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Cold Spring Harbor, NY, United States

Spector D.L.,Cold Spring Harbor Laboratory
Cold Spring Harbor perspectives in biology | Year: 2011

Nuclear speckles, also known as interchromatin granule clusters, are nuclear domains enriched in pre-mRNA splicing factors, located in the interchromatin regions of the nucleoplasm of mammalian cells. When observed by immunofluorescence microscopy, they usually appear as 20-50 irregularly shaped structures that vary in size. Speckles are dynamic structures, and their constituents can exchange continuously with the nucleoplasm and other nuclear locations, including active transcription sites. Studies on the composition, structure, and dynamics of speckles have provided an important paradigm for understanding the functional organization of the nucleus and the dynamics of the gene expression machinery. Source


The life span of a mammalian mRNA is determined, in part, by the binding of regulatory proteins and small RNA-guided complexes. The conserved endonuclease activity of Argonaute2 requires extensive complementarity between a small RNA and its target and is not used by animal microRNAs, which pair with their targets imperfectly. Here we investigate the endonucleolytic function of Ago2 and other nucleases by transcriptome-wide profiling of mRNA cleavage products retaining 5' phosphate groups in mouse embryonic stem cells (mESCs). We detect a prominent signature of Ago2-dependent cleavage events and validate several such targets. Unexpectedly, a broader class of Ago2-independent cleavage sites is also observed, indicating participation of additional nucleases in site-specific mRNA cleavage. Within this class, we identify a cohort of Drosha-dependent mRNA cleavage events that functionally regulate mRNA levels in mESCs, including one in the Dgcr8 mRNA. Together, these results highlight the underappreciated role of endonucleolytic cleavage in controlling mRNA fates in mammals. Copyright (c) 2010 Elsevier Inc. All rights reserved. Source


Park S.J.,Cold Spring Harbor Laboratory
Nature Genetics | Year: 2014

Naturally occurring genetic variation in the universal florigen flowering pathway has produced major advancements in crop domestication. However, variants that can maximize crop yields may not exist in natural populations. Here we show that tomato productivity can be fine-tuned and optimized by exploiting combinations of selected mutations in multiple florigen pathway components. By screening for chemically induced mutations that suppress the bushy, determinate growth habit of field tomatoes, we isolated a new weak allele of the florigen gene SINGLE FLOWER TRUSS (SFT) and two mutations affecting a bZIP transcription factor component of the 'florigen activation complex' (ref. 11). By combining heterozygous mutations, we pinpointed an optimal balance of flowering signals, resulting in a new partially determinate architecture that translated to maximum yields. We propose that harnessing mutations in the florigen pathway to customize plant architecture and flower production offers a broad toolkit to boost crop productivity. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. Source


Huang Z.J.,Cold Spring Harbor Laboratory
Neuron | Year: 2014

The mammalian neocortex gives rise to a wide range of mental activities and consists of a constellation of interconnected areas that are built from a set of basic circuit templates. Major obstacles to understanding cortical architecture include the diversity of cell types, their highly recurrent local and global connectivity, dynamic circuit operations, and a convoluted developmental assembly process rooted in the genome. With our increasing knowledge of gene expression and developmental genetic principles, it is now feasible to launch a program of genetic dissection of cortical circuits through systematic targeting of cell types and fate mapping of neural progenitors. Strategic design of even a modest number of mouse driver lines will facilitate efforts tocompile a cell type parts list, build a Cortical Cell Atlas, establish experimental access to modern tools, integrate studies across levels, and provide coordinates for tracing developmental trajectory from circuit assembly to functional operation. © 2014 Elsevier Inc. Source


Mills A.A.,Cold Spring Harbor Laboratory
Nature Reviews Cancer | Year: 2010

The discovery that cancer can be governed above and beyond the level of our DNA presents a new era for designing therapies that reverse the epigenetic state of a tumour cell. Understanding how altered chromatin dynamics leads to malignancy is essential for controlling tumour cells while sparing normal cells. Polycomb and trithorax group proteins are evolutionarily conserved and maintain chromatin in the 'off' or 'on' states, thereby preventing or promoting gene expression, respectively. Recent work highlights the dynamic interplay between these opposing classes of proteins, providing new avenues for understanding how these epigenetic regulators function in tumorigenesis. © 2010 Macmillan Publishers Limited. All rights reserved. Source

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