pages (March 2001)

Pol II Docking and Pausing at Growth and Stress Genes in C. elegans

Genome-wide binding sites of OsMADS1 and the distribution of binding sites in different regions of annotated genes. Genome-wide binding sites of OsMADS1.

Baekgyu Kim, Kyowon Jeong, V. Narry Kim Molecular Cell

Dynamic Regulation of Nucleosome Positioning in the Human Genome

Volume 5, Issue 4, Pages (November 2013)

Volume 20, Issue 9, Pages (August 2017)

Volume 50, Issue 2, Pages (April 2013)

Volume 21, Issue 9, Pages (November 2017)

Volume 66, Issue 4, Pages e4 (May 2017)

Volume 47, Issue 4, Pages (August 2012)

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains Chunhui Hou, Li Li, Zhaohui S.

Alex Charles Tuck, David Tollervey Cell

Schematic drawing of alternatively-spliced GFP reporter gene.

Antisense expression associates with larger gene expression variability. Antisense expression associates with larger gene expression variability. (A–D)

Divergent Transcription from Active Promoters

Universal Alternative Splicing of Noncoding Exons

Comparison of transcriptome changes in Cnot6l−/− MII eggs with other experimental data. Comparison of transcriptome changes in Cnot6l−/− MII eggs with.

Michael J Dye, Nick J Proudfoot Molecular Cell

Barc knockdown causes intron retention of short, GC-rich introns with weak splice sites. barc knockdown causes intron retention of short, GC-rich introns.

Pol II pausing over other gene classes.

Stefan Bresson, Alex Tuck, Desislava Staneva, David Tollervey

Single-cell atlas of lincRNA expression during mESC to NPC differentiation. Single-cell atlas of lincRNA expression during mESC to NPC differentiation.

Exon Tethering in Transcription by RNA Polymerase II

Manfred Schmid, Agnieszka Tudek, Torben Heick Jensen Cell Reports

Defining the Status of RNA Polymerase at Promoters

Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation Robert Ietswaart, Stefanie.

Integrated mRNA and microRNA expression and DNA methylation clusters.

Volume 16, Issue 6, Pages (August 2016)

Volume 11, Issue 7, Pages (May 2015)

Origins and Impacts of New Mammalian Exons

by Leighton J. Core, Joshua J. Waterfall, and John T. Lis

Fig. 2 Combined transcriptome profiling, ChIP-seq, and ATAC-seq analysis identifies 14 highly plausible direct targets of Runx. Combined transcriptome.

Presentation transcript:

The nuclear RNA degradation landscape of mESCs. The nuclear RNA degradation landscape of mESCs. (A) Half-lives of mRNAs and lincRNAs, calculated from RNA-seq decay curves following actinomycin D–mediated transcription shut-off. Messenger RNAs are shown in black, lincRNAs in red, and lincRNAs highlighted in this study in green. A running median trend line for mRNAs is shown in blue. (B) Box plot summary of lincRNA and mRNA half-lives (bar = median; notches = 1.58 × IQR/sqrt(n)), with the distributions tested for similarity using the Wilcoxon rank sum test. The three plots show low expressed (<40 normalised counts), high expressed (>40 normalised counts), or all transcripts (left to right). (C) Length of non-genome-encoded oligonucleotide tails detected on RNA fragments captured by Mtr4 CRAC. Oligo(A) tails correspond to degradation intermediates and oligo(C/G/T) tails are shown as a negative control. (D) Metaplots showing the distribution of Pol II Native Elongating Transcript sequencing (NET-seq) (top) and Mtr4 CRAC (middle) RNA fragments around the start and end of mRNA exons and introns (first three and the last exon shown). Mtr4 CRAC RNA fragments with non-genome-encoded 3′ oligo(A) tails, corresponding to initial Mtr4 recruitment sites, are shown separately (bottom). (E) An example of Mtr4 CRAC reads mapping near the 3′ end of an intron (β-actin intron 1). Individual sequencing reads corresponding to fragments with 3′ oligo(A) tails are shown as red bars, with an alignment of these sequences below (highlighting in red the non-genome-encoded oligo(A) tails). (F) Total distribution of RNA fragments bound to Pol II (NET-seq) or Mtr4 (CRAC) around mRNA TSSs, in the sense (top) and antisense (bottom) directions. “Sense PROMPTs” are defined as short, prematurely terminated transcripts originating from TSSes in the sense direction and “antisense PROMPTs” are similar transcripts that arise in the upstream antisense orientation (see diagram). Mtr4 A-tailed read (as for D) distributions are shown in green. See also Fig S5. Alex C Tuck et al. LSA 2018;1:e201800124 © 2018 Tuck et al.