Genome Biology: The 3′ end of the story: deciphering combinatorial interactions that control mRNA fate.

November 29, 2017

Authors Penalva LOF Sanford JR Precise control of messenger RNA (mRNA) fate—its translation, stability, and localization—is required for accurate eukaryotic gene expression and is of fundamental importance to human health and disease. Initial efforts to determine how the cell controls these processes focused on “who done it?” We now understand that many of the clues […]

BMC Genomics: Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer

October 3, 2017

Yu-Chiao Chiu, Li-Ju Wang, Tzu-Hung Hsiao, Eric Y. Chuang & Yidong Chen Abstract Background With the advances in high-throughput gene profiling technologies, a large volume of gene interaction maps has been constructed. A higher-level layer of gene-gene interaction, namely modulate gene interaction, is composed of gene pairs of which interaction strengths are modulated by (i.e., dependent on) the expression level […]

BMC Bioinformatics: XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation

October 3, 2017

Yuanhang Liu, Ping Wu, Jingqi Zhou, Teresa L. Johnson-Pais, Zhao Lai, Wasim H. Chowdhury, Ronald Rodriguez & Yidong Chen Abstract Background RNA sequencing (RNA-seq) is a high throughput technology that profiles gene expression in a genome-wide manner. RNA-seq has been mainly used for testing differential expression (DE) of transcripts between two conditions and has recently been used for testing differential alternative polyadenylation (APA). […]

Science Signaling: Evaluation of the selectivity and sensitivity of isoform- and mutation-specific RAS antibodies

September 26, 2017

Andrew M. Waters1,2, Irem Ozkan-Dagliyan3, Angelina V. Vaseva1,4, View ORCID ProfileNicole Fer2, Leslie A. Strathern2, View ORCID ProfileG. Aaron Hobbs1, View ORCID ProfileBasile Tessier-Cloutier5, View ORCID ProfileWilliam K. Gillette2, View ORCID ProfileRachel Bagni2, View ORCID ProfileGordon R. Whiteley2, James L. Hartley2, Frank McCormick2,6, Adrienne D. Cox1,3,7, Peter J. Houghton4, David G. Huntsman5, View ORCID ProfileMark R. Philips8, and View ORCID ProfileChanning J. Der1,3,* Abstract There is intense interest in developing therapeutic […]

JoVE: Genome-wide Analysis of HDAC Inhibitor-mediated Modulation of microRNAs and mRNAs in B Cells Induced to Undergo Class-switch DNA Recombination and Plasma Cell Differentiation

September 20, 2017

Helia N Sanchez 1, Tian Shen 2, Dawn Garcia 3, Zhao Lai 3, Paolo Casali 1, Hong Zan 4 Abstract Antibody responses are accomplished through several critical B cell-intrinsic processes, including somatic hypermutation (SHM), class-switch DNA recombination (CSR), and plasma cell differentiation. In recent years, epigenetic modifications or factors, such as histone deacetylation and microRNAs (miRNAs), have been shown to interact with B-cell genetic programs to […]

Nature Communications: Cross-talk between miR-471-5p and autophagy component proteins regulates LC3-associated phagocytosis (LAP) of apoptotic germ cells

September 19, 2017

Subbarayalu Panneerdoss, Suryavathi Viswanadhapalli, Nourhan Abdelfattah, Benjamin C. Onyeagucha, Santosh Timilsina, Tabrez A. Mohammad, Yidong Chen, Michael Drake, Kristiina Vuori, T. Rajendra Kumar & Manjeet K. Rao Abstract Phagocytic clearance of apoptotic germ cells by Sertoli cells is vital for germ cell development and differentiation. Here, using a tissue-specific miRNA transgenic mouse model, we show that interaction between miR-471-5p and autophagy member proteins regulates the clearance of […]

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 […]

Familial Cancer: Discovery of mutations in homologous recombination genes in African-American women with breast cancer

September 2, 2017

Yuan Chun Ding 1, Aaron W Adamson 1, Linda Steele 1, Adam M Bailis 2, Esther M John 3 4, Gail Tomlinson 5 6, Susan L Neuhausen 7 Abstract African-American women are more likely to develop aggressive breast cancer at younger ages and experience poorer cancer prognoses than non-Hispanic Caucasians. Deficiency in the repair of DNA by homologous recombination (HR) is associated with cancer development, suggesting that mutations in genes […]

Human Genetics: RNA processing as an alternative route to attack glioblastoma

September 1, 2017

Fabiana Marcelino Meliso, Christopher G Hubert, Pedro A Favoretto Galante, Luiz O Penalva Genomic analyses have become an important tool to identify new avenues for therapy. This is especially true for cancer types with extremely poor outcomes since our lack of effective therapies offers no tangible clinical starting point to build upon. The highly malignant […]

Human Genetics: From mechanisms to therapy: RNA processing’s impact on human genetics

September 1, 2017

Authors Luiz O Penalva, Jeremy R Sanford Protein-coding genes defy the one gene-one enzyme paradigm, in part, through the process of alternative pre-mRNA splicing. This mode of gene regulation is critical for generating protein isoforms with specific functions in development and homeostasis (Kalsotra and Cooper 2011). Alternative pre-mRNA processing not only expands the protein-coding capacity […]