Dynamic changes in RNA-protein interactions and RNA secondary structure in mammalian erythropoiesis.

Two features of eukaryotic RNA molecules that regulate their post-transcriptional fates are RNA secondary structure and RNA-binding protein (RBP) interaction sites. However, a comprehensive global overview of the dynamic nature of these sequence features during erythropoiesis has never been obtained. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approach to reveal the global landscape of RNA secondary structure and RBP-RNA interaction sites and the dynamics of these features during this important developmental process.

Using RNA Affinity Purification Followed by Mass Spectrometry to Identify RNA-Binding Proteins (RBPs).

RNA-binding proteins (RBPs) perform key functions in posttranscriptional regulation, adding complexity to the RNA life cycle. RNA interactome capture techniques have been applied to various organisms of interest and detected hundreds of RBPs, some with uncharacterized functions. However, even in many well-studied organisms, the primary sequence motif for most RBPs remains unknown.

Computationally Characterizing Protein-Bound Long Noncoding RNAs and Their Secondary Structure Using Protein Interaction Profile Sequencing (PIP-Seq) in Plants.

Two major components of posttranscriptional regulation are RNA-protein interactions and RNA secondary structure. While noncoding RNAs are far more abundant than messenger RNAs in eukaryotic systems, their functions remain largely unstudied. Evidence suggests that RNA-protein interactions and RNA secondary structure also regulate the function of long noncoding RNAs (lncRNAs), which are noncoding RNAs over 200 nucleotides (nt) in length.

An integrated genomic approach identifies persistent tumor suppressive effects of transforming growth factor-β in human breast cancer.

Introduction: Transforming growth factor-βs (TGF-βs) play a dual role in breast cancer, with context-dependent tumor-suppressive or pro-oncogenic effects. TGF-β antagonists are showing promise in early-phase clinical oncology trials to neutralize the pro-oncogenic effects. However, there is currently no way to determine whether the tumor-suppressive effects of TGF-β are still active in human breast tumors at the time of surgery and treatment, a situation that could lead to adverse therapeutic responses.

Tpl2 knockout keratinocytes have increased biomarkers for invasion and metastasis.

Skin cancer is the most common form of cancer in the USA, with an estimated two million cases diagnosed annually. Tumor progression locus 2 (Tpl2), also known as MAP3K8, is a serine/threonine protein kinase in the mitogen-activated protein kinase signal transduction cascade. Tpl2 was identified by our laboratory as having a tumor suppressor function in skin carcinogenesis, with the absence of this gene contributing to heightened inflammation and increased skin carcinogenesis.