Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs

Summary Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq). Notably, mNET-seq patterns specific for different Pol II CTD phosphorylation states reveal weak co-transcriptional splicing and poly(A) signal-independent Pol II termination of lincRNAs as compared to pre-mRNAs. In addition, lincRNAs are mostly restricted to chromatin, since they are rapidly degraded by the RNA exosome. We also show that a lincRNA-specific co-transcriptional RNA cleavage mechanism acts to induce premature termination. In effect, functional lincRNAs must escape from this targeted nuclear surveillance process.

[1]  T. Jensen,et al.  Dealing with pervasive transcription. , 2013, Molecular cell.

[2]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[3]  C. Kai,et al.  CAGE: cap analysis of gene expression , 2006, Nature Methods.

[4]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[5]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[6]  Z. Dominski,et al.  Formation of the 3' end of histone mRNA: getting closer to the end. , 2007, Gene.

[7]  H. Kimura,et al.  Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing , 2015, Cell.

[8]  Cole Trapnell,et al.  Computational methods for transcriptome annotation and quantification using RNA-seq , 2011, Nature Methods.

[9]  L. Steinmetz,et al.  Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality , 2013, Nature Structural &Molecular Biology.

[10]  David G. Knowles,et al.  The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.

[11]  J. Steitz,et al.  Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix , 2014, Nature Structural &Molecular Biology.

[12]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[13]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[14]  A. Hyman,et al.  The human cap-binding complex is functionally connected to the nuclear RNA exosome , 2013, Nature Structural &Molecular Biology.

[15]  J. Manley,et al.  The RNA polymerase II CTD coordinates transcription and RNA processing. , 2012, Genes & development.

[16]  T. Jensen,et al.  The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis. , 2015, Cell reports.

[17]  David L. Spector,et al.  3′ End Processing of a Long Nuclear-Retained Noncoding RNA Yields a tRNA-like Cytoplasmic RNA , 2008, Cell.

[18]  Philippe Gautier,et al.  DGCR8 Acts as an Adaptor for the Exosome Complex to Degrade Double-Stranded Structured RNAs , 2015, Molecular cell.

[19]  Alex P. Reynolds,et al.  Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution , 2015, Cell.

[20]  Affymetrix Encode Transcriptome.  Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. , 2009 .

[21]  I. Bozzoni,et al.  Primary microRNA transcripts are processed co-transcriptionally , 2008, Nature Structural &Molecular Biology.

[22]  Mihaela Zavolan,et al.  Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. , 2012, Cell reports.

[23]  M. Carmo-Fonseca,et al.  Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide , 2016, Nature Protocols.

[24]  M. Gullerová,et al.  Swiss army knives: non-canonical functions of nuclear Drosha and Dicer , 2015, Nature Reviews Molecular Cell Biology.

[25]  A. Ruthenburg,et al.  Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. , 2015, Cell reports.

[26]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[27]  T. Owa,et al.  Splicing factor SF3b as a target of the antitumor natural product pladienolide , 2007, Nature Chemical Biology.

[28]  J. Steitz,et al.  Widespread Inducible Transcription Downstream of Human Genes. , 2015, Molecular cell.

[29]  Manolis Kellis,et al.  The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. , 2013, Developmental cell.

[30]  T. Jensen,et al.  RNA decay machines: the exosome. , 2013, Biochimica et biophysica acta.

[31]  D. Bartel,et al.  lincRNAs: Genomics, Evolution, and Mechanisms , 2013, Cell.

[32]  Alastair R W Kerr,et al.  Co-transcriptional degradation of aberrant pre-mRNA by Xrn2 , 2012, The EMBO journal.

[33]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[34]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[35]  J. Mattick.  The Genetic Signatures of Noncoding RNAs , 2009, PLoS genetics.

[36]  P. Sharp,et al.  Detained introns are a novel, widespread class of post-transcriptionally spliced introns , 2015, Genes & development.

[37]  N. Proudfoot,et al.  Poly(A) signals control both transcriptional termination and initiation between the tandem GAL10 and GAL7 genes of Saccharomyces cerevisiae , 1998, The EMBO journal.

[38]  Howard Y. Chang,et al.  Unique features of long non-coding RNA biogenesis and function , 2015, Nature Reviews Genetics.

[39]  D. Eick,et al.  Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. , 2013, Biochimica et biophysica acta.

[40]  Thomas Bonfert,et al.  Widespread disruption of host transcription termination in HSV-1 infection , 2015, Nature Communications.

[41]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[42]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[43]  Wei Wu,et al.  NONCODEv4: exploring the world of long non-coding RNA genes , 2013, Nucleic Acids Res..

[44]  Alexander J. Federation,et al.  RNA Exosome-Regulated Long Non-Coding RNA Transcription Controls Super-Enhancer Activity , 2015, Cell.

[45]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[46]  Nicolas Descostes,et al.  Threonine‐4 of mammalian RNA polymerase II CTD is targeted by Polo‐like kinase 3 and required for transcriptional elongation , 2012, The EMBO journal.

[47]  C. Mello,et al.  CapSeq and CIP-TAP Identify Pol II Start Sites and Reveal Capped Small RNAs as C. elegans piRNA Precursors , 2012, Cell.

[48]  Mihaela Zavolan,et al.  Genome-wide Analysis of Pre-mRNA 3 0 End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3 0 UTR Length , 2012 .

[49]  Melissa J. Moore,et al.  Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation , 2009, Cell.

[50]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[51]  D. Tollervey,et al.  Transcriptome-wide Analysis of Exosome Targets , 2012, Molecular cell.

[52]  V. Kim,et al.  Regulation of microRNA biogenesis , 2014, Nature Reviews Molecular Cell Biology.

[53]  K. Struhl.  Transcriptional noise and the fidelity of initiation by RNA polymerase II , 2007, Nature Structural &Molecular Biology.

[54]  P. Kapranov,et al.  The Landscape of long noncoding RNA classification. , 2015, Trends in genetics : TIG.

[55]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[56]  Tsung-Cheng Chang,et al.  Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins , 2016, Cell.

[57]  Daniel R. Zerbino,et al.  Ensembl 2014 , 2013, Nucleic Acids Res..

[58]  Monika S. Kowalczyk,et al.  Intragenic enhancers act as alternative promoters. , 2012, Molecular cell.