Transcription Gene regulation
|
|
- Doreen Banks
- 6 years ago
- Views:
Transcription
1 Transcription Gene regulation The machine that transcribes a gene is composed of perhaps 50 proteins, including RNA polymerase, the enzyme that converts DNA code into RNA code. A crew of transcription factors grabs hold of the DNA just above the gene at a site called the core promoter, while associated activators bind to enhancer regions farther upstream of the gene to rev up transcription. Working as a tightly knit machine, these proteins transcribe a single gene into messenger RNA. The messenger RNA winds its way out of the nucleus to the factories that produce proteins, where it serves as a blueprint for production of a specific protein Lecture WS 2004/05 Bioinformatics III 1 a
2 Transcription in E.coli and in Eucaryotes Procaryotes Eucaryotes Genes are grouped into operons Genes are not grouped in operons mrna may contain transcript of several genes (poly-cistronic) each mrna contains only transcript of a single gene (mono-cistronic) Transcription and translation are coupled. Transcript is translated already during transcription. Transcription and translation are NOT coupled. Transcription takes place in nucleus, translation in cytosol. Gene regulation takes place by modification of transcription rate Gene regulation via transcription rate AND by RNA-processing, RNA stability etc. 3. Lecture WS 2004/05 Bioinformatics III 2
3 Promoter prediction in E.coli To analyze E.coli promoters, one may align a set of promoter sequences by the position that marks the known transcription start site (TSS) and search for conserved regions in the sequences. E.coli promoters are found to contain 3 conserved sequence features - a region approximately 6 bp long with consensus TATAAT at position a region approximately 6 bp long with consensus TTGACA at position a distance between these 2 regions of ca. 17 bp that is relatively constant 3. Lecture WS 2004/05 Bioinformatics III 3 a
4 Gene regulatory promoter network In E.coli, 240 transcription factors have been verified that regulate 3000 genes. Binding site matrics are available for more than 55 E.coli TFs (Robison et al. 1998) In S. cerevisae, genome-wide binding analysis of 106 transcription factors indicates that more than one-third of the promoter regions that were bound by regulators were bound by 2 or more regulators. Highly connected network of transcriptional regulators. 3. Lecture WS 2004/05 Bioinformatics III 4
5 Feasibility of computational motif search? Computational identification of transcription factor binding sites is difficult because they consist of short, degenerate sequences that occur frequently by chance. The problem is not easy to define (therefore: it is complex ) because - the motif is of unknown size - the motif might not be well conserved between promoters - the sequences used to search for the motif do not necessarily represent the complete promoter - genes with promoters to be analyzed are in many cases grouped together by a clustering algorithm which has its own limitations. 3. Lecture WS 2004/05 Bioinformatics III 5
6 Strategy 1 Arrival of microarray gene-expression data. Group of genes with similar expression profile (e.g. those that are activated at the same time in the cell cycle) one may assume that this profile ist, at least partly, caused by and reflected in a similar structure of the regions involved in transcription regulation. Search for common motifs in < 1000 base upstream regions. Sofar used: detection of single motifs (representing transcription-factor binding sites) common to the promoter sequences of putatively co-regulated genes. Better: search for simultaneous occurrence of 2 or more sites at a given distance interval! Search becomes more sensitive. 3. Lecture WS 2004/05 Bioinformatics III 6
7 Motif identifaction A flowchart to illustrate the two different approaches for motif identification. We analyzed 800 bp upstream from the translation start sites of the five genes from the yeast gene family PHO by the publicly available systems MEME (alignment) and RSA (exhaustive search). MEME was run on both strands, one occurrence per sequence mode, and found the known motif ranked as second best. RSA Tools was run with oligo size 6 and noncoding regions as background, as set by the demo mode of the system. The wellconserved heptamer of the motifs used by MEME to build the weight matrix is printed in bold. Ohler, Niemann Trends Gen 17, 2 (2001) 3. Lecture WS 2004/05 Bioinformatics III 7
8 Strategy 2: Exhaustive motiv search in upstream regions Exploit the finding that relevant motifs are often repeated many times, possibly with small variations, in the upstream region for the regulatory action to be effective. Search upstream region for overrepresented motifs (1) Group genes based on the overrepresented motifs (2) Analyze sets of genes that share motifs for coregulation in microarray exp. (3) Consider overrepresented motifs labelling sets of co-regulated genes as candidate binding sites. Cora et al. BMC Bioinformatics 5, 57 (2004) 3. Lecture WS 2004/05 Bioinformatics III 8
9 Exhaustive motiv search in upstream regions Exploit Cora et al. BMC Bioinformatics 5, 57 (2004) 3. Lecture WS 2004/05 Bioinformatics III 9
10 Exhaustive motiv search in upstream regions Cora et al. BMC Bioinformatics 5, 57 (2004) 3. Lecture WS 2004/05 Bioinformatics III 10
11 Exhaustive motiv search in upstream regions Cora et al. BMC Bioinformatics 5, 57 (2004) 3. Lecture WS 2004/05 Bioinformatics III 11
12 Recently published tools for promoter finding Ohler, Niemann Trends Gen 17, 2 (2001) 3. Lecture WS 2004/05 Bioinformatics III 12
13 Position-specific weight matrix Popular approach when list of genes available that share TF binding motif; Good multiple sequence alignment available. Alignment matrix: lists # of occurrences of each letter at each position of an alignment Hertz, Stormo (1999) Bioinformatics 15, Lecture WS 2004/05 Bioinformatics III 13
14 Position-specific weight matrix Examples of matrices used by YRSA 3. Lecture WS 2004/05 Bioinformatics III 14
15 Exp. Identification of TF binding site: DNase 1 Footprinting A protein bound to a specific DNA sequence will interfere with the digestion of that region by DNase I. An end-labelled DNA probe is incubated with a protein extract or a purified DNA-binding factor. The unprotected DNA is then partially digested with DNase I such that on average every DNA molecule is cut once. Digestion products are then resolved by electrophoresis. Comparison of the DNase I digestion pattern in the presence and absence of protein will allow the identification of a footprint (protected region) * * * * Denaturing PAGE Footprint 3. Lecture WS 2004/05 Bioinformatics III 15
16 Gel retardation assays Gel Shifts Electro Mobility Shift Assay (EMSA) Band Shift No protein add protein Incubating a purified protein, or a complex mixture of proteins e.g. nuclear or cell extract, with a 32 P end-labelled DNA fragment containing the putative protein binding site (from promoter region). * * Non-denaturing PAGE Reaction products are then analysed on a nondenaturing polyacrylamide gel. The specificity of the DNA-binding protein for the putative binding site is established by competition experiments using DNA fragments or oligonucleotides containing a binding site for the protein of interest, or other unrelated DNA sequences. Free DNA probe Retarded mobility due to protein binding 3. Lecture WS 2004/05 Bioinformatics III 16
17 3D structures of transcription factors 1A02.pdb 1AM9.pdb 1AU7.pdb TFs bind with very different binding modes. Some are sensitive for DNA conformation. 1CIT.pdb 1GD2.pdb 1H88.pdb 2 TFs bound! 3. Lecture WS 2004/05 Bioinformatics III 17
18 DNA conformation Canonical and mechanically distorted forms of helical DNA (from left to right: A-DNA, B-DNA, overstretched S-DNA,32 overtwisted P-DNA33). Conformational fluctuations of a B- DNA oligomer with an alternating GA sequence. The snapshots (100 ps intervals) from a simulation at 300 K using explicit solvent and counterions show axis and backbone fluctuations E. Giudice, R. Lavery (2002) Acc. Chem. Res. 35, Lecture WS 2004/05 Bioinformatics III 18
19 DNA conformation Induced base opening within B-DNA. Images show the conformational changes associated with moving thymine (bold) into the major groove of an oligomer with an alternating GA sequence. E. Giudice, R. Lavery (2002) Acc. Chem. Res. 35, Lecture WS 2004/05 Bioinformatics III 19
20 EM low-resolution structure of TF machinery Single particle images 3D reconstruction of TFIID Nogales et al. Science (1999) 3. Lecture WS 2004/05 Bioinformatics III 20
21 Identification of individual components Position of IIB and IIA on the TFIID structure and mapping of the TBP. The blue mesh corresponds to the holo-tfiid, with the A, B, and C lobes indicated. (A) The green mesh corresponds to the density difference between the holo-tfiid and the TFIID-IIB complex. (B) The magenta and green meshes show the density difference between the holo-tfiid and the trimeric complex TFIID-IIA-IIB. The density depicted in light green can be attributed to TFIIB by comparison with (A), and the magenta density therefore corresponds to IIA. (C) The yellow mesh shows the density difference between the holo-tfiid and TFIID that is bound to the TBP antibody. Nogales et al. Science (1999) 3. Lecture WS 2004/05 Bioinformatics III 21
22 database for eukaryotic transcription factors: TRANSFAC BIOBase / TU Braunschweig / GBF Relational database 6 flat files: FACTOR interaction of TFs SITE their DNA binding site GENE through which they regulate these target genes CELL factor source MATRIX TF nucleotide weight matrices CLASS classification scheme of TFs Wingender et al. (1998) J Mol Biol 284, Lecture WS 2004/05 Bioinformatics III 22
23 database for eukaryotic transcription factors: TRANSFAC BIOBase / TU Braunschweig / GBF Matys et al. (2003) Nucl Acid Res 31, Lecture WS 2004/05 Bioinformatics III 23
24 Match TM Search for putative TF binding sites in DNA sequences based on weight matrices. Use 2 values to score putative hits: Matrix similarity score: quality of a match between the sequence and the whole matrix [0,1] Core similarity score: quality of a match between the sequence and the core sequence of a matrix which consists of the five most conserved consecutive positions in a matrix [0,1] Profile: set of matrices and their cut-offs designed for function-driven searches Special profiles available for immune-cells, muscle cells, liver cells, and for cellcycle. Matys et al. (2003) Nucl Acid Res 31, Lecture WS 2004/05 Bioinformatics III 24
25 database for eukaryotic transcription factors: TRANSFAC BIOBase / TU Braunschweig / GBF Matys et al. (2003) Nucl Acid Res 31, Lecture WS 2004/05 Bioinformatics III 25
26 TRANSFAC classification 1 Superclass basic domains 3 Superclass: Helix-turn-helix 1.1 Leuzine zipper factors (bzip) 1.2 Helix-loop-helix factors (bhlh) 4 Superclass: beta-scaffold 1.3 bhlh-bzip Factors with Minor Groove 1.4 NF-1 Contacts 1.5 RF-X 1.6 bhsh 5 Superclass: others 2 Superclass: Zinc-coordinating DNA-binding domains 2.1 Cys4 zinc finger of nuclear receptor type 2.2 diverse Cys4 zinc fingers 2.3 Cys2His2 zinc finger domains 2.4 Cys6 cysteine-zinc cluster 2.5 Zinc fingers of alternating composition 3. Lecture WS 2004/05 Bioinformatics III 26
27 Eintrag für 1.1 Leuzine-Zippers TRANSFAC classification 3. Lecture WS 2004/05 Bioinformatics III 27
28 TRANSFAC classification 3. Lecture WS 2004/05 Bioinformatics III 28
29 TRANSFAC classification 3. Lecture WS 2004/05 Bioinformatics III 29
30 Summary Large databases available (e.g. TRANSFAC) with information about promoter sites. Information verified experimentally. Microarray data allows searching for common motifs of coregulated genes. Also possible: common GO annotation etc. TF binding motifs are frequently overrepresented in 1000 bp upstream region. Clear function of this is unknown. (Same as in proline-rich recognition sequences.) Relatively few TFs regulate large number of genes. Complex regulatory network, Thursday lecture Lecture WS 2004/05 Bioinformatics III 30
V10 Transcriptional Gene regulation networks
V10 Transcriptional Gene regulation networks The machine that transcribes a gene is composed of perhaps 50 proteins, including RNA polymerase, the enzyme that converts DNA code into RNA code. A crew of
More informationComplex Transcription Machinery
Complex Transcription Machinery Subunits of the Basal Txn Apparatus Stepwise Assembly of the Pre-initiation Complex Interplay of Activators, Co-regulators and RNA Polymerase at the Promoter Divide and
More informationMolecular Biology (BIOL 4320) Exam #1 March 12, 2002
Molecular Biology (BIOL 4320) Exam #1 March 12, 2002 Name KEY SS# This exam is worth a total of 100 points. The number of points each question is worth is shown in parentheses after the question number.
More informationEnhancers. Activators and repressors of transcription
Enhancers Can be >50 kb away from the gene they regulate. Can be upstream from a promoter, downstream from a promoter, within an intron, or even downstream of the final exon of a gene. Are often cell type
More informationChapter 14 Regulation of Transcription
Chapter 14 Regulation of Transcription Cis-acting sequences Distance-independent cis-acting elements Dissecting regulatory elements Transcription factors Overview transcriptional regulation Transcription
More informationTranscription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme, RNA polymerase.
Transcription in Bacteria Transcription in Bacteria Transcription in Bacteria Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme,
More informationStructure/function relationship in DNA-binding proteins
PHRM 836 September 22, 2015 Structure/function relationship in DNA-binding proteins Devlin Chapter 8.8-9 u General description of transcription factors (TFs) u Sequence-specific interactions between DNA
More informationRegulation of gene expression. (Lehninger pg )
Regulation of gene expression (Lehninger pg. 1072-1085) Today s lecture Gene expression Constitutive, inducible, repressible genes Specificity factors, activators, repressors Negative and positive gene
More informationChIP. November 21, 2017
ChIP November 21, 2017 functional signals: is DNA enough? what is the smallest number of letters used by a written language? DNA is only one part of the functional genome DNA is heavily bound by proteins,
More informationYear III Pharm.D Dr. V. Chitra
Year III Pharm.D Dr. V. Chitra 1 Genome entire genetic material of an individual Transcriptome set of transcribed sequences Proteome set of proteins encoded by the genome 2 Only one strand of DNA serves
More informationDNA Function: Information Transmission
DNA Function: Information Transmission DNA is called the code of life. What does it code for? *the information ( code ) to make proteins! Why are proteins so important? Nearly every function of a living
More informationAnnouncement Structure Analysis
Announcement Structure Analysis BSC 4439/BSC 5436: Biomedical Informatics: Structure Analysis Spring 2019, CB117 Monday and Wednesday 12:00 1:15pm Office hour: Monday and Wednesday 1:15 2pm Topics include
More informationSynthetic cells: do bacteria need all its genes? No.
NO NEED TO REFER TO THE SLIDES. بسم هللا الرحمن الرحيم Do we need all the non coding regions of the DNA? Two weeks ago, they discovered that the genome of a plant is very small (recall that plant genome
More informationBiotechnology Unit 3: DNA to Proteins. From DNA to RNA
From DNA to RNA Biotechnology Unit 3: DNA to Proteins I. After the discovery of the structure of DNA, the major question remaining was how does the stored in the 4 letter code of DNA direct the and of
More informationGenome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human. Supporting Information
Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human Angela Re #, Davide Corá #, Daniela Taverna and Michele Caselle # equal contribution * corresponding author,
More informationM1 - Biochemistry. Nucleic Acid Structure II/Transcription I
M1 - Biochemistry Nucleic Acid Structure II/Transcription I PH Ratz, PhD (Resources: Lehninger et al., 5th ed., Chapters 8, 24 & 26) 1 Nucleic Acid Structure II/Transcription I Learning Objectives: 1.
More informationDNA Transcription. Dr Aliwaini
DNA Transcription 1 DNA Transcription-Introduction The synthesis of an RNA molecule from DNA is called Transcription. All eukaryotic cells have five major classes of RNA: ribosomal RNA (rrna), messenger
More informationTranscription. DNA to RNA
Transcription from DNA to RNA The Central Dogma of Molecular Biology replication DNA RNA Protein transcription translation Why call it transcription and translation? transcription is such a direct copy
More informationGene Regulation in Eukaryotes
Gene Regulation in Eukaryotes The latest estimates are that a human cell, a eukaryotic cell, contains 20,000 25,000 genes. Some of these are expressed in all cells all the time. These so-called housekeeping
More informationMake the protein through the genetic dogma process.
Make the protein through the genetic dogma process. Coding Strand 5 AGCAATCATGGATTGGGTACATTTGTAACTGT 3 Template Strand mrna Protein Complete the table. DNA strand DNA s strand G mrna A C U G T A T Amino
More informationExpression of the genome. Books: 1. Molecular biology of the gene: Watson et al 2. Genetics: Peter J. Russell
Expression of the genome Books: 1. Molecular biology of the gene: Watson et al 2. Genetics: Peter J. Russell 1 Transcription 1. Francis Crick (1956) named the flow of information from DNA RNA protein the
More informationLecture 11. Initiation of RNA Pol II transcription. Transcription Initiation Complex
Lecture 11 *Eukaryotic Transcription Gene Organization RNA Processing 5 cap 3 polyadenylation splicing Translation Initiation of RNA Pol II transcription Consensus sequence of promoter TATA Transcription
More informationMotivation From Protein to Gene
MOLECULAR BIOLOGY 2003-4 Topic B Recombinant DNA -principles and tools Construct a library - what for, how Major techniques +principles Bioinformatics - in brief Chapter 7 (MCB) 1 Motivation From Protein
More informationGENETICS - CLUTCH CH.10 TRANSCRIPTION.
!! www.clutchprep.com CONCEPT: OVERVIEW OF TRANSCRIPTION Transcription is the process of using DNA as a template to RNA RNA polymerase is the enzyme that transcribes DNA - There are many different types
More informationI. Gene Expression Figure 1: Central Dogma of Molecular Biology
I. Gene Expression Figure 1: Central Dogma of Molecular Biology Central Dogma: Gene Expression: RNA Structure RNA nucleotides contain the pentose sugar Ribose instead of deoxyribose. Contain the bases
More informationSelected Techniques Part I
1 Selected Techniques Part I Gel Electrophoresis Can be both qualitative and quantitative Qualitative About what size is the fragment? How many fragments are present? Is there in insert or not? Quantitative
More informationChapters 31-32: Ribonucleic Acid (RNA)
Chapters 31-32: Ribonucleic Acid (RNA) Short segments from the transcription, processing and translation sections of each chapter Slide 1 RNA In comparison with DNA RNA utilizes uracil in place of thymine
More informationChem 465 Biochemistry II
Chem 465 Biochemistry II Name: 2 points Multiple choice (4 points apiece): 1. Which of the following is not true of trna molecules? A) The 3'-terminal sequence is -CCA. B) Their anticodons are complementary
More informationGENES AND CHROMOSOMES V. Lecture 7. Biology Department Concordia University. Dr. S. Azam BIOL 266/
1 GENES AND CHROMOSOMES V Lecture 7 BIOL 266/4 2014-15 Dr. S. Azam Biology Department Concordia University 2 CELL NUCLEUS AND THE CONTROL OF GENE EXPRESSION An Overview of Gene Regulation in Eukaryotes
More informationÜbung V. Einführung, Teil 1. Transktiptionelle Regulation TFBS
Übung V Einführung, Teil 1 Transktiptionelle Regulation TFBS Transcription Factors These proteins promote transcription 1. Bind DNA 2. Activate Transcription These two functions usually reside on separate
More informationMultiple choice questions (numbers in brackets indicate the number of correct answers)
1 Multiple choice questions (numbers in brackets indicate the number of correct answers) February 1, 2013 1. Ribose is found in Nucleic acids Proteins Lipids RNA DNA (2) 2. Most RNA in cells is transfer
More informationEukaryotic & Prokaryotic Transcription. RNA polymerases
Eukaryotic & Prokaryotic Transcription RNA polymerases RNA Polymerases A. E. coli RNA polymerase 1. core enzyme = ββ'(α)2 has catalytic activity but cannot recognize start site of transcription ~500,000
More informationDNA Transcription. Visualizing Transcription. The Transcription Process
DNA Transcription By: Suzanne Clancy, Ph.D. 2008 Nature Education Citation: Clancy, S. (2008) DNA transcription. Nature Education 1(1) If DNA is a book, then how is it read? Learn more about the DNA transcription
More informationوراثة األحياء الدقيقة Microbial Genetics
وراثة األحياء الدقيقة Microbial Genetics د. تركي محمد الداود مكتب 2 ب 45 أساسيات في علم الوراثة Fundamentals of Genetics Lecture 4 Physical Chemistry of Nucleic Acids DNA and RNA molecules can appear in
More informationChapter 25: Regulating Eukaryotic Transcription The Ligand Responsive Activators
Chapter 25: Regulating Eukaryotic Transcription The Ligand Responsive Activators At least 5 potential gene expression control points Superfamily of Gene Regulators Activation of gene structure Initiation
More informationTranscription in Eukaryotes
Transcription in Eukaryotes Biology I Hayder A Giha Transcription Transcription is a DNA-directed synthesis of RNA, which is the first step in gene expression. Gene expression, is transformation of the
More informationTranscription factors
Atlas of Genetics and Cytogenetics in Oncology and Haematology Transcription factors I Introduction * II Initiation of transcription III Transcription factors family pdf version I Introduction III.1 Helix-Turn-Helix
More informationChapter 17 Lecture. Concepts of Genetics. Tenth Edition. Regulation of Gene Expression in Eukaryotes
Chapter 17 Lecture Concepts of Genetics Tenth Edition Regulation of Gene Expression in Eukaryotes Chapter Contents 17.1 Eukaryotic Gene Regulation Can Occur at Any of the Steps Leading from DNA to Protein
More informationCHAPTERS , 17: Eukaryotic Genetics
CHAPTERS 14.1 14.6, 17: Eukaryotic Genetics 1. Review the levels of DNA packing within the eukaryote nucleus. Label each level. (A similar diagram is on pg 188 of your textbook.) 2. How do the coding regions
More informationTRANSCRIPTION COMPARISON OF DNA & RNA TRANSCRIPTION. Umm AL Qura University. Sugar Ribose Deoxyribose. Bases AUCG ATCG. Strand length Short Long
Umm AL Qura University TRANSCRIPTION Dr Neda Bogari TRANSCRIPTION COMPARISON OF DNA & RNA RNA DNA Sugar Ribose Deoxyribose Bases AUCG ATCG Strand length Short Long No. strands One Two Helix Single Double
More informationTranscription Eukaryotic Cells
Transcription Eukaryotic Cells Packet #20 1 Introduction Transcription is the process in which genetic information, stored in a strand of DNA (gene), is copied into a strand of RNA. Protein-encoding genes
More informationDNA & DNA : Protein Interactions BIBC 100
DNA & DNA : Protein Interactions BIBC 100 Sequence = Information Alphabet = language L,I,F,E LIFE DNA = DNA code A, T, C, G CAC=Histidine CAG=Glutamine GGG=Glycine Protein = Protein code 20 a.a. LIVE EVIL
More informationTranscription is the first stage of gene expression
Transcription is the first stage of gene expression RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides The RNA is complementary to the
More information(c) 2014 Dr. Alice Heicklen & Dr. Deborah Mowshowitz, Columbia University, New York, NY. Last update 02/26/ :57 PM
C2006/F2402 '14 OUTLINE OF LECTURE #11 (c) 2014 Dr. Alice Heicklen & Dr. Deborah Mowshowitz, Columbia University, New York, NY. Last update 02/26/2014 12:57 PM Handouts: 10C -- Typical Eukaryotic Gene,
More informationComputational Biology I LSM5191 (2003/4)
Computational Biology I LSM5191 (2003/4) Aylwin Ng, D.Phil Lecture Notes: Transcriptome: Molecular Biology of Gene Expression I Flow of information: DNA to polypeptide DNA Start Exon1 Intron Exon2 Termination
More informationTRANSCRIPTION AND PROCESSING OF RNA
TRANSCRIPTION AND PROCESSING OF RNA 1. The steps of gene expression. 2. General characterization of transcription: steps, components of transcription apparatus. 3. Transcription of eukaryotic structural
More informationGene Expression Transcription/Translation Protein Synthesis
Gene Expression Transcription/Translation Protein Synthesis 1. Describe how genetic information is transcribed into sequences of bases in RNA molecules and is finally translated into sequences of amino
More informationGene Expression: Transcription, Translation, RNAs and the Genetic Code
Lecture 28-29 Gene Expression: Transcription, Translation, RNAs and the Genetic Code Central dogma of molecular biology During transcription, the information in a DNA sequence (a gene) is copied into a
More informationGene Identification in silico
Gene Identification in silico Nita Parekh, IIIT Hyderabad Presented at National Seminar on Bioinformatics and Functional Genomics, at Bioinformatics centre, Pondicherry University, Feb 15 17, 2006. Introduction
More informationBIO 311C Spring Lecture 36 Wednesday 28 Apr.
BIO 311C Spring 2010 1 Lecture 36 Wednesday 28 Apr. Synthesis of a Polypeptide Chain 5 direction of ribosome movement along the mrna 3 ribosome mrna NH 2 polypeptide chain direction of mrna movement through
More information17.5 Eukaryotic Transcription Initiation Is Regulated by Transcription Factors That Bind to Cis-Acting Sites
17.5 Eukaryotic Transcription Initiation Is Regulated by Transcription Factors That Bind to Cis-Acting Sites 1 Section 17.5 Transcription regulatory proteins, transcription factors, target cis-acting sites
More informationGene Expression Technology
Gene Expression Technology Bing Zhang Department of Biomedical Informatics Vanderbilt University bing.zhang@vanderbilt.edu Gene expression Gene expression is the process by which information from a gene
More informationCELL BIOLOGY - CLUTCH CH. 7 - GENE EXPRESSION.
!! www.clutchprep.com CONCEPT: CONTROL OF GENE EXPRESSION BASICS Gene expression is the process through which cells selectively to express some genes and not others Every cell in an organism is a clone
More informationGene expression DNA RNA. Protein DNA. Replication. Initiation Elongation Processing Export. DNA RNA Protein. Transcription. Degradation.
Gene expression DNA RNA Protein DNA DNA Degradation RNA Degradation Protein Replication Transcription Translation Initiation Elongation Processing Export Initiation Elongation Processing Targeting Chapter
More informationBS 50 Genetics and Genomics Week of Oct 24
BS 50 Genetics and Genomics Week of Oct 24 Additional Practice Problems for Section Question 1: The following table contains a list of statements that apply to replication, transcription, both, or neither.
More informationDNA. Is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses.
Is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. Genetic information is encoded as a sequence of nucleotides (guanine,
More informationBiology. Biology. Slide 1 of 39. End Show. Copyright Pearson Prentice Hall
Biology Biology 1 of 39 12-3 RNA and Protein Synthesis 2 of 39 Essential Question What is transcription and translation and how do they take place? 3 of 39 12 3 RNA and Protein Synthesis Genes are coded
More informationBiology. Biology. Slide 1 of 39. End Show. Copyright Pearson Prentice Hall
Biology Biology 1 of 39 12-3 RNA and Protein Synthesis 2 of 39 12 3 RNA and Protein Synthesis Genes are coded DNA instructions that control the production of proteins. Genetic messages can be decoded by
More informationUNIT 3 GENETICS LESSON #41: Transcription
UNIT 3 GENETICS LESSON #41: Transcription Objective: Explain how transcription converts a gene into a singlestranded RNA molecule. Suppose you want to play a game but you need tokens and you only have
More informationFermentation. Lesson Overview. Lesson Overview 13.1 RNA
13.1 RNA THINK ABOUT IT DNA is the genetic material of cells. The sequence of nucleotide bases in the strands of DNA carries some sort of code. In order for that code to work, the cell must be able to
More information6.047 / Computational Biology: Genomes, Networks, Evolution Fall 2008
MIT OpenCourseWare http://ocw.mit.edu 6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms.
More informationCharacterizing DNA binding sites high throughput approaches Biol4230 Tues, April 24, 2018 Bill Pearson Pinn 6-057
Characterizing DNA binding sites high throughput approaches Biol4230 Tues, April 24, 2018 Bill Pearson wrp@virginia.edu 4-2818 Pinn 6-057 Reviewing sites: affinity and specificity representation binding
More informationReading for lecture 2
Reading for lecture 2 1. Structure of DNA and RNA 2. Information storage by DNA 3. The Central Dogma Voet and Voet, Chapters 28 (29,30) Alberts et al, Chapters 5 (3) 1 5 4 1 3 2 3 3 Structure of DNA and
More informationNOTES Gene Expression ACP Biology, NNHS
Name Date Block NOTES Gene Expression ACP Biology, NNHS Model 1: Transcription the process of genes in DNA being copied into a messenger RNA 1. Where in the cell is DNA found? 2. Where in the cell does
More informationBioinformatics: Microarray Technology. Assc.Prof. Chuchart Areejitranusorn AMS. KKU.
Introduction to Bioinformatics: Microarray Technology Assc.Prof. Chuchart Areejitranusorn AMS. KKU. ความจร งเก ยวก บ ความจรงเกยวกบ Cell and DNA Cell Nucleus Chromosome Protein Gene (mrna), single strand
More informationIntroduction to Bioinformatics Online Course: IBT
Introduction to Bioinformatics Online Course: IBT Multiple Sequence Alignment Building Multiple Sequence Alignment Lec5: Interpreting your MSA Using Logos Using Logos - Logos are a terrific way to generate
More informationThe Genetic Code and Transcription. Chapter 12 Honors Genetics Ms. Susan Chabot
The Genetic Code and Transcription Chapter 12 Honors Genetics Ms. Susan Chabot TRANSCRIPTION Copy SAME language DNA to RNA Nucleic Acid to Nucleic Acid TRANSLATION Copy DIFFERENT language RNA to Amino
More informationDNA Binding Domains: Structural Motifs. Effector Domain. Zinc Fingers. Zinc Fingers, continued. Zif268
DNA Binding Domains: Structural Motifs Studies of known transcription factors have found several motifs of protein design to allow sequence-specific binding of DNA. We will cover only three of these motifs:
More informationChapter 11. Transcription. The biochemistry and molecular biology department of CMU
Chapter 11 Transcription The biochemistry and molecular biology department of CMU Transcription The synthesis of RNA molecules using DNA strands as the templates so that the genetic information can be
More informationRNA Expression of the information in a gene generally involves production of an RNA molecule transcribed from a DNA template. RNA differs from DNA
RNA Expression of the information in a gene generally involves production of an RNA molecule transcribed from a DNA template. RNA differs from DNA that it has a hydroxyl group at the 2 position of the
More informationAP Biology Gene Expression/Biotechnology REVIEW
AP Biology Gene Expression/Biotechnology REVIEW Multiple Choice Identify the choice that best completes the statement or answers the question. 1. Gene expression can be a. regulated before transcription.
More informationTranscription. The sugar molecule found in RNA is ribose, rather than the deoxyribose found in DNA.
Transcription RNA (ribonucleic acid) is a key intermediary between a DNA sequence and a polypeptide. RNA is an informational polynucleotide similar to DNA, but it differs from DNA in three ways: RNA generally
More informationThemes: RNA and RNA Processing. Messenger RNA (mrna) What is a gene? RNA is very versatile! RNA-RNA interactions are very important!
Themes: RNA is very versatile! RNA and RNA Processing Chapter 14 RNA-RNA interactions are very important! Prokaryotes and Eukaryotes have many important differences. Messenger RNA (mrna) Carries genetic
More informationChromatographic Separation of the three forms of RNA Polymerase II.
Chromatographic Separation of the three forms of RNA Polymerase II. α-amanitin α-amanitin bound to Pol II Function of the three enzymes. Yeast Pol II. RNA Polymerase Subunit Structures 10-7 Subunit structure.
More informationThe Structure of Proteins The Structure of Proteins. How Proteins are Made: Genetic Transcription, Translation, and Regulation
How Proteins are Made: Genetic, Translation, and Regulation PLAY The Structure of Proteins 14.1 The Structure of Proteins Proteins - polymer amino acids - monomers Linked together with peptide bonds A
More informationDifferential Gene Expression
Biology 4361 Developmental Biology Differential Gene Expression June 19, 2008 Differential Gene Expression Overview Chromatin structure Gene anatomy RNA processing and protein production Initiating transcription:
More informationTranscription in Prokaryotes. Jörg Bungert, PhD Phone:
Transcription in Prokaryotes Jörg Bungert, PhD Phone: 352-273-8098 Email: jbungert@ufl.edu Objectives Understand the basic mechanism of transcription. Know the function of promoter elements and associating
More informationnature methods A paired-end sequencing strategy to map the complex landscape of transcription initiation
nature methods A paired-end sequencing strategy to map the complex landscape of transcription initiation Ting Ni, David L Corcoran, Elizabeth A Rach, Shen Song, Eric P Spana, Yuan Gao, Uwe Ohler & Jun
More informationReplication Review. 1. What is DNA Replication? 2. Where does DNA Replication take place in eukaryotic cells?
Replication Review 1. What is DNA Replication? 2. Where does DNA Replication take place in eukaryotic cells? 3. Where does DNA Replication take place in the cell cycle? 4. 4. What guides DNA Replication?
More informationSection C: The Control of Gene Expression
Section C: The Control of Gene Expression 1. Each cell of a multicellular eukaryote expresses only a small fraction of its genes 2. The control of gene expression can occur at any step in the pathway from
More informationActivation of a Floral Homeotic Gene in Arabidopsis
Activation of a Floral Homeotic Gene in Arabidopsis By Maximiliam A. Busch, Kirsten Bomblies, and Detlef Weigel Presentation by Lis Garrett and Andrea Stevenson http://ucsdnews.ucsd.edu/archive/graphics/images/image5.jpg
More informationDifferential Gene Expression
Biology 4361 Developmental Biology Differential Gene Expression September 28, 2006 Chromatin Structure ~140 bp ~60 bp Transcriptional Regulation: 1. Packing prevents access CH 3 2. Acetylation ( C O )
More informationIB BIO I Replication/Transcription/Translation Van Roekel/Madden. Name Date Period. D. It separates DNA strands. (Total 1 mark)
Name Date Period 1. What is the function of helicase? A. It forms bonds between DNA nucleotides. B. It adds new nucleotides to the DNA helix. C. It forms the DNA helix. D. It separates DNA strands. 2.
More informationThe Little Things About the Little Things Inside of Us The Eukaryotic Genome and Its Expression
The Little Things About the Little Things Inside of Us The Eukaryotic Genome and Its Expression What Are the Characteristics of the Eukaryotic Genome? Key differences between eukaryotic and prokaryotic
More informationFig Ch 17: From Gene to Protein
Fig. 17-1 Ch 17: From Gene to Protein Basic Principles of Transcription and Translation RNA is the intermediate between genes and the proteins for which they code Transcription is the synthesis of RNA
More informationDifferential Gene Expression
Developmental Biology Biology 4361 Differential Gene Expression October 13, 2005 core transcription initiation site 5 promoter 3 TATAT +1 upstream downstream Basal transcription factors (eukaryotes) TFIID
More informationEukaryotic Gene Expression Prof. P. N. Rangarajan Department of Biochemistry Indian Institute of Science, Bangalore
Eukaryotic Gene Expression Prof. P. N. Rangarajan Department of Biochemistry Indian Institute of Science, Bangalore Module No. # 01 Lecture No. # 04 Gene Regulation in Eukaryotes: Proximal and Distal Promoter
More informationChapter 8 Lecture Outline. Transcription, Translation, and Bioinformatics
Chapter 8 Lecture Outline Transcription, Translation, and Bioinformatics Replication, Transcription, Translation n Repetitive processes Build polymers of nucleotides or amino acids n All have 3 major steps
More informationRNA POLYMERASE FUNCTIONS E-BOOK
08 March, 2018 RNA POLYMERASE 1 2 3 FUNCTIONS E-BOOK Document Filetype: PDF 431.06 KB 0 RNA POLYMERASE 1 2 3 FUNCTIONS E-BOOK It catalyzes the transcription of DNA to synthesize precursors of mrna and
More informationGenome-Scale Predictions of the Transcription Factor Binding Sites of Cys 2 His 2 Zinc Finger Proteins in Yeast June 17 th, 2005
Genome-Scale Predictions of the Transcription Factor Binding Sites of Cys 2 His 2 Zinc Finger Proteins in Yeast June 17 th, 2005 John Brothers II 1,3 and Panayiotis V. Benos 1,2 1 Bioengineering and Bioinformatics
More informationControl of Eukaryotic Genes
Control of Eukaryotic Genes 2007-2008 The BIG Questions How are genes turned on & off in eukaryotes? How do cells with the same genes differentiate to perform completely different, specialized functions?
More informationThe nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Nucleic acids are macromolecules composed of chains of mononucleotides joined by phosphodiester bonds. The nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are universal
More informationControl of Eukaryotic Genes. AP Biology
Control of Eukaryotic Genes The BIG Questions How are genes turned on & off in eukaryotes? How do cells with the same genes differentiate to perform completely different, specialized functions? Evolution
More informationIntroduction to Microarray Data Analysis and Gene Networks. Alvis Brazma European Bioinformatics Institute
Introduction to Microarray Data Analysis and Gene Networks Alvis Brazma European Bioinformatics Institute A brief outline of this course What is gene expression, why it s important Microarrays and how
More informationControl of Eukaryotic Genes. AP Biology
Control of Eukaryotic Genes The BIG Questions How are genes turned on & off in eukaryotes? How do cells with the same genes differentiate to perform completely different, specialized functions? Evolution
More informationGenomics and Gene Recognition Genes and Blue Genes
Genomics and Gene Recognition Genes and Blue Genes November 3, 2004 Eukaryotic Gene Structure eukaryotic genomes are considerably more complex than those of prokaryotes eukaryotic cells have organelles
More informationPractice Exam A. Briefly describe how IL-25 treatment might be able to help this responder subgroup of liver cancer patients.
Practice Exam 2007 1. A special JAK-STAT signaling system (JAK5-STAT5) was recently identified in which a gene called TS5 becomes selectively transcribed and expressed in the liver upon induction by a
More informationLecture Summary: Regulation of transcription. General mechanisms-what are the major regulatory points?
BCH 401G Lecture 37 Andres Lecture Summary: Regulation of transcription. General mechanisms-what are the major regulatory points? RNA processing: Capping, polyadenylation, splicing. Why process mammalian
More informationChapter 3. DNA, RNA, and Protein Synthesis
Chapter 3. DNA, RNA, and Protein Synthesis 4. Transcription Gene Expression Regulatory region (promoter) 5 flanking region Upstream region Coding region 3 flanking region Downstream region Transcription
More informationBISHOPAgEd.Weebly.com. Weeks: Dates: 1/18-1/29 Unit: RNA &Protein Synthesis. Monday Tuesday Wednesday Thursday Friday. FFA Meeting 6pm 27 E
Ms. King BISHOPAgEd.Weebly.com Name: Period: Weeks: 21-22 Dates: 1/18-1/29 Unit: RNA &Protein Synthesis Monday Tuesday Wednesday Thursday Friday 18 NO School 19 E 20 O RNA Part 1 FFA Meeting 6pm 21 E 22
More information