Abstract：
:Thousands of genes produce polyadenylated mRNAs that still contain one or more introns. These transcripts are known as retained intron RNAs (RI-RNAs). In the past 10 years, RI-RNAs have been linked to post-transcriptional alternative splicing in a variety of developmental contexts, but they can also be dead-end products fated for RNA decay. Here we discuss the role of intron retention in shaping gene expression programs, as well as recent evidence suggesting that the biogenesis and fate of RI-RNAs is regulated by nuclear organization. We discuss the possibility that proximity of RNA to nuclear speckles - biomolecular condensates that are highly enriched in splicing factors and other RNA binding proteins - is associated with choices ranging from efficient co-transcriptional splicing, export and stability to regulated post-transcriptional splicing and possible vulnerability to decay.
journal_name
Curr Opin Genet Devjournal_title
Current opinion in genetics & developmentauthors
Gordon JM,Phizicky DV,Neugebauer KMdoi
10.1016/j.gde.2020.11.002subject
Has Abstractpub_date
2020-12-05 00:00:00pages
67-76eissn
0959-437Xissn
1879-0380pii
S0959-437X(20)30148-9journal_volume
67pub_type
杂志文章,评审abstract：:Primordial germ cells (PGCs), the embryonic precursors of the gametes of the adult animal, can give rise to two types of pluripotent stem cells. In vivo, PGCs can give rise to embryonal carcinoma cells, the pluripotent stem cells of testicular tumors. Cultured PGCs exposed to a specific cocktail of growth factors give...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2003.08.010
更新日期：2003-10-01 00:00:00
abstract：:Hox proteins regulate specific sets of target genes to give rise to morphological distinctions along the anterior-posterior body axis of metazoans. Though they have high developmental specificity, Hox proteins have low DNA binding specificity, so how they select the appropriate target genes has remained enigmatic. The...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2005.06.009
更新日期：2005-08-01 00:00:00
abstract：:Whole-transcriptome analyses have established that the plant circadian clock regulates virtually every plant biological process and most prominently hormonal and stress response pathways. Systems biology efforts have successfully modeled the plant central clock machinery and an iterative process of model refinement an...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2010.08.010
更新日期：2010-12-01 00:00:00
abstract：:Much progress has been made in the past few years in understanding the mechanism and regulation of mRNA synthesis. This rapid progress has largely been due to the availability of cloned genes encoding components of the transcription machinery. Structural and biochemical studies are rapidly defining the architecture of...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(96)80044-x
更新日期：1996-04-01 00:00:00
abstract：:Unexpected relationships among the various aminoacyl-tRNA synthetases continue to be uncovered. The question arises - is this mainly the result of promiscuous exchange, or is the confusion really a reflection of the differential loss of past duplications? Phylogenetic analysis may yet provide the answer. ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(98)80030-0
更新日期：1998-12-01 00:00:00
abstract：:The digital reconstruction of the embryogenesis of model organisms from 3D+time data is revolutionizing practices in quantitative and integrative Developmental Biology. A manual and fully supervised image analysis of the massive complex data acquired with new microscopy technologies is no longer an option and automate...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2011.08.001
更新日期：2011-10-01 00:00:00
abstract：:Cell-cell and starvation signals are funneled through the phosphorelay to initiate sporulation by activating the transcription regulator SpoOA. Activation of SpoOA leads to synthesis of the transcription factors sigmaF and sigmaE. Substantial advances have been made in our understanding of the signal circuitry of the ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(96)80080-3
更新日期：1996-10-01 00:00:00
abstract：:The Selfish Operon Model postulates that the organization of bacterial genes into operons is beneficial to the constituent genes in that proximity allows horizontal cotransfer of all genes required for a selectable phenotype; eukaryotic operons formed for very different reasons. Horizontal transfer of selfish operons ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(99)00025-8
更新日期：1999-12-01 00:00:00
abstract：:Genetic conflicts arise when the evolutionary interests of two genetic elements are not aligned. Conflicts between genomes (e.g. pathogen versus host) or within the same genome (e.g. internal parasitic DNA sequences versus the rest of the host genome) can both foster 'molecular arms races', in which genes on both side...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2019.07.011
更新日期：2019-10-01 00:00:00
abstract：:During development and differentiation, early inductive processes that influence cell fate at a later stage leave marks at distinct gene loci that are maintained through several rounds of mitosis. The structure of chromatin is part of this epigenetic memory that restricts or permits differential expression of genes in...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(00)00175-1
更新日期：2001-04-01 00:00:00
abstract：:Models in developmental biology continue to yield valuable insights, yet do not play a strong role as guides to experiment. This may be because of the largely unexplored complexity of most developing organisms, and the fact that the most powerful models work at a very abstract level. In Dictyostelium discoideum, howev...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(05)80186-8
更新日期：1992-08-01 00:00:00
abstract：:Recent evidence suggests that dynamic three-dimensional genomic interactions in the nucleus exert critical roles in regulated gene expression. Here, we review a series of recent paradigm-shifting experiments that highlight the existence of specific gene networks within the self-organizing space of the nucleus. These g...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2009.07.005
更新日期：2009-10-01 00:00:00
abstract：:Bladder cancer is the 5th commonest cancer and two major risk factors are smoking and occupational chemical exposure. There is also evidence of a genetic component to its aetiology. Candidate gene studies have mostly focused on genes involved in adduct metabolism and DNA repair, including a recent consortium-based met...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2010.01.002
更新日期：2010-06-01 00:00:00
abstract：:Vertebrate neural crest cells are embryonic neuroepithelial cells that undergo an epithelial-mesenchymal transition, migrate throughout the embryo and form a wide variety of derivatives, including peripheral neurons and glia, pigment cells, and craniofacial cartilage, bone and teeth. Neural crest cell evolution and el...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章
doi：10.1016/j.gde.2008.11.006
更新日期：2008-12-01 00:00:00
abstract：:Our understanding of how roots develop in soil may be at the eve of significant transformations. The formidable expansion of imaging technologies enables live observations of the rhizosphere micro-pore architecture at unprecedented resolution. Granular matter physics provides ways to understand the microscopic fluctua...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2018.03.007
更新日期：2018-08-01 00:00:00
abstract：:In 2003, a p53-expressing adenovirus was approved as a cancer therapy drug in China. Consequently, there has been a surge in the need to understand the regulation of wild type p53 function in vivo. The majority of the progress made during the past two years has focused on the cellular factors and post-translational mo...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2004.12.008
更新日期：2005-02-01 00:00:00
abstract：:Recent technological and computational advances in understanding the transcriptional and chromatin features of single cells have begun answering longstanding questions in the extent and impact of biological heterogeneity. Here, we outline the intrinsic and extrinsic mechanisms that underlie the transcriptional and fun...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2015.11.004
更新日期：2016-04-01 00:00:00
abstract：:One of the ways in which higher eukaryotes receive messages from the environment is via cell surface receptor tyrosine kinases. These are transmembrane proteins with an extracellular binding domain that specifies the growth factor with which it will interact, and an intracellular domain that encodes the tyrosine kinas...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(94)90085-x
更新日期：1994-02-01 00:00:00
abstract：:A rooted phylogenetic tree of the kinetoplastid protozoa has been constructed that, together with a comparative analysis of editing of several genes, leads to the surprising conclusion that extensive or pan-editing with multiple overlapping guide RNAs is more ancient than 5'-editing. The mechanism of editing is still ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(94)90075-2
更新日期：1994-12-01 00:00:00
abstract：:Transcription is the first step in gene expression, and its regulation underlies multicellular development and the response to environmental changes. Most studies of transcriptional regulation have focused on the recruitment of RNA polymerase to promoters. However, recent work has shown that, for many promoters, post-...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2007.12.008
更新日期：2008-04-01 00:00:00
abstract：:The current state of the gene regulatory network for endomesoderm specification in sea urchin embryos is reviewed. The network was experimentally defined, and is presented as a predictive map of cis-regulatory inputs and functional regulatory gene interconnections (updated versions of the network and most of the under...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2004.06.004
更新日期：2004-08-01 00:00:00
abstract：:Human pluripotent stem cells derived from embryos (human Embryonic Stem Cells or hESCs) or generated by direct reprogramming of somatic cells (human Induced Pluripotent Stem Cells or hiPSCs) can proliferate almost indefinitely in vitro while maintaining the capacity to differentiate into a broad diversity of cell type...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2017.07.004
更新日期：2017-10-01 00:00:00
abstract：:Telomerase regulation and telomere shortening act as a strong tumor suppressor mechanism in human somatic cells. Point mutations in the promoter of telomerase reverse transcriptase (TERT) are the most frequent non-coding mutation in cancer. These TERT promoter mutations (TPMs) create de novo ETS factor binding sites u...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2020.02.001
更新日期：2020-02-01 00:00:00
abstract：:The largest subunit of eukaryotic RNA polymerase II has an unusual tandemly repeated heptapeptide sequence at its carboxyl terminus. The function of this evolutionarily conserved carboxy-terminal domain is unknown; however, new evidence links it to the formation of a large multi-component RNA polymerase II complex pos...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(95)80009-3
更新日期：1995-04-01 00:00:00
abstract：:Our understanding of the mechanism of action of retinoids has been greatly expanded by a series of recent findings. First, the three-dimensional structure of the ligand-binding domain of two retinoid receptors has been solved and suggests that ligand binding induces marked allosteric changes. Second, several co-factor...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(96)80085-2
更新日期：1996-10-01 00:00:00
abstract：:The detection of sequence variation with restriction fragment length polymorphisms is advancing our knowledge of plant genetics on several fronts. In the past year, there has been progress in genetic map construction, phylogeny studies, and the dissection of multigenic traits. In addition, new methods that are indepen...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(91)80051-m
更新日期：1991-06-01 00:00:00
abstract：:Multiple neural and non-neural cell types arise from the neural crest (NC) in vertebrate embryos. Recent work has provided evidence for multipotent stem cells and intermediate precursors in the early NC cell population as well as in various NC derivatives in embryos and even in adult. Advances have been made towards u...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2003.08.002
更新日期：2003-10-01 00:00:00
abstract：:The conversion of one cell type to another is defined as metaplasia (or sometimes it is referred to as transdifferentiation or cellular reprogramming). Metaplasia is important clinically and may predispose to the development of cancer. Barrett's metaplasia is one such example and is the focus of the present review. Ba...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2012.08.001
更新日期：2012-10-01 00:00:00
abstract：:The dystrophin-glycoprotein complex (DGC) is a multisubunit complex that connects the cytoskeleton of a muscle fiber to its surrounding extracellular matrix. Mutations in the DGC disrupt the complex and lead to muscular dystrophy. There are a few naturally occurring animal models of DGC-associated muscular dystrophy (...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(02)00309-x
更新日期：2002-06-01 00:00:00
abstract：:Pluripotency-associated transcription factors possess a pivotal role to maintain pluripotency in pluripotent stem cells as well as to induce pluripotency in somatic cells. They direct specific pattern of gene expression from the genome by co-operating with the genetic and epigenetic mechanisms. Recent findings reveale...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2014.08.004
更新日期：2014-10-01 00:00:00
