Oncotarget: Novel post-transcriptional and post-translational regulation of pro-apoptotic protein BOK and anti-apoptotic protein Mcl-1 determine the fate of breast cancer cells to survive or die

September 12, 2017

Benjamin Onyeagucha1,2, Panneerdoss Subbarayalu1,2, Nourhan Abdelfattah1,2, Subapriya Rajamanickam1,2, Santosh Timilsina1,2, Rosa Guzman1, Carla Zeballos2, Vijay Eedunuri1,2, Sanjay Bansal1, Tabrez Mohammad2, Yidong Chen1,3, Ratna K. Vadlamudi4, and Manjeet K. Rao1,2 ABSTRACT Deregulation of apoptosis is central to cancer progression and a major obstacle to effective treatment. The Bcl-2 gene family members play important roles in the regulation […]

BMC Genomics: A hierarchical model for clustering m6A methylation peaks in MeRIP-seq data

August 22, 2016

Xiaodong Cui, Jia Meng, Shaowu Zhang, Manjeet K. Rao, Yidong Chen & Yufei Huang Abstract Background The recent advent of the state-of-art high throughput sequencing technology, known as Methylated RNA Immunoprecipitation combined with RNA sequencing (MeRIP-seq) revolutionizes the area of mRNA epigenetics and enables the biologists and biomedical researchers to have a global view of N 6-Methyladenosine (m6A) on the transcriptome. Yet there […]

Clinical Cancer Research: Inhibition of FoxM1-Mediated DNA Repair by Imipramine Blue Suppresses Breast Cancer Growth and Metastasis

July 1, 2016

Subapriya Rajamanickam, Subbarayalu Panneerdoss, Aparna Gorthi, Santosh Timilsina, Benjamin Onyeagucha, Dmytro Kovalsky, Dmitri Ivanov, Martha A. Hanes, Ratna K. Vadlamudi, Yidong Chen, Alexander J. Bishop, Jack L. Arbiser and Manjeet K. Rao Abstract Purpose: The approaches aimed at inhibiting the ability of cancer cells to repair DNA strand breaks have emerged as promising targets for treating cancers. Here, we assessed the potential of imipramine blue (IB), a novel analog of antidepressant imipramine, to suppress breast cancer growth and metastasis by inhibiting […]

Biology of Reproduction: Rhox8 Ablation in the Sertoli Cells Using a Tissue-Specific RNAi Approach Results in Impaired Male Fertility in Mice

July 1, 2015

Joshua P. Welborn, Matthew G. Davis, Steven D. Ebers, Genna R. Stodden, Kanako Hayashi, Joseph L. Cheatwood, Manjeet K. Rao, James A. MacLean, II Abstract The reproductive homeobox X-linked, Rhox, genes encode transcription factors that are selectively expressed in reproductive tissues. While there are 33 Rhox genes in mice, only Rhox and Rhox8 are expressed in Sertoli cells, suggesting that they may regulate the expression of somatic-cell gene products […]

BMC Genomics: HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data

April 21, 2015

Xiaodong Cui, Jia Meng, Manjeet K Rao, Yidong Chen & Yufei Huang Abstract Background Methylated RNA Immunoprecipitation combined with RNA sequencing (MeRIP-seq) is revolutionizing the de novo study of RNA epigenomics at a higher resolution. However, this new technology poses unique bioinformatics problems that call for novel and sophisticated statistical computational solutions, aiming at identifying and […]

Journal of Biological Chemistry: Hormone-induced and DNA Demethylation-induced Relief of a Tissue-specific and Developmentally Regulated Block in Transcriptional Elongation*

December 19, 2014

Abstract Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox […]

Nucleic Acids Research: MeT-DB: a database of transcriptome methylation in mammalian cells

November 6, 2014

Hui Liu, Mario A Flores, Jia Meng, Lin Zhang, Xinyu Zhao, Manjeet K. Rao, Yidong Chen, Yufei Huang Abstract Methyltranscriptome is an exciting new area that studies the mechanisms and functions of methylation in transcripts. The MethylTranscriptome DataBase (MeT-DB, http://compgenomics.utsa.edu/methylation/) is the first comprehensive resource for N6-methyladenosine (m6A) in the mammalian transcriptome. It includes a database that records publicly available data sets from […]

Methods: A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package

October 1, 2014

Author links open overlay panelJiaMenga,  ZhiliangLua,  HuiLiub,  LinZhangb,  ShaowuZhangc, YidongChende, Manjeet K.Raoef,  YufeiHuanggd Abstract Despite the prevalent studies of DNA/Chromatin-related epigenetics, such as, histone modifications and DNA methylation, RNA epigenetics has not drawn deserved attention until a new affinity-based sequencing approach MeRIP-Seq was developed and applied to survey the global mRNA N6-methyladenosine (m6A) in mammalian cells. As a marriage of […]

Oncogene: Androgen receptor and microRNA-21 axis downregulates transforming growth factor beta receptor II (TGFBR2) expression in prostate cancer

July 31, 2014

S Mishra 1, J J Deng 1, P S Gowda 1, M K Rao 1, C-L Lin 2, C L Chen 2, T Huang 3, L-Z Sun 4 Abstract Prostate cancer cells escape growth inhibition from transforming growth factor β (TGFβ) by downregulating TGFβ receptors. However, the mechanism by which cancer cells downregulate TGFβ receptors in the prostate is not clear. Here, we showed that coordinated action of miR-21 and […]

Journal of Biological Chemistry: The RHOX Homeodomain Proteins Regulate the Expression of Insulin and Other Metabolic Regulators in the Testis*

November 29, 2013

James A. MacLean II‡,§, Zhiying Hu§, Joshua P. Welborn‡, Hye-Won Song§,¶,‖, Manjeet K. Rao§,**, Chad M. Wayne§,‡‡ and Miles F. Wilkinson§,¶,‖1 Abstract Defects in cellular metabolism have been widely implicated in causing male infertility, but there has been little progress in understanding the underlying mechanism. Here we report that several key metabolism genes are regulated in […]