Abstract：
:Allele-specific gene expression can influence disease traits. Non-coding germline genetic variants that alter regulatory elements can cause allele-specific gene expression and contribute to cancer susceptibility. In tumors, both somatic copy number alterations and somatic single nucleotide variants have been shown to lead to allele-specific expression of genes, many of which are considered drivers of tumor growth. Here, we review recent studies revealing the pervasive presence of this phenomenon in cancer susceptibility and progression. Furthermore, we underscore the importance of careful experimental design and computational analysis for accurate allelic expression quantification and avoidance of false positives. Finally, we discuss additional methodological challenges encountered in cancer studies and in the burgeoning field of single-cell transcriptomics.
journal_name
Curr Opin Genet Devjournal_title
Current opinion in genetics & developmentauthors
Robles-Espinoza CD,Mohammadi P,Bonilla X,Gutierrez-Arcelus Mdoi
10.1016/j.gde.2020.10.007subject
Has Abstractpub_date
2020-12-28 00:00:00pages
10-19eissn
0959-437Xissn
1879-0380pii
S0959-437X(20)30146-5journal_volume
66pub_type
杂志文章,评审abstract：:The eukaryotic nucleus is a highly compartmentalized and dynamic environment. Chromosome territories are arranged nonrandomly within the nucleus and numerous studies have indicated that a gene's position in the nucleus can impact its transcriptional activity. Here, we focus on recent advances in our understanding of t...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2009.02.007
更新日期：2009-04-01 00:00:00
abstract：:The nuclear periphery has been implicated in gene regulation and it has been proposed that proximity to the nuclear lamina and inner nuclear membrane (INM) leads to gene repression. More recently, it appears that there is a correlation and interdependence between lamina associated domains (LADs), the epigenome and ove...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2013.11.021
更新日期：2014-04-01 00:00:00
abstract：:The Caenorhabditis elegans hermaphrodite vulva is one of the best studied models for signal transduction and cell fate determination during organogenesis. Systematic forward genetic screens have identified a complex and highly interconnected signaling network formed by the conserved EGFR, NOTCH, and WNT signaling path...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2015.01.006
更新日期：2015-06-01 00:00:00
abstract：:This is the year of the chimpanzee genome. Chimpanzee chromosome 22 has been sequenced and soon will be followed by the whole genome, and thousands of chimpanzee cDNA sequences are available for comparative analysis. Not only does this genomic information allow us to identify human-specific changes in particular genes...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2004.08.007
更新日期：2004-12-01 00:00:00
abstract：:Recent reprogramming studies indicate that mammalian, somatic cells have the potential to achieve pluripotent states and undergo cell type switching. Such cellular traits are observed under natural conditions in animals that regenerate complex organs. A number of invertebrates display the amazing trait of whole body r...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2012.09.006
更新日期：2012-10-01 00:00:00
abstract：:Identification of new genes involved in muscle disorders has dramatically changed the traditional clinical classification of the large and heterogeneous group of the muscular dystrophies. Results obtained in recent years by positional candidate cloning have demonstrated the role of the sarcolemma and of the nuclear en...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(99)80041-0
更新日期：1999-06-01 00:00:00
abstract：:Molecular biological techniques have contributed greatly to the study of vertebrate ocular tissues. The specification of ocular tissues has been shown to be closely related to the expression of transcription factors encoded by genes such as Pax6 and microphthalmia. Lens-specific expression of the delta 1-crystallin ge...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(94)90137-r
更新日期：1994-10-01 00:00:00
abstract：:The transcription factor TFIIH is a versatile, multi-functional protein complex with multiple engagements. Apart from its role in basal transcription, TFIIH is intimately implicated in DNA repair and (probably) in cell cycle control (both of which are required to prevent carcinogenesis) as well as having possible role...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(96)90006-4
更新日期：1996-02-01 00:00:00
abstract：:Notch signaling has been implicated in a wide variety of processes from cell-fate decisions, tissue patterning and morphogenesis to human diseases and cancer. A model for Notch directly regulating gene expression has been proposed and at least two signaling pathways have been identified; however, the molecular mechani...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(98)80115-9
更新日期：1998-08-01 00:00:00
abstract：:Covalent modifications of histone proteins play key roles in transcription, DNA repair, recombination, and other such processes. Over a hundred histone modifications have been described, and a popular idea in the field is that the function of a single histone mark cannot be understood without understanding its combina...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2012.02.013
更新日期：2012-04-01 00:00:00
abstract：:The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2017.03.010
更新日期：2017-08-01 00:00:00
abstract：:Combinatorial regulation of eukaryotic transcription is mediated by proteins that associate in a specific manner to form multiprotein DNA-bound complexes. Substantial progress has recently been made towards the understanding of the molecular determinants of the protein-protein and protein-DNA interactions that govern ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(98)80010-5
更新日期：1998-10-01 00:00:00
abstract：:In this review we discuss the importance of genetic somatic mosaicism and its impact on brain diseases. We start from introducing the different types of somatic mutations, their frequencies and abundances across development and lifespan. We then describe how weakness in DNA repair mechanisms influences their prevalenc...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2020.05.002
更新日期：2020-12-01 00:00:00
abstract：:Genomic information from ancient human remains is beginning to show its full potential for learning about human prehistory. We review the last few years' dramatic finds about European prehistory based on genomic data from humans that lived many millennia ago and relate it to modern-day patterns of genomic variation. T...
journal_title：Current opinion in genetics & development
pub_type： 历史文章,杂志文章,评审
doi：10.1016/j.gde.2016.09.004
更新日期：2016-12-01 00:00:00
abstract：:All the aspects of transcription are controlled by complexes that modify or remodel chromatin at the level of individual genes, gene clusters, or whole chromosomes. The MSL complex that is responsible for dosage compensation in Drosophila is an example of complexes that operate at the whole-chromosome level on the tra...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2009.10.004
更新日期：2009-12-01 00:00:00
abstract：:Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mec...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2016.01.001
更新日期：2016-04-01 00:00:00
abstract：:Non-human primates (NHPs) have been proposed as good models for neurodevelopmental disorders due to close similarities to humans in terms of brain structure and cognitive function. The recent development of genome editing technologies has opened new avenues to generate and investigate genetically modified NHPs as mode...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2020.05.040
更新日期：2020-12-01 00:00:00
abstract：:The effort to map the entire human genome has led recently to the important milestone publication in late 1999 of the complete sequence of chromosome 22. This has been facilitated by increasingly sophisticated tools for genetic analysis and the ensuing wealth of detailed genetic information. The quest for genetic fact...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(00)00082-4
更新日期：2000-06-01 00:00:00
abstract：:Hepatocytes differentiate from the endoderm during embryonic development. Recent studies show, however, that hepatocytes can also be derived from rare cells that reside in the pancreas, bone marrow, and brain. Indeed, the latest discoveries indicate that embryonic hepatocytes normally arise by diversion of an endoderm...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(00)00234-3
更新日期：2001-10-01 00:00:00
abstract：:The recent identification of Wnt-7a as a signalling molecule in dorsal/ventral patterning means that we now have a known signal for control of each of the three limb axes. Fibroblast growth factors can allow proximal/distal patterning and Sonic hedgehog gene expression signals anterior/posterior patterning. Networks o...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(95)90052-i
更新日期：1995-08-01 00:00:00
abstract：:Subsets of patients with common cancers belong to families in which the predisposition is inherited in a regular Mendelian fashion. Genes underlying these cancers are now recognized in colorectal cancer (APC, mismatch repair genes, LKB1) and in breast cancer (BRCA1, BRCA2) whereas, in prostate cancer, a locus in chrom...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(98)80085-3
更新日期：1998-06-01 00:00:00
abstract：:Over the past year, interest has focused on identifying signalling molecules--including Wnts, Sonic hedgehog, BMP-4, and noggin--that divert somitic mesodermal cells into the muscle lineage, either by induction or derepression. New mouse mutants have also provided insights into somite formation and differentiation, as...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(97)80011-1
更新日期：1997-10-01 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
abstract：:A wealth of pharmacological data point to the involvement of catecholamine metabolism in a number of psychiatric and behavioral disorders. Furthermore, evidence points to many of these affective disorders having a moderate to large genetic component. These observations have provided the impetus to search for differenc...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(94)90031-0
更新日期：1994-06-01 00:00:00
abstract：:A number of prokaryotic and eukaryotic genomes are currently being sequenced. Already, the nucleotide sequences of four yeast chromosomes and of 2.2 Mb from Caenorhabditis elegans have been reported. Human genomic sequences have also been used in comparative studies with both mouse and Fugu rubripes. ...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/0959-437x(95)80050-6
更新日期：1995-06-01 00:00:00
abstract：:Loss of the retinoblastoma protein, pRb, appears to have a role in several human tumor types. Mice lacking pRb have been produced as models of human disease, but have a different spectrum of affected tissues. Recent work shows that the tumorigenic effects of pRb may be revealed only after additional genetic alteration...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(95)90057-8
更新日期：1995-02-01 00:00:00
abstract：:In eukaryotes, the genetic material is stored in the nucleus, which is enclosed in a double lipid bilayer, the nuclear envelope (NE). It protects the genome from physical stress and separates it from the rest of the cell. On top of this physical function, growing evidence shows that the nuclear periphery contributes t...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2012.12.001
更新日期：2013-04-01 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：:Unexpected patterns of neuroblast, angioblast and myoblast movement and tissue organization have been defined using lineage tracing and transplantation methods. The most novel and enigmatic new data derive from analyses of genes in the Hox- and Pax-gene families. In addition to the characterization of expression patte...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/s0959-437x(05)80175-3
更新日期：1992-08-01 00:00:00
abstract：:Cornelia de Lange Syndrome (CdLS) is a rare multiple malformation disorder with characteristic facial features, growth and cognitive retardation, and many other abnormalities. CdLS individuals were recently shown to have heterozygous mutations in a previously uncharacterised gene, NIPBL, which encodes delangin, a homo...
journal_title：Current opinion in genetics & development
pub_type： 杂志文章,评审
doi：10.1016/j.gde.2005.04.005
更新日期：2005-06-01 00:00:00
