Chromatin and Chromatin Remodeling Enzymes

555 Pages·2004·8.287 MB·English

by  Wu L.A., Allis C.D.

Preface
Acentralchallengeofthepost-genomiceraistounderstandhowthe30,000to
40,000uniquegenesinthehumangenomeareselectivelyexpressedorsilenced
tocoordinatecellulargrowthanddifferentiation.Thepackagingofeukaryotic
genomes in a complex of DNA, histones, and nonhistone proteins called
chromatinprovidesasurprisinglysophisticatedsystemthatplaysacriticalrole
in controlling the flow of genetic information. This packaging system has
evolved to index our genomes such that certain genes become readily access-
ible to the transcription machinery, while other genes are reversibly silenced.
Moreover, chromatin-based mechanisms of gene regulation, often involving
domainsofcovalentmodificationsofDNAandhistones,canbeinheritedfrom
onegenerationtothenext.Theheritabilityofchromatinstatesintheabsence
ofDNAmutationhascontributedgreatlytothecurrentexcitementinthefield
ofepigenetics.
Thepast5yearshavewitnessedanexplosionofnewresearchonchroma-
tinbiologyandbiochemistry.Chromatinstructureandfunctionarenowwidely
recognizedasbeingcriticaltoregulatinggeneexpression,maintaininggenomic
stability, and ensuring faithful chromosome transmission. Moreover, links be-
tweenchromatinmetabolismanddiseasearebeginningtoemerge.Theidenti-
fication of altered DNA methylation and histone acetylase activity in human
cancers,theuseofhistonedeacetylaseinhibitorsinthetreatmentofleukemia,
and the tumor suppressor activities of ATP-dependent chromatin remodeling
enzymesareexamplesthatlikelyrepresentjustthetipoftheiceberg.
Assuch,thefieldisattractingnewinvestigatorswhoenterwithlittlefirst
hand experience with the standard assays used to dissect chromatin structure
and function. In addition, even seasoned veterans are overwhelmed by the
rapid introduction of new chromatin technologies. Accordingly, we sought to
bring together a useful ‘‘go-to’’ set of chromatin-based methods that would
update and complement two previous publications in this series, Volume 170
(Nucleosomes)andVolume304(Chromatin).Whilemanyoftheclassicproto-
colsinthosevolumesremainastimelynowaswhentheywerewritten,itisour
hopethepresentserieswillfillinthegapsforthenextseveralyears.
This3-volumesetofMethodsinEnzymologyprovidesnearlyonehundred
procedurescoveringthefullrangeoftools—bioinformatics,structuralbiology,
biophysics, biochemistry, genetics, and cell biology—employed in chromatin
research.Volume375includesahistonedatabase,methodsforpreparationof
xv
xvi preface
histones,histonevariants,modifiedhistonesanddefinedchromatinsegments,
protocolsfornucleosomereconstitutionandanalysis,andcytologicalmethods
forimagingchromatinfunctionsinvivo.Volume376includeselectronmicro-
scopy and biophysical protocols for visualizing chromatin and detecting chro-
matin interactions, enzymological assays for histone modifying enzymes, and
immunochemical protocols for the in situ detection of histone modifications
and chromatin proteins. Volume 377 includes genetic assays of histones and
chromatin regulators, methods for the preparation and analysis of histone
modifying and ATP-dependent chromatin remodeling enzymes, and assays
fortranscriptionandDNArepaironchromatintemplates.Weareexceedingly
gratefultotheverylargenumberofcolleaguesrepresentingthefield’sleading
laboratories, who have taken the time and effort to make their technical
expertiseavailableinthisseries.
Finally, we wish to take the opportunity to remember Vincent Allfrey,
AndreiMirzabekov,HaroldWeintraub,AbrahamWorcel,andespeciallyAlan
Wolffe,co-editorofVolume304(Chromatin).Alloftheseindividualshadkey
rolesinshapingthechromatinfieldintowhatitistoday.
C. David Allis
Carl Wu
Editors’ Note: Additional methods can be found in Methods in Enzymology,
Vol. 371 (RNA Polymerases and Associated Factors, Part D) Section III
Chromatin,SankarL.AdhyaandSusanGarges,Editors.
METHODS IN ENZYMOLOGY
EDITORS-IN-CHIEF
John N. Abelson Melvin I. Simon
DIVISIONOFBIOLOGY
CALIFORNIAINSTITUTEOFTECHNOLOGY
PASADENA,CALIFORNIA
FOUNDINGEDITORS
Sidney P. Colowick and Nathan O. Kaplan
Contributors to Volume 375
Articlenumbersareinparenthesesandfollowingthenamesofcontributors.
Affiliationslistedarecurrent.
Chad Alexander (3), The University of Hinrich Boeger (11), Department of
Tennessee-Oak Ridge Graduate School Structural Biology, Stanford University
of Genome Science and Technology, SchoolofMedicine,Stanford,California
Oak Ridge National Laboratory, Life 94305
SciencesDivision,OakRidge,Tennessee
37831-8080 William M. Bonner (5), Laboratory of
Molecular Pharmacology, National
Genevie`ve Almouzni (8), Institut Curie, Cancer Institute, Bethesda, Maryland
Section de Recherche, F-75248, Paris 20892
Cedex05,France
Michael Bruno (14), Division of Gene
Satoshi Ando (18), Department of Mo-
Regulation and Expression, The Well-
lecularLifeScience,SchoolofMedicine,
come Trust Biocentre, Department of
Tokai University, Kanagawa 259-1193,
Biochemistry, University of Dundee,
Japan
Dundee, DD1 5EH, Scotland, United
YunheBao(2),DepartmentofBiochemis- Kingdom.
try and Molecular Biology, Colorado
GerardJ.Bunick(3),LifeSciencesDiv-
State University, FortCollins, Colorado
ision, Oak Ridge National Laboratory,
80523-1870
OakRidge,Tennessee37831-8080
Blaine Bartholomew (13), Department
of Biochemistry & Molecular Biology, MichaelBustin(21),NationalCancerIn-
Southern Illinois University School of stitute, National Institutes of Health,
Medicine, Carbondale, Illinois Bethesda,Maryland20892
62901-4413
AnneE.Carpenter(23),WhiteheadInsti-
David P. Bazett-Jones (28), Programme tuteforBiomedicalResearch,Cambridge,
in Cell Biology, Hospital for Sick Massachusetts02142
Children, Toronto, Ontario M5G 1X8,
Gustavo Carrero (26), Department of
Canada
Mathematical and Statistical Sciences,
AndrewS.Belmont(23),Departmentof Faculty of Science, University of
CellandStructuralBiology,Universityof Alberta, Edmonton, Alberta T6G 2E1,
Illinois at Urbana-Champaign, Urbana, Canada
Illinois61801
David Carter (29), Laboratory of Chro-
LeiseBerven(16),Children’sMedicalRe- matin and Gene Expression, Babraham
search Institute, Westmead, New South Institute, Cambridge CB2 4AT, United
Wales2415,Australia Kingdom
YehuditBirger(21),NationalCancerIn- Fre´de´ricCatez(21),NationalCancerIn-
stitute, National Institutes of Health, stitute, National Institutes of Health,
Bethesda,Maryland20892 Bethesda,Maryland20892
ix
x contributors to volume 375
Lyubomira Chakalova (29), Laboratory Pamela N. Dyer (2), Department of Bio-
ofChromatinandGeneExpression,Bab- chemistryandMolecularBiology,Color-
raham Institute, Cambridge CB2 4AT, ado State University, Fort Collins,
UnitedKingdom Colorado80523-1870
Srinivas Chakravarthy (2), Department Raji S. Edayathumangalam (2), Depart-
ofBiochemistryandMolecularBiology, mentofBiochemistryandMolecularBiol-
Colorado State University,Fort Collins, ogy, Colorado State University, Fort
Colorado80523-1870 Collins,Colorado80523-1870
Lakshmi N. Changolkar (15), Depart- Thomas G. Fazzio (6), Fred Hutchinson
mentofAnimalBiology,SchoolofVeter- Cancer Research Center, Seattle, Wash-
inary Medicine, University of ington98109-1024
Pennsylvania,Philadelphia,Pennsylvania
Andrew Flaus (14), Division of Gene
19104
Regulation and Expression, The Well-
LisaAnnCirillo(9),DepartmentofCell comeTrustBiocentre,DepartmentofBio-
Biology, Neurobiology, and Anatomy, chemistry,UniversityofDundee,Dundee,
Medical College of Washington, DD15EH,Scotland,UnitedKingdom.
Milwaukee,Wisconsin53149
PeterFraser(29),LaboratoryofChroma-
PeterR.Cook(24),TheSirWilliamDunn tinandGeneExpression,BabrahamInsti-
SchoolofPathology,UniversityofOxford, tute, Cambridge CB2 4AT, United
OxfordOX13RE,UnitedKingdom Kingdom
EllenCrawford(26),DepartmentofOn- SusanM.Gasser(22),DepartmentofMo-
cology,FacultyofMedicine,Universityof lecular Biology, University of Geneva,
Alberta and Cross Cancer Institute, 1211Geneva4,Switzerland
Edmonton,AlbertaT6G2E1,Canada
Stanislaw A. Gorski (25), National
WouterdeLaat(30),DepartmentofCell Cancer Institute, National Institutes of
Biology, ErasmusMC, 3015 GE Rotter-
Health,Bethesda,Maryland20892
dam,TheNetherlands
JoachimGriesenbeck(11),Departmentof
GerdadeVries(26),DepartmentofMath-
Structural Biology, Stanford University
ematical and StatisticalSciences, Faculty
SchoolofMedicine,Stanford,California
ofScience,UniversityofAlberta,Edmon-
94305
ton,AlbertaT6G2E1,Canada
Graham Dellaire (28), Programme in FrankGrosveld(30),DepartmentofCell
Biology, ErasmusMC, 3015 GE Rotter-
CellBiology,HospitalforSickChildren,
dam,TheNetherlands
Toronto,OntarioM5G1X8,Canada
JohnD.Diller(10),DepartmentofBio- B.LeifHanson(3),TheUniversityofTen-
chemistryandMolecularBiology,Center nessee-Oak Ridge Graduate School of
for Gene Regulation, The Pennsylvania Genome Science and Technology, Life
State University, University Park, Sciences Divison, Oak Ridge National
Pennsylvania16802 Laboratory, Oak Ridge, Tennessee
37831-8080
Charles E. Ducker (10), Departmentof
Biochemistry and Molecular Biology, Joel M. Harp (3), Department of Bio-
CenterforGeneRegulation,ThePennsyl- chemistryandCenterforStructuralBiol-
vania State University, University Park, ogy, Vanderbilt University, Nashville,
Pennsylvania16802 Tennessee37232-8725
contributors to volume375 xi
Keiji Hashimoto (17), Core Research for Karolin Luger (2), Department of Bio-
Evolutional Science and Technology, chemistryandMolecularBiology,Color-
Saitama332-0012,Japan ado State University, Fort Collins,
Colorado80523-1870
JeffreyJ.Hayes(12),DepartmentofBio-
chemistry and Biophysics, University of James G. McNally (27), Laboratory of
Rochester Medical Center, Rochester, ReceptorBiologyandGeneExpression,
NewYork14642 NationalCancerInstitute,NationalInsti-
tutes of Health, Bethesda, Maryland
Florence Hediger (22), Department of
20892
MolecularBiology,UniversityofGeneva,
1211Geneva4,Switzerland Tom Misteli (25) National Cancer Insti-
tute, National Institutes of Health,
MichaelJ.Hendzel(26),Departmentof
Bethesda,Maryland20892
Oncology, University of Alberta and
Cross Cancer Instutite, Edmonton, CraigA.Mizzen(19),DepartmentofCell
AlbertaT6G1Z2,Canada & Structural Biology, University of
MikiHieda(24),SirWilliamDunnSchool Illinois at Urbana-Champaign, Urbana,
Illinois61801
of Pathology, University of Oxford,
OxfordOX13RE,UnitedKingdom SetsuoMorishita(17),DepartmentofMo-
Stefan R. Kassabov (13), Department of lecularBiology,SchoolofScience,Nagoya
University,Nagoya464-8601,Japan
Biochemistry & Molecular Biology,
Southern Illinois University School of Uma M. Muthurajan (2), Department of
Medicine, Carbondale, Illinois
Biochemistry and Molecular Biology,
62901-4413
ColoradoState University, Fort Collins,
HiroshiKimura(24),HorizontalMedical Colorado80523-1870
ResearchOrganization,SchoolofMedi- Frank R. Neumann (22), Department of
cine,KyotoUniversity,Kyoto606-8510,
MolecularBiology,UniversityofGeneva,
Japan
1211Geneva4,Switzerland
Roger D. Kornberg (11), Departmentof RozaliaNisman(28),ProgrammeinCell
Structural Biology, Stanford University Biology, Hospital for Sick Children,
SchoolofMedicine,Stanford,California
Toronto,OntarioM5G1X8,Canada
94305
TomOwen-Hughes(14),DivisionofGene
David Landsman (1) NationalCenterfor Regulation and Expression, The Well-
BiotechnologyInformation,NationalLi- comeTrustBiocentre,DepartmentofBio-
braryofMedicine,NationalInstitutesof chemistry,UniversityofDundee,Dundee,
Health,Bethesda,Maryland20894 DD15EHScotland,UnitedKingdom.
PaulJ.Laybourn(7),DepartmentofBio- John R. Pehrson (15), Department of
chemistryandMolecularBiology,Color- Animal Biology, School of Veterinary
ado State University, Fort Collins, Medicine, University of Pennsylvania,
Colorado80523-1870 Philadelphia,Pennsylvania19104
Jae-HwanLim(21),NationalCancerInsti- CraigL.Peterson(4)UniversityofMas-
tute, National Institutes of Health, sachusetts Medical School, Worchester,
Bethesda,Maryland20892 Massachusetts01605
xii contributors to volume 375
RobertD.Phair(25),BioInformaticsSer- Erik Splinter (30), Department of Cell
vices,Rockville,Maryland20854 Biology, ErasmusMC, 3015 GE Rotter-
dam,TheNetherlands
Duane R. Pilch (5), Laboratory of Mo-
lecular Pharmacology, National Cancer Diana A. Stavreva (27), Laboratory of
Institute,Bethesda,Maryland20892 ReceptorBiologyandGeneExpression,
NationalCancerInstitute,NationalInsti-
YuriV. Postnikov (21), National Cancer tutesofHealth,Bethesda,Maryland20892
Institute, National Institutes of Health,
Bethesda,Maryland20892 J. Seth Strattan (11), Department of
Structural Biology, Stanford University
DannyRangasamy(16),TheJohnCurtin SchoolofMedicine,Stanford,California
School of Medical Research, Australian
94305
NationalUniversity,Canberra,Australia
CapitalTerritory2601,Australia Steven A. Sullivan (1), National Center
forBiotechnologyInformation,National
Dominique Ray-Gallet (8), Institut LibraryofMedicine,NationalInstitutes
Curie, Section de Recherche, F-75248, ofHealth,Bethesda,Maryland20894
ParisCedex05,France
Ulrica Svensson (16), The John Curtin
ChristopheRedon(5),LaboratoryofMo- School of Medical Research, Australian
lecular Pharmacology, National Cancer NationalUniversity,Canberra,Australian
Institute,Bethesda,Maryland20892 CapitalTerritory2601,Australia
RaymondReeves(20),SchoolofMolecu- AngelaTaddei(22),DepartmentofMo-
larBiosciences,Biochemistry/Biophysics, lecular Biology, University of Geneva,
Washington State University, Pullman, 1211Geneva4,Switzerland
Washington99164-4660
John Th’ng (26), Northwestern Ontario
Patricia Ridgway (16), The John Curtin Regional Cancer Centre, Thunder Bay,
School of Medical Research, Australian OntarioP7A7T1,Canada
National University, Canberra, Austra-
David John Tremethick (16), The John
lianCapitalTerritory2601,Australia
CurtinSchoolofMedicalResearch,Aus-
ChunRuan(10),DepartmentofBiochem- tralian National University, Canberra,
istry and Molecular Biology, Center for Australian Capital Territory 2601,
GeneRegulation,ThePennsylvaniaState Australia
University,UniversityPark,Pennsylvania
Toshio Tsukiyama (6), Fred Hutchinson
16802
Cancer Research Center, Seattle, Wash-
Olga A. Sedelnikova (5), Laboratory ington98109-1024
of Molecular Pharmacology, National JayC.Vary,Jr.(6),MolecularandCellu-
Cancer Institute, Bethesda, Maryland
lar Biology Program, University of
20892
Washington,Seattle,Washington98195
MichaelA.Shogren-Knaak(4),Univer- Cindy L. White (2), Department of Bio-
sity of Massachusetts Medical School, chemistryandMolecularBiology,Color-
Worchester,Massachusetss01605 ado State University, Fort Collins,
Colorado80523-1870
Robert T. Simpson (10), Department of
Biochemistry and Molecular Biology, SriwanWongwisansri(7),Departmentof
CenterforGeneRegulation,ThePennsyl- Biochemistry and Molecular Biology,
vania State University, University Park, ColoradoState University, FortCollins,
Pennsylvania16802 Colorado80523-1870
contributors to volume375 xiii
KinyaYoda(17,18),BioscienceandBio- Chunyang Zheng (12), Department of
technology Center, Nagoya University, BiochemistryandBiophysics,University
Nagoya,464-8601,Japan ofRochesterMedicalCenter,Rochester,
NewYork14642
Kenneth S. Zaret (9), Cell and Devel-
opmental Biology Program, Fox Chase
CancerCenter,Philadelphia,Pennsylva-
nia19111
[1] mining corehistone sequencesfrompublic proteindatabases 3
[1] Mining Core Histone Sequences from Public
Protein Databases
By Steven A. Sullivan and David Landsman
Introduction
Constructinganonlinedatabaseofhistonesandhistonefold-containing
proteins has allowed our group to analyze histone sequence variation in
some detail.1,2 Here, we describe how we have inventoried core histone
protein sequences as part of this project. The issues involved in such an
undertaking are for the most part not unique to histone sequences. Our
methods and observations should be broadly applicable to studies of
protein families that are highly represented inpublicsequencedatabases.
Considerations
Ourinitialgoalwastocollectasmanyreportedhistonesequencesaswe
could find. Among the considerations that came into play were the
following.
1. Sourcing of sequences. Several excellent public sequence reposi-
tories make protein sequences available to researchers. We relied on the
protein database maintained by the National Center for Biotechnology
Information (NCBI), which is updated frequently and has been compiled
from worldwide sources, including Swiss-Prot,3 the Protein Information
Resource (PIR),4 the Protein Research Foundation (PRF) (http://
www.prf.or.jp/en/), the Protein Data Bank (PDB),5 and translations
from annotated coding regions in GenBank6 and RefSeq,7 a curated,
nonredundant set of sequences.
1S.Sullivan,D.W.Sink,K.L.Trout,I.Makalowska,P.M.Taylor,A.D.Baxevanis,and
D.Landsman,NucleicAcidsRes.30,341(2002).
2S.A.SullivanandD.Landsman,Proteins52,454(2003).
3B.Boeckmann,A.Bairoch,R.Apweiler,M.C.Blatter,A.Estreicher,E.Gasteiger,M.J.
Martin,K.Michoud,C.O’Donovan,I.Phan,S.Pilbout,andM.Schneider,NucleicAcids
Res.31,365(2003).
4C. H. Wu, L. S. Yeh, H. Huang, L. Arminski, J. Castro-Alvear, Y. Chen, Z. Hu, P.
Kourtesis,R.S.Ledley,B.E.Suzek,C.R.Vinayaka,J.Zhang,andW.C.Barker,Nucleic
AcidsRes.31,345(2003).
5J.Westbrook,Z.Feng,L.Chen,H.Yang,andH.M.Berman,NucleicAcidsRes.31,489
(2003).
METHODSINENZYMOLOGY,VOL.375 0076-6879/04$35.00
4 histone bioinformatics [1]
2. Sequence-harvesting tools. In general, a sequence database search is
a similarity search of either the actual sequence data or its annotation. We
find that both must be targeted in order to maximize the sequence harvest,
because sequence-based searches alone can miss small or ambiguous
sequence fragments that have been deposited in the public databases, and
text-based searches can miss ‘‘cryptic’’ histones, that is, those with
inadequate or incorrect annotation.
For text-based searches of sequence annotation we used the Entrez
search engine at the NCBI Web site (http://www.ncbi.nlm.nih.gov/Entrez).
For sequence-based searching we used several varieties of the popular
Basic Local Alignment Search Tool (BLAST) pairwise alignment algo-
rithm. The most commonly used sequence similarity search tools find
‘‘hits’’ based on pairwise alignments of each sequence in the database to
either the query sequence alone, for example, in the case of BLAST, or a
query profile derived from a previously aligned set of similar sequences, for
example, in the case of PSI-BLAST or HMMER.8,9 The latter tools are
better at finding highly divergent members of a protein family but can be
expected to return false positives, requiring further filtering of results.
PSI-BLAST is actually a hybrid tool that performs one round of standard
BLAST, using a user-supplied query sequence, and then builds a profile
from the alignment of the initial BLAST results, which becomes the query
for the next round of BLAST. The process is reiterated until ‘‘conver-
gence’’ is reached, that is, until no more new matches are found above
the cutoff score. Ideally this should take fewer than 10 iterations, but con-
vergence can be elusive when the query sequence matches a diverse and
perhaps distantly related set of proteins. This was more difficult to interpret
with searches for nonhistone proteins containing the histone fold than for
harvesting core histone sequences. With the latter we found that seven iter-
ations were sufficient to reach either convergence or the point at which all
the ‘‘new’’ hits appeared by other criteria to be false positives. PSI-BLAST
routinely returned a small number of true-positive matches to the query
sequences that gapped protein BLAST (BLASTPGP) had missed.
Reasonably fast BLASTPGP and PSI-BLAST servers are available at
the NCBI Web site (http://www.ncbi.nlm.nih.gov/BLAST). One advantage
of the NCBI Web site PSI-BLAST implementation over a command-line
6D.A.Benson,I.Karsch-Mizrachi,D.J.Lipman,J.Ostell,andD.L.Wheeler,NucleicAcids
Res.31,23(2003).
7K.D.Pruitt,T.Tatusova,andD.R.Maglott,NucleicAcidsRes.31,34(2003).
8S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J.
Lipman,NucleicAcidsRes.25,3389(1997).
9S.R.Eddy,Bioinformatics14,755(1998).