Seq'ing identity and function in a repeat-derived noncoding RNA world.

Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology
Rachel J O'Neill

Abstract

Innovations in high-throughout sequencing approaches are being marshaled to both reveal the composition of the abundant and heterogeneous noncoding RNAs that populate cell nuclei and lend insight to the mechanisms by which noncoding RNAs influence chromosome biology and gene expression. This review focuses on some of the recent technological developments that have enabled the isolation of nascent transcripts and chromatin-associated and DNA-interacting RNAs. Coupled with emerging genome assembly and analytical approaches, the field is poised to achieve a comprehensive catalog of nuclear noncoding RNAs, including those derived from repetitive regions within eukaryotic genomes. Herein, particular attention is paid to the challenges and advances in the sequence analyses of repeat and transposable element-derived noncoding RNAs and in ascribing specific function(s) to such RNAs.

References

Jul 1, 1976·Proceedings of the National Academy of Sciences of the United States of America·M ThomasR W Davis
Jan 1, 1990·Molecular and Cellular Biology·C I BrannanS M Tilghman
May 1, 1986·Journal of Immunological Methods·S J BoguslawskiR J Carrico
Jan 1, 1986·Journal of Cell Science. Supplement·E G FeyS Penman
Jul 7, 1972·Science·D S HolmesJ Bonner
Mar 11, 2000·Molecular Biology of the Cell·T Pederson
Nov 20, 2001·EMBO Reports·J S Mattick
Feb 14, 2003·Bioinformatics·A LefebvreJ Alexandre
Jun 7, 2003·Science·Lee Zou, Stephen J Elledge
Dec 1, 1957·Biochimica Et Biophysica Acta·G FELSENFELD, A RICH
Jan 17, 2004·Nucleic Acids Research·J Ramon GoñiModesto Orozco
Oct 30, 2004·Proceedings of the National Academy of Sciences of the United States of America·Christopher N ToppR Kelly Dawe
Sep 6, 2005·Science·John S Mattick
Nov 3, 2005·EMBO Reports·Durdica Ugarkovic
Dec 7, 2005·Proceedings of the National Academy of Sciences of the United States of America·Eliane El AchkarMichelle Debatisse
Oct 3, 2006·Molecular Carcinogenesis·Qi WuKaren M Vasquez
Oct 24, 2007·Molecular and Cellular Biology·Deepankar RoyMichael R Lieber
May 27, 2008·Genome Research·Zhaoshi JiangEvan E Eichler
Jan 24, 2009·Nature Reviews. Molecular Cell Biology·V Narry KimMikiko C Siomi
Apr 25, 2009·PLoS Genetics·John S Mattick
Jun 13, 2009·Progress in Molecular and Subcellular Biology·Rachel J O'Neill, Dawn M Carone
Nov 10, 2009·Genome Biology·Ana C Marques, Chris P Ponting
Feb 13, 2010·Cold Spring Harbor Protocols·Stephen T Smale
May 5, 2010·Annual Review of Genomics and Human Genetics·Judith D Brown, Rachel J O'Neill
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
Jan 21, 2011·Nature·L Stirling Churchman, Jonathan S Weissman
Apr 20, 2011·Cold Spring Harbor Symposia on Quantitative Biology·H BierhoffI Grummt
Nov 11, 2011·Heredity·J D BrownR J O'Neill

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Citations

Mar 12, 2020·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Beth A Sullivan
Sep 14, 2020·DNA Repair·Cathrine Broberg Vågbø, Geir Slupphaug

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Methods Mentioned

BETA
RNA-seq
PRO-seq
ChAR-seq
proximity ligation
proximity-ligation
immunoprecipitation
DRIP-seq
affinity purification
ChIRP
RAP

Software Mentioned

Bowtie2
ChAR
MARGI
GRID
RepeatMasker
seq
RepARK
CHART
BWA
MapR

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