Quantitative immunopeptidomics reveals a tumor stroma-specific target for T cell therapy.

T cell receptor (TCR)-based immunotherapy has emerged as a promising therapeutic approach for the treatment of patients with solid cancers. Identifying peptide-human leukocyte antigen (pHLA) complexes highly presented on tumors and rarely expressed on healthy tissue in combination with high-affinity TCRs that when introduced into T cells can redirect T cells to eliminate tumor but not healthy tissue is a key requirement for safe and efficacious TCR-based therapies. To discover promising shared tumor antigens that could be targeted via TCR-based adoptive T cell therapy, we employed population-scale immunopeptidomics using quantitative mass spectrometry across ~1500 tumor and normal tissue samples.

Regulated dicing of pre-mir-144 via reshaping of its terminal loop.

Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2).

Library Selection with a Randomized Repertoire of (βα)-Barrel Enzymes Results in Unexpected Induction of Gene Expression.

The potential of the frequently encountered (βα)-barrel fold to acquire new functions was tested by an approach combining random mutagenesis and selection . For this purpose, the genes encoding 52 different phosphate-binding (βα)-barrel proteins were subjected to error-prone PCR and cloned into an expression plasmid. The resulting mixed repertoire was used to transform different auxotrophic strains, each lacking an enzyme with a phosphate-containing substrate.

The nuclear matrix protein Matr3 regulates processing of the synaptic microRNA-138-5p.

microRNA-dependent post-transcriptional control represents an important gene-regulatory layer in post-mitotic neuronal development and synaptic plasticity. We recently identified the brain-enriched miR-138 as a negative regulator of dendritic spine morphogenesis in rat hippocampal neurons. A potential involvement of miR-138 in cognition is further supported by a recent GWAS study on memory performance in a cohort of aged (>60 years) individuals.

Publisher Correction: Regulation of microRNA biogenesis and its crosstalk with other cellular pathways.

The legend of Figure 2 neglected to acknowledge that part b was adapted with permission from ref., Elsevier and that part d, third panel from the left was reproduced from ref., Springer Nature Limited.

Author Correction: Regulation of microRNA biogenesis and its crosstalk with other cellular pathways.

In Figure 1b, the GHG sequence motif in the primary microRNA has been moved to the basal stem and the ruler of the basal stem has been shortened to more precisely delineate 11 base pairs. The changes have been made in the HTML and PDF versions of the manuscript.

Regulation of microRNA biogenesis and its crosstalk with other cellular pathways.

MicroRNAs (miRNAs) are short non-coding RNAs that inhibit the expression of target genes by directly binding to their mRNAs. miRNAs are transcribed as precursor molecules, which are subsequently cleaved by the endoribonucleases Drosha and Dicer. Mature miRNAs are bound by a member of the Argonaute (AGO) protein family to form the RNA-induced silencing complex (RISC) in a process termed RISC loading.

Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors.

Cleavage factor II (CF II) is a poorly characterized component of the multiprotein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not.

LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs.

LIN28 is a bipartite RNA-binding protein that post-transcriptionally inhibits the biogenesis of let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remain poorly understood because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD), which binds a GGAG-like element in the precursor, and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U)GAU motif.

Identification of microRNA Precursor-Associated Proteins.

MicroRNA (miRNA) biogenesis is regulated intricately at multiple levels. In addition to transcriptional control of pri-miRNA loci, sequence as well as structural features of the pri-miRNA-stem loop determine its processing efficiency by the endonucleases Drosha and Dicer. On the one hand, general features are necessary to allow a hairpin to be recognized by the processing machinery; on the other hand, specific sequence motifs of individual miRNA precursors can be read by RNA binding proteins (RBPs) that regulate processing, leading to increased or decreased levels of functional miRNAs.

Interactions, localization, and phosphorylation of the mA generating METTL3-METTL14-WTAP complex.

-methyladenine (mA) is found on many eukaryotic RNAs including mRNAs. mA modification has been implicated in mRNA stability and turnover, localization, or translation efficiency. A heterodimeric enzyme complex composed of METTL3 and METTL14 generates mA on mRNAs.

A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis.

During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs.

Structural and functional insights into the fly microRNA biogenesis factor Loquacious.

In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing.

The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation.

TRIM-NHL proteins are conserved among metazoans and control cell fate decisions in various stem cell linages. The Drosophila TRIM-NHL protein Brain tumor (Brat) directs differentiation of neuronal stem cells by suppressing self-renewal factors. Brat is an RNA-binding protein and functions as a translational repressor.

Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins.

Early B-cell factor 1 (Ebf1) is a key transcriptional determinant of B-lymphocyte differentiation whose DNA-binding domain has no sequence similarity to other transcription factor families. Here we report the crystal structure of an Ebf1 dimer bound to its palindromic recognition site. The DNA-binding domain adopts a pseudoimmunoglobulin-like fold with novel topology, but is structurally similar to the Rel homology domains of NFAT and NF-κB.

SMADs stimulate miRNA processing.

MicroRNAs (miRNAs) are potent regulators of gene expression. Consequently, miRNA expression is tightly regulated itself. In this issue, Hata and coworkers provide mechanistic insights into how SMAD proteins regulated the biogenesis of a specific subset of human miRNAs.

Early B cell factor 1 regulates B cell gene networks by activation, repression, and transcription- independent poising of chromatin.

The transcription factor early B cell factor-1 (Ebf1) is a key determinant of B lineage specification and differentiation. To gain insight into the molecular basis of Ebf1 function in early-stage B cells, we combined a genome-wide ChIP sequencing analysis with gain- and loss-of-function transcriptome analyses. Among 565 genes that are occupied and transcriptionally regulated by Ebf1, we identified large sets involved in (pre)-B cell receptor and Akt signaling, cell adhesion, and migration.

Transcription factor EBF restricts alternative lineage options and promotes B cell fate commitment independently of Pax5.

Alternative lineage restriction and B cell fate commitment require the transcription factor Pax5, but the function of early B cell factor (EBF) in these processes remains mostly unexplored. Here we show that in the absence of EBF, 'expandable' and clonal lymphoid progenitor cells retained considerable myeloid potential. Conversely, ectopic expression of EBF in multipotential progenitor cells directed B cell generation at the expense of myeloid cell fates.