SAMPATH P

Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition

Published date : 08 Jan 2018

In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome-association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs.

type
Journal Paper
journal
Development, 8 Jan 2018, Vol 145, Issue 1, doi: 10.1242/dev.159566
Impact Factor
5.843

EGF hijacks miR-198/FSTL1 wound-healing switch and steers a two-pronged pathway toward metastasis

Published date : 21 Aug 2017

Epithelial carcinomas are well known to activate a prolonged wound-healing program that promotes malignant transformation. Wound closure requires the activation of keratinocyte migration via a dual-state molecular switch. This switch involves production of either the anti-migratory microRNA miR-198 or the pro-migratory follistatin-like 1 (FSTL1) protein from a single transcript; miR-198 expression in healthy skin is down-regulated in favor of FSTL1 upon wounding, which enhances keratinocyte migration and promotes re-epithelialization.

type
Journal Paper
journal
The Journal of Experimental Medicine, 2017,doi: 10.1084/jem.20170354
Impact Factor
11.991

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

Published date : 08 Dec 2014

Background
Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies.

Results

type
Journal Paper
journal
BMC Genomics 2014, 15(Suppl 9):S7 doi:10.1186/1471-2164-15-S9-S7
Impact Factor
4.04

Role of Translationally Regulated Genes in Embryonic Stem Cell Differentiation: Integration of Transciptome and Translational State Profiling

Published date : 29 Aug 2012

This chapter describes a method for genome-wide identification of translationally regulated genes during embryonic stem cell differentiation using integrated transcriptome and translation state profiling. Previous attempts at identification of translationally regulated genes have focused on measuring the fractionation of the mRNA molecules in the translated and untranslated fractions without considering the transcriptional status of these genes.

type
Book/Book Chapter
journal
Computational Biology of Embryonic Stem Cells, 2012, Vol. 1, Pg 180-192, ISBN : 978-1-60805-025-3

ModBase, a database of annotated comparative protein structure models, and associated resources

Published date : 30 Jan 2011

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains 10,355,444 reliable models for domains in 2,421,920 unique protein sequences.

type
Journal Paper
journal
Nuclei Acids Research 2011, Jan:39 (Database issue) D465-74, doi: 10.1093/nar/gkq1091
Impact Factor
7.836