Table of Contents

Volume 3, Issue 3

  May/June 2012

  Pages 105 - 153

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 Issue Catalogue (MARC XML)

EDITOR'S PREVIEW

Open Access Article

In this issue of Transcription

Barbara P. Rattner
Page 105
http://dx.doi.org/10.4161/trns.20354
Full Text | PDF




POINTS-OF-VIEW

Open Access Article

A conserved role for intragenic DNA methylation in alternative pre-mRNA splicing

Shalini Oberdoerffer
Pages 106 - 109
http://dx.doi.org/10.4161/trns.19816
Abstract | Full Text | PDF

DNA methylome analysis in a variety of species has revealed elevated 5-methylcytosine at exons relative to introns. These associations raised the possibility that intragenic DNA methylation aids the spliceosome in the process of exon definition. Here, I highlight recent genome-wide associations and direct evidence linking DNA methylation to pre-mRNA splicing.

Open Access Article

Selective role of Mediator tail module in the transcription of highly regulated genes in yeast

Suraiya A. Ansari and Randall H. Morse
Pages 110 - 114
http://dx.doi.org/10.4161/trns.19840
Abstract | Full Text | PDF

The tail module subunits of Mediator complex are targets of activators both in yeast and metazoans. Here we discuss recent evidence from studies in yeast for tail module specificity for SAGA-dependent, TATA-containing genes including highly regulated stress response genes, and for independent recruitment and function of the tail module.

Open Access Article

Multiple active centers of multi-subunit RNA polymerases

Yulia Yuzenkova, Mohammad Roghanian and Nikolay Zenkin
Pages 115 - 118
http://dx.doi.org/10.4161/trns.19887
Abstract | Full Text | PDF

The active center of multi-subunit RNA polymerase consists of two modules, the Mg²⁺ module, holding the catalytic Mg²⁺ ion, and a module made of a flexible domain, the Trigger Loop. Uniquely, the “TL module” can be substituted by “alternative modules,” thus changing the catalytic properties of the active center.

Open Access Article

p53 and metabolism: Old player in a new game

Nirmalya Sen, Yatendra Kumar Satija and Sanjeev Das
Pages 119 - 123
http://dx.doi.org/10.4161/trns.20094
Abstract | Full Text | PDF

Metabolic reprogramming is an integral part of tumorigenesis. Tumor suppressor p53 is a well studied transcription factor intimately linked with the control of cell cycle progression and apoptosis. Here, we discuss the emerging role of p53 in the transcriptional regulation of metabolism. This activity is a key component of p53 tumor suppression function.

Open Access Article

Cdc6: A multi-functional molecular switch with critical role in carcinogenesis

Thodoris G. Petrakis, Konstantinos Vougas and Vassilis G. Gorgoulis
Pages 124 - 129
http://dx.doi.org/10.4161/trns.20301
Abstract | PDF

Research in the last decade revealed an additional role for the Replication Licensing Factor Cdc6 in transcriptional regulation. This novel function has been linked to human cancer development. Here, we summarize all the findings arguing over a role of Cdc6 as a transcriptional repressor and shed light toward new research directions for this field.




RESEARCH PAPER

Open Access Article

The endoglycosidase heparanase enters the nucleus of T lymphocytes and modulates H3 methylation at actively transcribed genes via the interplay with key chromatin modifying enzymes

Yi Qing He, Elissa L. Sutcliffe, Karen L. Bunting, Jasmine Li, Katharine J. Goodall, Ivan K.A. Poon, Mark D. Hulett, Craig Freeman, Anjum Zafar, Russell L. McInnes, Toshiki Taya, Christopher R. Parish and Sudha Rao
Pages 130 - 145
http://dx.doi.org/10.4161/trns.19998
Abstract | Full Text | PDF

The methylation of histones is a fundamental epigenetic process regulating gene expression programs in mammalian cells. Dysregulated patterns of histone methylation are directly implicated in malignant transformation. Here, we report the unexpected finding that the invasive extracellular matrix degrading endoglycosidase heparanase enters the nucleus of activated human T lymphocytes and regulates the transcription of a cohort of inducible immune response genes by controlling histone H3 methylation patterns. It was found that nuclear heparanase preferentially associates with euchromatin. Genome-wide ChIP-on-chip analyses showed that heparanase is recruited to both the promoter and transcribed regions of a distinct cohort of transcriptionally active genes. Knockdown and overexpression of the heparanase gene also showed that chromatin-bound heparanase is a prerequisite for the transcription of a subset of inducible immune response genes in activated T cells. Furthermore, the actions of heparanase seem to influence gene transcription by associating with the demethylase LSD1, preventing recruitment of the methylase MLL and thereby modifying histone H3 methylation patterns. These data indicate that heparanase belongs to an emerging class of proteins that play an important role in regulating transcription in addition to their well-recognized extra-nuclear functions.




METHODS ARTICLE

Open Access Article

Efficient reconstitution of transcription elongation complexes for single-molecule studies of eukaryotic RNA polymerase II

Murali Palangat, Matthew H. Larson, Xiaopeng Hu, Averell Gnatt, Steven M. Block and Robert Landick
Pages 146 - 153
http://dx.doi.org/10.4161/trns.20269
Abstract | PDF

Single-molecule studies of RNA polymerase II (RNAP II) require high yields of transcription elongation complexes (TECs) with long DNA tethers upstream and downstream of the TEC. Here we report on a robust system to reconstitute both yeast and mammalian RNAP II with an efficiency of ~80% into TECs that elongate with an efficiency of ~90%, followed by rapid, high-efficiency tripartite ligation of long DNA fragments upstream and downstream of the reconstituted TECs. Single mammalian and yeast TECs reconstituted with this method have been successfully used in an optical-trapping transcription assay capable of applying forces that either assist or hinder transcript elongation.