Long noncoding RNAs (lncRNAs) are potentially important regulators of cell differentiation and development, but little is known about their roles in B lymphocytes. Using RNA-seq and de novo transcript assembly, we identified 4516 lncRNAs expressed in 11 stages of B-cell development and activation. Most of these lncRNAs have not been previously detected, even in the closely related T-cell lineage. Comparison with lncRNAs previously described in human B cells identified 185 mouse lncRNAs that have human orthologs. Using chromatin immunoprecipitation-seq, we classified 20% of the lncRNAs as either enhancer-associated (eRNA) or promoter-associated RNAs. We identified 126 eRNAs whose expression closely correlated with the nearest coding gene, thereby indicating the likely location of numerous enhancers active in the B-cell lineage. Furthermore, using this catalog of newly discovered lncRNAs, we show that PAX5, a transcription factor required to specify the B-cell lineage, bound to and regulated the expression of 109 lncRNAs in pro-B and mature B cells and 184 lncRNAs in acute lymphoblastic leukemia.

Adhesion and migration of T cells are controlled by chemokines and by adhesion molecules, especially integrins, and play critical roles in the normal physiological function of T lymphocytes. Using an RNA interference screen we have identified the WNK1 kinase as a regulator of both integrin-mediated adhesion and T cell migration. We demonstrate that WNK1 is a negative regulator of integrin-mediated adhesion, whereas it acts as a positive regulator of migration via OXSR1 and STK39 kinases and the SLC12A2 ion co-transporter. WNK1-deficient T cells home less efficiently to lymphoid organs, and migrate more slowly through them. Our results reveal that a pathway hitherto known only to regulate salt homeostasis in the kidney functions to balance T cell adhesion and migration.

The baculovirus insect cell expression system (BEVS) was used for the production of self-forming Porcine parvovirus-like particles (VLPs) in serum-free medium. A low multiplicity of infection (MOI) strategy was used to overcome an extra virus amplification step, undesirable in industrial production, and to minimize the virus passage effect. It was confirmed that the time of infection (TOI) and MOI are dependent variables. Higher cell densities were obtained at low MOIs, keeping a constant TOI; however, both volumetric and specific productivities were lower. In synchronous infection, at high MOI, the specific productivity decreased when the cells were infected in the late phase of growth. Product degradation due to cell lysis strongly influenced the optimal time of harvest (TOH). Time of harvest was found to be highly dependent on the MOI, and a direct relationship with the cell yield was obtained. Analysis of the culture medium reveals that glutamine depletion occurs in the late phase of the growth. Supplementation of glutamine to uninfected cell cultures resulted in an increased cell yield. Its addition to cultures infected in the middle phase of the growth curve was also able to restore the productivity levels, but addition to cells in their stationary phase caused no observable effect on product expression. The study clearly shows that for a specific TOI it is not obvious what the correct MOI should be to obtain the best volumetric productivity.

Edited by Michael IbbaKeywords: NMD ROD1 UPF1 a b s t r a c t RNA-binding proteins play a crucial role in the post-transcriptional regulation of gene expression. Polypyrimidine tract binding protein (PTB in humans) has been extensively characterized as an important splicing factor, and has additional functions in 3 0 end processing and translation. ROD1 is a PTB paralog containing four RRM (RNA recognition motif) domains. Here, we discover a function of ROD1 in nonsense-mediated mRNA decay (NMD). We show that ROD1 and the core NMD factor UPF1 interact and co-regulate an extensive number of target genes. Using a reporter system, we demonstrate that ROD1, similarly to UPF1 and UPF2, is required for the destabilization of a known NMD substrate. Finally, we show through RIP-seq that ROD1 and UPF1 associate with a significant number of common transcripts. Structured summary of protein interactions:ROD1 physically interacts with TMED10,

In the version of this article initially published, the citation of Figure 3 in the second paragraph of the third subsection (Chromatin: the nexus of phenotype and the environment) is incorrect. That should cite Figure 2, as follows: "From an evolutionary perspective, two extreme models of how such complexity might be generated and regulated can be envisaged 95 (Fig. 2). " The error has been corrected in the HTML and PDF versions of the article.Erratum: Sall1 is a transcriptional regulator defining microglia identity and function In the HTML version of this article initially published, the scale bar was missing from the inset in the top right image in Figure 2d; the bottom left plot in Figure 2e was incorrectly a duplicate of the adjacent plot at right; and the designations in Figure 4b (Sall1 f l and Sall1 creER/fl ) should have been Sall1 fl/fl and Sall1 CreER/fl (respectively). Also, the arrows in the designations above and below the plots in Supplementary Figure 3b were rendered as boxes; these should have been as follows: Sall1 +/+ →Cx3cr1 CreER -iDTR and Sall1 GFP/+ →Cx3cr1 CreER -iDTR. Finally, in Supplementary Figure 4f, the red (Ki67 + ) cells in the right set of images were not visible. These errors have been corrected for the HTML version of this article.