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Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions.

Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, Lissner MM, Natoli G, Black DL, Smale ST.

Cell. 2012 Jul 20;150(2):279-90. doi: 10.1016/j.cell.2012.05.043.


Splicing kinetics and transcript release from the chromatin compartment limit the rate of Lipid A-induced gene expression.

Pandya-Jones A, Bhatt DM, Lin CH, Tong AJ, Smale ST, Black DL.

RNA. 2013 Jun;19(6):811-27. doi: 10.1261/rna.039081.113. Epub 2013 Apr 24.


Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs.

Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R.

Genome Res. 2012 Sep;22(9):1616-25. doi: 10.1101/gr.134445.111.


Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

Iglesias MJ, Reilly SJ, Emanuelsson O, Sennblad B, Pirmoradian Najafabadi M, Folkersen L, Mälarstig A, Lagergren J, Eriksson P, Hamsten A, Odeberg J.

PLoS One. 2012;7(2):e32306. doi: 10.1371/journal.pone.0032306. Epub 2012 Feb 27. Erratum in: PLoS One. 2012;7(4): doi/10.1371/annotation/689ae222-9eb1-4f80-8ebe-6b80e8ad45ce. Jesus Iglesias, Maria [corrected to Iglesias, Maria Jesus].


A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation.

Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, Allred AL, Barish GD, Smale ST.

Cell. 2016 Mar 24;165(1):165-179. doi: 10.1016/j.cell.2016.01.020. Epub 2016 Feb 25.


Divergent transcription is associated with promoters of transcriptional regulators.

Lepoivre C, Belhocine M, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau JC, Puthier D, Spicuglia S.

BMC Genomics. 2013 Dec 23;14:914. doi: 10.1186/1471-2164-14-914.


The transcriptional regulator network of human inflammatory macrophages is defined by open chromatin.

Schmidt SV, Krebs W, Ulas T, Xue J, Baßler K, Günther P, Hardt AL, Schultze H, Sander J, Klee K, Theis H, Kraut M, Beyer M, Schultze JL.

Cell Res. 2016 Feb;26(2):151-70. doi: 10.1038/cr.2016.1. Epub 2016 Jan 5.


Gene-specific control of inflammation by TLR-induced chromatin modifications.

Foster SL, Hargreaves DC, Medzhitov R.

Nature. 2007 Jun 21;447(7147):972-8. Epub 2007 May 30. Erratum in: Nature. 2008 Jan 3;451(7174):102.


Quantification of co-transcriptional splicing from RNA-Seq data.

Herzel L, Neugebauer KM.

Methods. 2015 Sep 1;85:36-43. doi: 10.1016/j.ymeth.2015.04.024. Epub 2015 Apr 27.


The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing.

Abe K, Yamamoto R, Franke V, Cao M, Suzuki Y, Suzuki MG, Vlahovicek K, Svoboda P, Schultz RM, Aoki F.

EMBO J. 2015 Jun 3;34(11):1523-37. doi: 10.15252/embj.201490648. Epub 2015 Apr 20.


Regulation of macrophage inflammatory gene expression by the orphan nuclear receptor Nur77.

Pei L, Castrillo A, Tontonoz P.

Mol Endocrinol. 2006 Apr;20(4):786-94. Epub 2005 Dec 8.


Essential role of the IRF8-KLF4 transcription factor cascade in murine monocyte differentiation.

Kurotaki D, Osato N, Nishiyama A, Yamamoto M, Ban T, Sato H, Nakabayashi J, Umehara M, Miyake N, Matsumoto N, Nakazawa M, Ozato K, Tamura T.

Blood. 2013 Mar 7;121(10):1839-49. doi: 10.1182/blood-2012-06-437863. Epub 2013 Jan 14.


RNA sequencing reveals dynamic changes of mRNA abundance of cytochromes P450 and their alternative transcripts during mouse liver development.

Peng L, Yoo B, Gunewardena SS, Lu H, Klaassen CD, Zhong XB.

Drug Metab Dispos. 2012 Jun;40(6):1198-209. doi: 10.1124/dmd.112.045088. Epub 2012 Mar 20.


Localization and stability of introns spliced from the Pem homeobox gene.

Clement JQ, Maiti S, Wilkinson MF.

J Biol Chem. 2001 May 18;276(20):16919-30. Epub 2001 Feb 23.


Regulation of the processing of glucose-6-phosphate dehydrogenase mRNA by nutritional status.

Amir-Ahmady B, Salati LM.

J Biol Chem. 2001 Mar 30;276(13):10514-23. Epub 2000 Dec 21.


Transcriptional regulation of the human toll-like receptor 2 gene in monocytes and macrophages.

Haehnel V, Schwarzfischer L, Fenton MJ, Rehli M.

J Immunol. 2002 Jun 1;168(11):5629-37.


Nuclear to cytoplasmic translocation of heterogeneous nuclear ribonucleoprotein U enhances TLR-induced proinflammatory cytokine production by stabilizing mRNAs in macrophages.

Zhao W, Wang L, Zhang M, Wang P, Qi J, Zhang L, Gao C.

J Immunol. 2012 Apr 1;188(7):3179-87. doi: 10.4049/jimmunol.1101175. Epub 2012 Feb 17.


Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts.

Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X.

Circ Res. 2011 Dec 9;109(12):1332-41. doi: 10.1161/CIRCRESAHA.111.249433. Epub 2011 Oct 27.


Chromatin associated sense and antisense noncoding RNAs are transcribed from the var gene family of virulence genes of the malaria parasite Plasmodium falciparum.

Epp C, Li F, Howitt CA, Chookajorn T, Deitsch KW.

RNA. 2009 Jan;15(1):116-27. doi: 10.1261/rna.1080109. Epub 2008 Nov 26.

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