0	10	Functional	functional	JJ
11	19	analysis	analysis	NN
20	22	of	of	IN
23	33	cis-linked	cis-linked	JJ
34	44	regulatory	regulatory	JJ
45	54	sequences	sequence	NNS
55	57	in	in	IN
58	61	the	the	DT
62	65	HLA	HLA	NNP
66	69	DRA	DRA	NNP
70	78	promoter	promoter	NN
79	81	by	by	IN
82	95	transcription	transcription	NN
96	98	in	in	FW
99	104	vitro	vitro	FW
104	105	.	.	.

107	110	Two	two	CD
111	120	consensus	consensus	NN
121	130	sequences	sequence	NNS
130	131	,	,	,
132	138	called	call	VBN
139	140	X	X	NNP
141	144	and	and	CC
145	146	Y	Y	NNP
147	152	boxes	box	NNS
152	153	,	,	,
154	161	capable	capable	JJ
162	164	of	of	IN
165	172	binding	bind	VBG
173	180	nuclear	nuclear	JJ
181	189	proteins	protein	NNS
190	193	and	and	CC
194	204	regulating	regulate	VBG
205	215	expression	expression	NN
216	218	in	in	IN
219	220	B	B	NNP
221	226	cells	cell	NNS
227	231	have	have	VBP
232	236	been	be	VBN
237	244	defined	define	VBN
245	251	within	within	IN
252	255	the	the	DT
256	265	immediate	immediate	JJ
266	274	upstream	upstream	JJ
275	281	region	region	NN
282	284	of	of	IN
285	290	major	major	JJ
291	309	histocompatibility	histocompatibility	NN
310	317	complex	complex	NN
318	319	(	(	(
319	322	MHC	MHC	NNP
322	323	)	)	)
324	329	class	class	NN
330	332	II	ii	CD
333	342	promoters	promoter	NNS
342	343	.	.	.

344	350	Unlike	unlike	IN
351	356	other	other	JJ
357	362	class	class	NN
363	365	II	ii	CD
366	375	promoters	promoter	NNS
375	376	,	,	,
377	380	the	the	DT
381	387	HLA-DR	HLA-DR	NNP
388	393	alpha	alpha	NN
394	395	(	(	(
395	398	DRA	DRA	NNP
398	399	)	)	)
400	408	promoter	promoter	NN
409	413	also	also	RB
414	422	contains	contain	VBZ
423	426	one	one	CD
427	434	element	element	NN
435	444	identical	identical	JJ
445	447	to	to	TO
448	451	the	the	DT
452	453	“	``	``
453	460	octamer	octamer	NN
460	461	”	''	''
462	467	motif	motif	NN
468	470	of	of	IN
471	485	immunoglobulin	immunoglobulin	NN
486	494	variable	variable	JJ
495	501	region	region	NN
502	511	promoters	promoter	NNS
512	516	that	that	WDT
517	519	is	be	VBZ
520	531	responsible	responsible	JJ
532	535	for	for	IN
536	537	B	B	NNP
538	551	cell-specific	cell-specific	JJ
552	565	transcription	transcription	NN
565	566	.	.	.

567	571	This	this	DT
572	573	“	``	``
573	580	octamer	octamer	NN
580	581	”	''	''
582	584	in	in	IN
585	588	the	the	DT
589	596	context	context	NN
597	599	of	of	IN
600	603	DRA	DRA	NNP
604	611	appears	appear	VBZ
612	619	capable	capable	JJ
620	622	of	of	IN
623	630	binding	bind	VBG
631	635	both	both	CC
636	639	the	the	DT
640	650	ubiquitous	ubiquitous	JJ
651	652	(	(	(
652	657	OTF-1	otf-1	NN
657	658	)	)	)
659	662	and	and	CC
663	680	lymphoid-specific	lymphoid-specific	JJ
681	682	(	(	(
682	687	OTF-2	otf-2	NN
687	688	)	)	)
689	690	“	``	``
690	697	octamer	octamer	NN
697	698	”	''	''
699	706	binding	binding	NN
707	715	proteins	protein	NNS
715	716	,	,	,
717	720	but	but	CC
721	723	at	at	IN
724	729	least	least	JJS
730	733	one	one	CD
734	739	other	other	JJ
740	748	distinct	distinct	JJ
749	750	“	``	``
750	757	octamer	octamer	NN
757	758	”	''	''
759	766	complex	complex	NN
767	770	was	be	VBD
771	776	found	find	VBN
776	777	.	.	.

778	780	In	in	IN
781	786	order	order	NN
787	789	to	to	TO
790	802	characterize	characterize	VB
803	806	the	the	DT
807	815	function	function	NN
816	818	of	of	IN
819	829	cis-acting	cis-acting	JJ
830	838	elements	element	NNS
838	839	,	,	,
840	842	we	we	PRP
843	847	have	have	VBP
848	857	developed	develop	VBN
858	860	an	an	DT
861	863	in	in	FW
864	869	vitro	vitro	FW
870	876	system	system	NN
877	879	in	in	IN
880	885	which	which	WDT
886	887	a	a	DT
888	891	DRA	DRA	NNP
892	900	promoter	promoter	NN
901	910	construct	construct	NN
911	913	is	be	VBZ
914	925	transcribed	transcribe	VBN
926	930	more	more	RBR
931	942	efficiently	efficiently	RB
943	945	in	in	IN
946	954	extracts	extract	NNS
955	959	from	from	IN
960	961	B	B	NNP
962	967	cells	cell	NNS
968	972	than	than	IN
973	975	in	in	IN
976	984	extracts	extract	NNS
985	989	from	from	IN
990	995	class	class	NN
996	1007	II-negative	ii-negative	JJ
1008	1012	HeLa	HeLa	NNP
1013	1018	cells	cell	NNS
1018	1019	.	.	.

1020	1021	5	5	CD
1021	1022	’	'	SYM
1023	1031	deletion	deletion	NN
1032	1042	constructs	construct	NNS
1043	1048	which	which	WDT
1049	1055	lacked	lack	VBD
1056	1059	the	the	DT
1060	1061	Y	y	NN
1062	1065	box	box	NN
1065	1066	,	,	,
1067	1070	but	but	CC
1071	1079	retained	retain	VBD
1080	1083	the	the	DT
1084	1085	“	``	``
1085	1092	octamer	octamer	NN
1092	1093	”	''	''
1094	1099	motif	motif	NN
1100	1103	and	and	CC
1104	1108	TATA	TATA	NNP
1109	1112	box	box	NN
1113	1117	were	be	VBD
1118	1128	completely	completely	RB
1129	1137	inactive	inactive	JJ
1137	1138	,	,	,
1139	1142	and	and	CC
1143	1151	internal	internal	JJ
1152	1160	deletion	deletion	NN
1161	1163	of	of	IN
1164	1167	the	the	DT
1168	1169	Y	Y	NNP
1170	1173	box	box	NN
1174	1181	reduced	reduce	VBD
1182	1195	transcription	transcription	NN
1196	1198	by	by	IN
1199	1201	95	95	CD
1201	1202	%	%	NN
1202	1203	.	.	.

1204	1209	Using	use	VBG
1210	1221	supercoiled	supercoile	VBN
1221	1222	,	,	,
1223	1226	but	but	CC
1227	1230	not	not	RB
1231	1237	linear	linear	JJ
1238	1247	templates	template	NNS
1247	1248	,	,	,
1249	1251	we	we	PRP
1252	1260	observed	observe	VBD
1261	1272	differences	difference	NNS
1273	1275	in	in	IN
1276	1289	transcription	transcription	NN
1290	1302	efficiencies	efficiency	NNS
1303	1307	from	from	IN
1308	1317	templates	template	NNS
1318	1325	lacking	lack	VBG
1326	1328	or	or	CC
1329	1339	disrupting	disrupt	VBG
1340	1343	the	the	DT
1344	1345	X	X	NNP
1346	1355	consensus	consensus	NN
1356	1363	element	element	NN
1364	1368	that	that	WDT
1369	1376	reflect	reflect	VBP
1377	1384	effects	effect	NNS
1385	1387	of	of	IN
1388	1394	random	random	JJ
1395	1406	replacement	replacement	NN
1407	1409	of	of	IN
1410	1411	X	X	NNP
1412	1415	box	box	NN
1416	1425	sequences	sequence	NNS
1426	1428	in	in	IN
1429	1438	transient	transient	JJ
1439	1449	expression	expression	NN
1450	1456	assays	assay	NNS
1456	1457	.	.	.

1458	1471	Demonstration	demonstration	NN
1472	1474	of	of	IN
1475	1478	the	the	DT
1479	1487	complete	complete	JJ
1488	1498	dependence	dependence	NN
1499	1501	on	on	IN
1502	1505	the	the	DT
1506	1507	Y	y	NN
1508	1511	box	box	NN
1512	1514	in	in	IN
1515	1519	this	this	DT
1520	1526	system	system	NN
1527	1535	suggests	suggest	VBZ
1536	1540	that	that	IN
1540	1541	,	,	,
1542	1549	despite	despite	IN
1550	1553	its	its	PRP$
1554	1566	demonstrated	demonstrate	VBN
1567	1577	importance	importance	NN
1578	1580	in	in	IN
1581	1584	the	the	DT
1585	1588	DRA	DRA	NNP
1589	1597	promoter	promoter	NN
1597	1598	,	,	,
1599	1602	the	the	DT
1603	1606	DRA	DRA	NNP
1607	1608	“	``	``
1608	1615	octamer	octamer	NN
1615	1616	”	''	''
1617	1621	does	do	VBZ
1622	1625	not	not	RB
1626	1633	utilize	utilize	VB
1634	1639	OTF-2	otf-2	NN
1640	1642	in	in	IN
1643	1644	a	a	DT
1645	1651	manner	manner	NN
1652	1661	analogous	analogous	JJ
1662	1664	to	to	TO
1665	1679	immunoglobulin	immunoglobulin	NN
1680	1689	promoters	promoter	NNS
1690	1692	in	in	IN
1693	1694	B	B	NNP
1695	1700	cells	cell	NNS
1700	1701	.	.	.