The distribution of variation in regulatory gene segments, as present in MHC class II promoters.

Abstract:

:Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and mouse using extensive collections of published sequences together with unpublished sequences recently deposited by us in the EMBL gene bank using the Shannon entropy to quantify diversity. For comparison, we also apply our analysis to distantly related MHC class II promoters, as well as to class I promoters and to class II coding regions. We observe a high level of intraspecies variability, which in mouse but not in man is localized to a significant extent near the binding sites of transcription factors-sites that are conserved over longer evolutionary distances. This localization may both indicate and enhance heterozygote advantage, as the presence of two functionally different promoters would be expected to confer flexibility in the immune response.

journal_name

Genome Res

journal_title

Genome research

authors

Cowell LG,Kepler TB,Janitz M,Lauster R,Mitchison NA

doi

10.1101/gr.8.2.124

subject

Has Abstract

pub_date

1998-02-01 00:00:00

pages

124-34

issue

2

eissn

1088-9051

issn

1549-5469

journal_volume

8

pub_type

杂志文章
  • Characterization of Alu repeats that are associated with trinucleotide and tetranucleotide repeat microsatellites.

    abstract::The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of m...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.7.7.716

    authors: Yandava CN,Gastier JM,Pulido JC,Brody T,Sheffield V,Murray J,Buetow K,Duyk GM

    更新日期:1997-07-01 00:00:00

  • The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.

    abstract::RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.189621.115

    authors: Cieslik M,Chugh R,Wu YM,Wu M,Brennan C,Lonigro R,Su F,Wang R,Siddiqui J,Mehra R,Cao X,Lucas D,Chinnaiyan AM,Robinson D

    更新日期:2015-09-01 00:00:00

  • Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells.

    abstract::Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.2431504

    authors: Hattori N,Abe T,Hattori N,Suzuki M,Matsuyama T,Yoshida S,Li E,Shiota K

    更新日期:2004-09-01 00:00:00

  • The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine.

    abstract::ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicin...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.092841.109

    authors: Biesecker LG,Mullikin JC,Facio FM,Turner C,Cherukuri PF,Blakesley RW,Bouffard GG,Chines PS,Cruz P,Hansen NF,Teer JK,Maskeri B,Young AC,NISC Comparative Sequencing Program.,Manolio TA,Wilson AF,Finkel T,Hwang P,Arai A

    更新日期:2009-09-01 00:00:00

  • A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

    abstract::The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a ch...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.253435.119

    authors: Pettersson ME,Rochus CM,Han F,Chen J,Hill J,Wallerman O,Fan G,Hong X,Xu Q,Zhang H,Liu S,Liu X,Haggerty L,Hunt T,Martin FJ,Flicek P,Bunikis I,Folkvord A,Andersson L

    更新日期:2019-11-01 00:00:00

  • The landscape of histone modifications across 1% of the human genome in five human cell lines.

    abstract::We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including th...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.5704207

    authors: Koch CM,Andrews RM,Flicek P,Dillon SC,Karaöz U,Clelland GK,Wilcox S,Beare DM,Fowler JC,Couttet P,James KD,Lefebvre GC,Bruce AW,Dovey OM,Ellis PD,Dhami P,Langford CF,Weng Z,Birney E,Carter NP,Vetrie D,Dunham I

    更新日期:2007-06-01 00:00:00

  • Spidey: a tool for mRNA-to-genomic alignments.

    abstract::We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing error...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.195301

    authors: Wheelan SJ,Church DM,Ostell JM

    更新日期:2001-11-01 00:00:00

  • Active Alu element "A-tails": size does matter.

    abstract::Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.384802

    authors: Roy-Engel AM,Salem AH,Oyeniran OO,Deininger L,Hedges DJ,Kilroy GE,Batzer MA,Deininger PL

    更新日期:2002-09-01 00:00:00

  • A matter of life or death: how microsatellites emerge in and vanish from the human genome.

    abstract::Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.122937.111

    authors: Kelkar YD,Eckert KA,Chiaromonte F,Makova KD

    更新日期:2011-12-01 00:00:00

  • Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution.

    abstract::Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosa...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.230433.117

    authors: Naqvi S,Bellott DW,Lin KS,Page DC

    更新日期:2018-04-01 00:00:00

  • Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast.

    abstract::Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.164996.113

    authors: McManus CJ,May GE,Spealman P,Shteyman A

    更新日期:2014-03-01 00:00:00

  • Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors.

    abstract::Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor bindi...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.257576.119

    authors: Cusack M,King HW,Spingardi P,Kessler BM,Klose RJ,Kriaucionis S

    更新日期:2020-10-01 00:00:00

  • Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing.

    abstract::Genomic structural variation (SV) is a major determinant for phenotypic variation. Although it has been extensively studied in humans, the nucleotide resolution structure of SVs within the widely used model organism Drosophila remains unknown. We report a highly accurate, densely validated map of unbalanced SVs compri...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.142646.112

    authors: Zichner T,Garfield DA,Rausch T,Stütz AM,Cannavó E,Braun M,Furlong EE,Korbel JO

    更新日期:2013-03-01 00:00:00

  • Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution.

    abstract::Somatic L1 retrotransposition events have been shown to occur in epithelial cancers. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.196238.115

    authors: Ewing AD,Gacita A,Wood LD,Ma F,Xing D,Kim MS,Manda SS,Abril G,Pereira G,Makohon-Moore A,Looijenga LH,Gillis AJ,Hruban RH,Anders RA,Romans KE,Pandey A,Iacobuzio-Donahue CA,Vogelstein B,Kinzler KW,Kazazian HH Jr,Sol

    更新日期:2015-10-01 00:00:00

  • A bioinformatics-based strategy identifies c-Myc and Cdc25A as candidates for the Apmt mammary tumor latency modifiers.

    abstract::The epistatically interacting modifier loci (Apmt1 and Apmt2) accelerate the polyoma Middle-T (PyVT)-induced mammary tumor. To identify potential candidate genes loci, a combined bioinformatics and genomics strategy was used. On the basis of the assumption that the loci were functioning in the same or intersecting pat...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.210502

    authors: Cozma D,Lukes L,Rouse J,Qiu TH,Liu ET,Hunter KW

    更新日期:2002-06-01 00:00:00

  • Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk.

    abstract::Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.133728.111

    authors: Brinkman AB,Gu H,Bartels SJ,Zhang Y,Matarese F,Simmer F,Marks H,Bock C,Gnirke A,Meissner A,Stunnenberg HG

    更新日期:2012-06-01 00:00:00

  • The first five years of single-cell cancer genomics and beyond.

    abstract::Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.191098.115

    authors: Navin NE

    更新日期:2015-10-01 00:00:00

  • Cloning of 559 potential exons of genes of human chromosome 21 by exon trapping.

    abstract::Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6.8.747

    authors: Chen H,Chrast R,Rossier C,Morris MA,Lalioti MD,Antonarakis SE

    更新日期:1996-08-01 00:00:00

  • An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

    abstract::Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.146084.112

    authors: Wang Y,Lu J,Yu J,Gibbs RA,Yu F

    更新日期:2013-05-01 00:00:00

  • Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels.

    abstract::Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6.1.58

    authors: Martinez JM,Breidenbach HH,Cawthon R

    更新日期:1996-01-01 00:00:00

  • Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum.

    abstract::The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical m...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.1555203

    authors: Bankier AT,Spriggs HF,Fartmann B,Konfortov BA,Madera M,Vogel C,Teichmann SA,Ivens A,Dear PH

    更新日期:2003-08-01 00:00:00

  • Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure.

    abstract::Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.106252.110

    authors: Storlazzi CT,Lonoce A,Guastadisegni MC,Trombetta D,D'Addabbo P,Daniele G,L'Abbate A,Macchia G,Surace C,Kok K,Ullmann R,Purgato S,Palumbo O,Carella M,Ambros PF,Rocchi M

    更新日期:2010-09-01 00:00:00

  • HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

    abstract::Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessin...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.220640.117

    authors: Yang T,Zhang F,Yardımcı GG,Song F,Hardison RC,Noble WS,Yue F,Li Q

    更新日期:2017-11-01 00:00:00

  • Interaction between the X chromosome and an autosome regulates size sexual dimorphism in Portuguese Water Dogs.

    abstract::Size sexual dimorphism occurs in almost all mammals. In Portuguese Water Dogs, much of the difference in skeletal size between females and males is due to the interaction between a Quantitative Trait Locus (QTL) on the X-chromosome and a QTL linked to Insulin-like Growth Factor 1 (IGF-1) on the CFA 15 autosome. In fem...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3712705

    authors: Chase K,Carrier DR,Adler FR,Ostrander EA,Lark KG

    更新日期:2005-12-01 00:00:00

  • A role for palindromic structures in the cis-region of maize Sirevirus LTRs in transposable element evolution and host epigenetic response.

    abstract::Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length o...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.193763.115

    authors: Bousios A,Diez CM,Takuno S,Bystry V,Darzentas N,Gaut BS

    更新日期:2016-02-01 00:00:00

  • ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm.

    abstract::Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.242362.118

    authors: Bozek M,Cortini R,Storti AE,Unnerstall U,Gaul U,Gompel N

    更新日期:2019-05-01 00:00:00

  • Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays.

    abstract::Mutational analysis of large genes with complex genomic structures plays an important role in medical genetics. Technical limitations associated with current mutation screening protocols have placed increased emphasis on the development of new technologies to simplify these procedures. High-density arrays of >90,000-o...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.8.12.1245

    authors: Hacia JG,Sun B,Hunt N,Edgemon K,Mosbrook D,Robbins C,Fodor SP,Tagle DA,Collins FS

    更新日期:1998-12-01 00:00:00

  • Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project.

    abstract::CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.2171704

    authors: Chen R,Sodergren E,Weinstock GM,Gibbs RA

    更新日期:2004-04-01 00:00:00

  • A nuclear matrix attachment site in the 4q35 locus has an enhancer-blocking activity in vivo: implications for the facio-scapulo-humeral dystrophy.

    abstract::Facio-scapulo-humeral dystrophy (FSHD), a muscular hereditary disease with a prevalence of 1 in 20,000, is caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. Earlier, we demonstrated the existence in the vicinity of the D4Z4 repeat of a nuclear matrix attachment site, FR-MAR, efficient in no...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6620908

    authors: Petrov A,Allinne J,Pirozhkova I,Laoudj D,Lipinski M,Vassetzky YS

    更新日期:2008-01-01 00:00:00

  • Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors.

    abstract::Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.107961.110

    authors: Robbins CM,Tembe WA,Baker A,Sinari S,Moses TY,Beckstrom-Sternberg S,Beckstrom-Sternberg J,Barrett M,Long J,Chinnaiyan A,Lowey J,Suh E,Pearson JV,Craig DW,Agus DB,Pienta KJ,Carpten JD

    更新日期:2011-01-01 00:00:00