Spotlight

Managing the Chromatin Landscape… and a Bunch of Signaling Trails along with it

SATB1, expanded as special AT-rich binding protein 1, has emerged in recent years as an important player in the maintenance of chromatin organization in living cells. This article studies the rise of SATB1 to the status of a global gene regulator and contributions of Prof. Sanjeev Galande, who leads a research laboratory at IISER Pune, to this effect.

Like signposts guiding tourists in a new land, in a cellular context, molecules are aided by signals, markers, and regulators pointing them to the next step. At the level of gene regulation, SATB1 protein has emerged as one such master regulator with a key role in organizing the chromatin (chromosomal material inside the nucleus of a cell).

SATB1 is highly expressed in the thymus, a specialized organ of the immune system where T cells learn to distinguish a foreign cell or material from that of body’s own. Sanjeev Galande’s association with SATB1 runs long. As a postdoctoral fellow at the Burnham Institute (La Jolla, USA) and then at the Lawrence Berkeley National Laboratory in the late ′90s, Galande was studying a few proteins that bind chromatin and alter its organization, especially in the background of cancer. This was the time SATB1 was known as a chromatin binding protein with an unusual binding sequence; its involvement in chromatin organization was just beginning to be addressed.

Taking a short detour from his work on chromatin binding of certain nuclear enzymes, Galande grabbed a chance to work on SATB1, a protein he thought could potentially be important in more than one pathway. One of the first questions he addressed on SATB1 was related to it being chewed up by protein-cutting enzymes (proteases) during apoptosis, a process by which select cells die in the interest of the body.

In investigating why SATB1 is being targeted by cellular proteases in this system, Galande made a crucial discovery: SATB1 contains a PDZ-like domain, making it the only known chromatin associated protein with such a domain (Mol. Cell. Biol. 21:5591-5604). Proteins that contain PDZ domain seem to be capable of communicating with other proteins thus acting like signaling hubs; in short, the identification of this domain in SATB1 revealed a possible new function of SATB1. “I could see how SATB1 might bridge multiple signaling pathways to chromatin level regulation of gene expression. After returning to India, this formed the focus of my research,” recalls Galande.

With a group of enthusiastic graduate students, at the National Centre for Cell Sciences (NCCS) in Pune, Galande began to investigate SATB1 functions at two levels: defining a molecular mechanism for SATB1 function and assessing SATB1’s reach across multiple signaling pathways.

Prof. Sanjeev Galande (far right, sitting) with his group members

In the first of a series of publications to follow, Galande’s group showed that presence or absence of a phosphoryl group on one of SATB1’s amino acids (Ser 185) switched the role of SATB1 from activation to repression of gene expresson (Mol. Cell 22:231-243). This provided a mechanism by which SATB1 can coordinate its interactions with other DNA-binding proteins.

It has been proposed by other researchers in this field that SATB1 tethers certain regions of the chromatin to nuclear matrix as if placing a pin on a poster board. Such protein mediated bridging was thought to bring together distant regions of the chromatin leaving out loops of chromatin in between.

Using the MHC gene locus and home-grown assays, the Galande laboratory confirmed SATB1 as one of the components required for such tethering; in addition, they also defined the precise regions that constitute the loops and the anchored regions of the chromatin.

An important observation they made in this regard is that the loop organization of the MHC locus is altered upon introducing a signal of infection and that this in turn altered the transcription activity of the genes in MHC locus (Nat. Cell Biol. 9:45-56).

“Through these experiments, for the first time, we had showed that a change in higher-order structure of the chromatin is linked to transcriptional output. We then proposed that SATB1 acts as an intermediary that links the two aspects. It is now widely accepted that chromatin organizer proteins such as SATB1 have regulatory roles in gene expression,” describes Galande.

Talking about how learning and designing new technologies has paid well, Galande says, “When we realized that SATB1 may be coordinating multiple signaling pathways, we used the microarray technology to probe it further. This method was quite new for us at that time, but well used elsewhere… our lab picked up this technique and carried out the entire process—from hybridization to analysis. This was a useful exercise as it gave us insightful findings on how differential gene expression occurs in the various models we have chosen to study SATB1 function.”

Among the many pathways that SATB1 has been implicated through this microarray analysis, the Galande group chose the well characterized wnt signaling pathway to probe the role of SATB1. This study revealed that SATB1 regulates wnt signaling by recruiting beta-catenin protein, effectively placing SATB1 as an important modulator in the wnt signaling pathway (PLoS Biol. 8:e1000296).

Galande’s laboratory has moved to IISER Pune in 2010 and has been working on various themes centered on SATB1 unearthing newer roles for the protein. Some of the questions they are asking are what regulates the balance between pluripotency and differentiation in a human stem cell model system; what role might global regulators such as SATB1 have in the development of a complex body plan comparing invertebrate and vertebrate model systems; and how SATB1 regulates cell migration, which have implications in understanding early developmental processes and disease conditions such as cancer.

Galande has also been involved in setting up the Centre of Excellence in Epigenetics at IISER Pune with funds from the Department of Biotechnology (Government of India). The Centre provides a focal point for a team of scientists interested in addressing the mechanism and evolution of epigenetic regulation in a variety of model systems. Recently, in collaboration with Sanjay Gupta’s group at ACTREC in Mumbai, the Centre has developed HIstome, an extensive database of histone proteins. This database is described in greater detail below.

Research in Sanjeev Galande’s laboratory is funded by the Department of Biotechnology and the Department of Science and Technology (India) and the Wellcome Trust (UK). For more information on published and ongoing work from Galande laboratory, visit http://www.iiserpune.ac.in/~sanjeev/

HIstome: A one-stop information portal for all epigenetic players

HIstome is a recently developed database that provides information about human histone proteins, which are involved in packaging the chromosomal material in a cell. Research article reporting the database has been published in the journal Nucleic Acids Research (40:D337-D342) and the database website has been functional since earlier this year (http://www.histome.net/).

The HIstome database is extensive and interactive. Here, one can obtain information on human histones (with work underway to extend this to other species), their variants and modifications; sites of modifications; enzymes that modify, sequence of those enzymes, and the enzyme substrates; sequence of proteins as well as genes, and promoter sequences too.

“This is a useful database for any epigenetics related work. Based on a reviewer’s suggestion, we have included a disease module considering that many histone variants have been implicated in cancer. The website had begun to receive hits from various parts of the world even within the first few days of being set up,” said Sanjeev Galande, one of the senior authors involved in developing the database, pointing to the growing popularity of the database.

“Soon we are planning to extend this database from human to several other models such as mouse, Drosophila, zebrafish etc. The new version will also have the capability to compare results between different model systems,” added Galande.

Farhat Habib, a scientist associated with the Centre of Excellence in Epigenetics based out of IISER Pune and one of the primary authors on this publication, has described HIstome on www.indiabioscience.org along with useful pointers to researchers interested in building a database; his article can be accessed here.

The work was a collaborative effort between research group of Sanjeev Galande (CoE in Epigenetics, IISER Pune) and Sanjay Gupta (ACTREC, Mumbai). Other researchers involved in this study were Satyajeet Khare, who was a postdoctoral fellow with Galande and performed part of this work when as a graduate student with Gupta; Farhat Habib of CoE in Epigenetics, IISER Pune; Rahul Sharma of CoE in Epigenetics, IISER Pune; and Nikhil Gadewal of ACTREC, Mumbai.

-Reported by Shanti Kalipatnapu

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