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encode and the parts of the human genome

STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE PART C-STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2018年 72卷 28-37页

作者： Kaiser, Marie, I Bielefeld Univ Dept Philosophy Postfach 10 01 31 D-33501 Bielefeld Germany

This paper examines a specific kind of part-whole relations that exist in the molecular genetic domain. The central question is under which conditions a particular molecule, such as a DNA sequence, is a biological part of the human genome. I address this question by analyzing how biologists in fact partition the human genome into parts. This paper thus presents a case study in the metaphysics of biological practice. I develop a metaphysical account of genomic parthood by analyzing the investigative and reasoning practices in the encode (ENCyclopedia Of DNA Elements) project. My account reveals two conditions that determine whether a molecule is a part of the human genome (i.e., a genomic part). First, genomic parts must possess a causal role function in the genome as a whole, that is, their functions must contribute to the genome directing the overall functioning of the cell. Second, genomic parts must have a specific chemical structure and be actual segments of the DNA sequence of the genome.

关键词： Part-whole relation encode Genome Causal role function Structure

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Deciphering encode

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TRENDS IN GENETICS 2016年第4期32卷 238-249页

作者： Diehl, Adam G. Boyle, Alan P. Univ Michigan Dept Computat Med & Bioinformat Ann Arbor MI 48109 USA Univ Michigan Dept Human Genet Ann Arbor MI 48109 USA

The encode project represents a major leap from merely describing and comparing genomic sequences to surveying them for direct indicators of function. The astounding quantity of data produced by the encode consortium can serve as a map to locate specific landmarks, guide hypothesis generation, and lead us to principles and mechanisms underlying genome biology. Despite its broad appeal, the size and complexity of the repository can be intimidating to prospective users. We present here some background about the encode data, survey the resources available for accessing them, and describe a few simple principles to help prospective users choose the data type(s) that best suit their needs, where to get them, and how to use them to their best advantage.

关键词： encode genomics gene regulation ChIP-seq RNA-seq DNase-seq

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PLANT PHYSIOLOGY 2010年第3期153卷 1372-1384页

作者： Haselier, Andre Akbari, Hana Weth, Agnes Baumgartner, Werner Frentzen, Margrit Rhein Westfal TH Aachen Univ Inst Biol 1 Unit Bot D-52056 Aachen Germany Rhein Westfal TH Aachen Univ Inst Biol 2 Unit Cellular Neurobion D-52056 Aachen Germany

Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the formation of cytidinediphosphate diacylglycerol, an essential precursor of anionic phosphoglycerolipids like phosphatidylglycerol or -inositol. In plant cells, CDS isozymes are located in plastids, mitochondria, and microsomes. Here, we show that these isozymes are encoded by five genes in Arabidopsis (Arabidopsis thaliana). Alternative translation initiation or alternative splicing of CDS2 and CDS4 transcripts can result in up to 10 isoforms. Most of the cDNAs encoding the various plant isoforms were functionally expressed in yeast and rescued the nonviable phenotype of the mutant strain lacking CDS activity. The closely related genes CDS4 and CDS5 were found to encode plastidial isozymes with similar catalytic properties. Inactivation of both genes was required to obtain Arabidopsis mutant lines with a visible phenotype, suggesting that the genes have redundant functions. Analysis of these Arabidopsis mutants provided further independent evidence for the importance of plastidial phosphatidylglycerol for structure and function of thylakoid membranes and, hence, for photoautotrophic growth.

关键词： arabidopsis encode plastidial Genes Thylakoid Membrane Isoenzymes Diglycerides Arabidopsis coding Phosphatidylglycerols

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A comparative analysis of encode and Cistrome in the context of TF binding signal

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BMC GENOMICS 2024年第SUPPL 3期25卷 1页

作者： Perna, Stefano Pinoli, Pietro Ceri, Stefano Wong, Limsoon Nanyang Technol Univ Lee Kong Chian Sch Med 9 Nanyang Dr Singapore 636921 Singapore Politecn Milan Dept Elect Informat & Bioengn 32 Piazza Leonardo da Vinci I-20133 Milan Italy Natl Univ Singapore Sch Comp 13 Comp Dr Singapore 117417 Singapore

BackgroundWith the rise of publicly available genomic data repositories, it is now common for scientists to rely on computational models and preprocessed data, either as control or to discover new knowledge. However, different repositories adhere to the different principles and guidelines, and data processing plays a significant role in the quality of the resulting datasets. Two popular repositories for transcription factor binding sites data - encode and Cistrome - process the same biological samples in alternative ways, and their results are not always consistent. Moreover, the output format of the processing (BED narrowPeak) exposes a feature, the signalValue, which is seldom used in consistency checks, but can offer valuable insight on the quality of the *** provide evidence that data points with high signalValue(s) (top 25% of values) are more likely to be consistent between encode and Cistrome in human cell lines K562, GM12878, and HepG2. In addition, we show that filtering according to said high values improves the quality of predictions for a machine learning algorithm that detects transcription factor interactions based only on positional information. Finally, we provide a set of practices and guidelines, based on the signalValue feature, for scientists who wish to compare and merge narrowPeaks from encode and *** signalValue feature is an informative feature that can be effectively used to highlight consistent areas of overlap between different sources of TF binding sites that expose it. Its applicability extends to downstream to positional machine learning algorithms, making it a powerful tool for performance tweaking and data aggregation.

关键词： Transcription Factors Database SignalValue encode Cistrome

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Insights from encode on Missing Proteins: Why β-Defensin Expression Is Scarcely Detected

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JOURNAL OF PROTEOME RESEARCH 2015年第9期14卷 3635-3644页

作者： Fan, Yang Zhang, Yue Xu, Shaohang Kong, Nannan Zhou, Yang Ren, Zhe Deng, Yamei Lin, Liang Ren, Yan Wang, Quanhui Zi, Jin Wen, Bo Liu, Siqi Chinese Acad Sci Beijing Inst Genom Key Lab Genome Sci & Informat Beijing 100101 Peoples R China BGI Shenzhen Beishan Ind Zone Shenzhen 518083 Peoples R China Chinese Acad Sci Grad Univ Beijing 100049 Peoples R China

beta-Defensins (DEFBs) have a variety of functions. The majority of these proteins were not identified in a recent proteome survey. Neither protein detection nor the analysis of transcriptomic data based on RNA-seq data for three liver cancer cell lines identified any expression products. Extensive investigation into DEFB transcripts in over 70 cell lines offered similar results. This fact naturally begs the question Why are DEFB genes scarcely expressed? After examining DEFB gene annotation and the physicochemical properties of its protein products, we postulated that regulatory elements could play a key role in the resultant poor transcription of DEFB genes. Four regions containing DEFB genes and six adjacent regions on chromosomes 6, 8, and 20 were carefully investigated using The Encyclopedia of DNA Elements (encode) information, such as that of DNase I hypersensitive sites (DHSs), transcription factors (TFs), and histone modifications. The results revealed that the intensities of these encode features were globally weaker than those in the adjacent regions. Impressively, DEFB-related regions on chromosomes 6 and 8 containing several non-DEFB genes had lower encode feature intensities, indicating that the absence of DEFB mRNAs might not depend on the gene family but may be reliant upon gene location and chromatin structure.

关键词： CHPP missing proteins beta-defensin encode DHS histone modification TF proteome

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Junk or functional DNA? encode and the function controversy

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BIOLOGY & PHILOSOPHY 2014年第6期29卷 807-831页

作者： Germain, Pierre-Luc Ratti, Emanuele Boem, Federico European Inst Oncol IEO Dept Expt Oncol Milan Italy Univ Milan Dipartimento Sci Salute I-20139 Milan Italy

In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (encode) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of 'Junk DNA'. This provoked a heated reaction from evolutionary biologists, who among other things claimed that encode adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concerning the nature of the encode project, the relevant notion of function and the claim that most of our genome is junk. We argue that evolutionary accounts of function presuppose functions as 'causal roles', and that selection is but a useful proxy for relevant functions, which might well be unsuitable to biomedical research. Taking a closer look at the discovery process in which encode participates, we argue that encode's strategy of biochemical signatures successfully identified activities of DNA elements with an eye towards causal roles of interest to biomedical research. We argue that encode's controversial claim of functionality should be interpreted as saying that 80 % of the genome is engaging in relevant biochemical activities and is very likely to have a causal role in phenomena deemed relevant to biomedical research. Finally, we discuss ambiguities in the meaning of junk DNA and in one of the main arguments raised for its prevalence, and we evaluate the impact of encode's results on the claim that most of our genome is junk.

关键词： Biological function Causal role Selected effect encode Junk DNA

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Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the encode project

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GENE 2014年第1期545卷 80-87页

作者： Pundhir, Sachin Hannibal, Tine Dahlbaek Bang-Berthelsen, Claus Heiner Wegener, Anne-Marie Karin Pociot, Flemming Holmberg, Dan Gorodkin, Jan Univ Copenhagen Ctr Noncoding RNA Technol & Hlth DK-1870 Frederiksberg C Denmark Univ Copenhagen IKVH DK-1870 Frederiksberg C Denmark Univ Copenhagen Fac Hlth & Med Sci ISIM Immunol DK-2200 Copenhagen N Denmark Lund Univ BMC EMV Immunol S-22184 Lund Sweden Herlev Univ Hosp Dept Pediat E DK-2730 Herlev Denmark

The Cd247 gene encodes for a transmembrane protein important for the expression and assembly of TCR/CD3 complex on the surface of T lymphocytes. Down-regulation of CD247 has functional consequences in systemic autoimmunity and has been shown to be associated with Type 1 Diabetes in NOD mouse. In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (encode) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites, supported by histone marks and ChIP-seq data, that specifically have features of an enhancer and a promoter, respectively. We also identified a putative long non-coding RNA from the characteristically long first intron of the Cd247 gene. The long non-coding RNA annotation is supported by manual annotations from the Gencode project in human and our expression quantification analysis performed in NOD and B6 mice using qRT-PCR. Furthermore, 17 of the 23 SNPs already known to be implicated with T1D were observed within the long non-coding RNA region in mouse. The spatially conserved regulatory elements identified in this study have the potential to enrich our understanding of the role of Cd247 gene in autoimmune diabetes. (C) 2014 Elsevier B.V. All rights reserved.

关键词： CD247 cis-regulatory sequence IncRNA high-throughput sequencing encode UCSC genome browser

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Meta-analysis and prioritization of human skin pigmentation-associated GWAS-SNPs using encode data-based web-tools

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ARCHIVES OF DERMATOLOGICAL RESEARCH 2019年第3期311卷 163-171页

作者： Ganguly, Kausik Saha, Tania Saha, Arpan Dutta, Tithi Banerjee, Souradeep Sengupta, Debmalya Bhattacharya, Sreyashi Ghosh, Sampurna Sengupta, Mainak Univ Calcutta Dept Genet Kolkata India

Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype. In the present study, which, to our knowledge, is the first of its kind, we tried to analyze and prioritize 519 non-coding SNPs and 24 3UTR SNPs emerging from 14 different human skin pigmentation-related GWAS, primarily using several encode-based web-tools like rSNPBase, RegulomeDB, HaploReg, etc., most of which incorporate experimentally validated evidences in their predictions. Using this comprehensive, in-silico, analytical approach, we successfully prioritized all the pigmentation-associated GWAS-SNPs and tried to annotate pigmentation-related functionality to them, which would pave the way for deeper understanding of the molecular basis of human skin pigmentation variations.

关键词： Pigmentation GWAS encode SNP Melanin

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Chitinase genes responsive to cold encode antifreeze proteins in winter cereals

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PLANT PHYSIOLOGY 2000年第3期124卷 1251-1263页

作者： Yeh, S Moffatt, BA Griffith, M Xiong, F Yang, DSC Wiseman, SB Sarhan, F Danyluk, J Xue, YQ Hew, CL Doherty-Kirby, A Lajoie, G Univ Waterloo Dept Biol Waterloo ON N2L 3G1 Canada Univ Toronto Deppt Lab Med & Pathobiol Toronto ON Canada McMaster Univ Dept Biochem Hamilton ON L8N 3Z5 Canada Univ Quebec Dept Sci Biol Montreal PQ H3C 3P8 Canada Univ Waterloo Dept Chem Waterloo ON N2L 3G1 Canada

Antifreeze proteins similar to two different chitinases accumulate during cold acclimation in winter rye (Secale cereale). To determine whether these cold-responsive chitinases require post-translational modification to bind to ice, cDNAs coding for two different full-length chitinases were isolated from a cDNA library produced from cold-acclimated winter rye leaves. CHT9 is a 1,193-bp clone that encodes a 31.7-kD class I chitinase and CHT46 is a 998-bp clone that codes for a 24.8-kD class II chitinase. Chitinase-antifreeze proteins purified from the plant were similar in mass to the predicted mature products of CHT9 and CHT46, thus indicating that there was little chemical modification of the amino acid sequences in planta. To confirm these results, the mature sequences of CHT9 and CHT46 were expressed in Escherichia coli and the products of both cDNAs modified the growth of ice. Transcripts of both genes accumulated late in cold acclimation in winter rye. Southern analysis of winter rye genomic DNA indicated the presence of a small gene family homologous to CHT46. In hexaploid wheat, CHT46 homologs marred to the homeologous group 1 chromosomes and were expressed in response to cold and drought. We conclude that two novel cold-responsive genes encoding chitinases with ice-binding activity may have arisen in winter rye and other cereals through gene duplication.

关键词： .Chitinases encode Ontario Canada Cereals accumulate cold acclimation antifreeze Responsive to Cold Proteins in Winter winter rye

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Comparison of encode region SNPs between Cebu Filipino and Asian HapMap samples

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JOURNAL OF HUMAN GENETICS 2007年第9期52卷 729-737页

作者： Marvelle, Amanda F. Lange, Leslie A. Qin, Li Wang, Yunfei Lange, Ethan M. Adair, Linda S. Mohlke, Karen L. Univ N Carolina Sch Med Dept Genet Chapel Hill NC 27599 USA Univ N Carolina Sch Med Dept Nutr Chapel Hill NC 27599 USA Univ N Carolina Sch Publ Hlth Dept Nutr Chapel Hill NC 27599 USA Univ N Carolina Sch Publ Hlth Dept Biostat Chapel Hill NC 27599 USA

Patterns of linkage disequilibrium (LD) act as the framework for designing efficient association studies;these patterns are being studied and catalogued by The International HapMap Project. The current study assessed the transferability of tag SNPs chosen from HapMap panels to a cohort of 80 individuals from metro Cebu, Philippines, who participated in the Cebu Longitudinal Health and Nutrition Survey (CLHNS). The analyses focused on 627 single nucleotide polymorphisms (SNPs) in the central 40 kb within each of the 10 HapMap encode regions. The similarity between the genetic variants in Cebu Filipino samples and HapMap panels was examined using allele frequency estimates, measures of pairwise linkage disequilibrium (LD), and haplotype frequency estimates. For these measures, strong correlations were observed between the Cebu Filipino samples and the Asian panels from HapMap, with the strongest correlations observed with the Han Chinese from Beijing (CHB) panel. Tag SNPs selected using the HapMap CHB panel were particularly effective at representing the genetic variation in Cebu Filipino samples. These results suggest that the HapMap data will be an effective resource for future studies in Cebu Filipino samples.

关键词： linkage disequilibrium SNPs HapMap encode population variation Philippines

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